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Compendium of Plant Genomes
Chittaranjan Kole Editor
The Mango
Genome
Series Editor
Chittaranjan Kole, Raja Ramanna Fellow, Government of India,
ICAR-National Research Center on Plant Biotechnology, Pusa,
New Delhi, India
Whole-genome sequencing is at the cutting edge of life sciences in the new
millennium. Since the first genome sequencing of the model plant Arabidopsis
thaliana in 2000, whole genomes of about 100 plant species have been
sequenced and genome sequences of several other plants are in the pipeline.
Research publications on these genome initiatives are scattered on dedicated
web sites and in journals with all too brief descriptions. The individual
volumes elucidate the background history of the national and international
genome initiatives; public and private partners involved; strategies and
genomic resources and tools utilized; enumeration on the sequences and their
assembly; repetitive sequences; gene annotation and genome duplication. In
addition, synteny with other sequences, comparison of gene families and most
importantly potential of the genome sequence information for gene pool
characterization and genetic improvement of crop plants are described.
Interested in editing a volume on a crop or model plant?
Please contact Prof. C. Kole, Series Editor, at ckoleorg@gmail.com
More information about this series at http://www.springer.com/series/11805

Chittaranjan Kole
Editor
The Mango Genome
123
Editor
Chittaranjan Kole
ICAR-National Institute
for Plant Biotechnology
Raja Ramanna Fellow
Government of India
New Delhi, India
ISSN 2199-4781 ISSN 2199-479X (electronic)

ISBN 978-3-030-47828-5 ISBN 978-3-030-47829-2 (eBook)
https://doi.org/10.1007/978-3-030-47829-2
© Springer Nature Switzerland AG 2021

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The use of general descriptive names, registered names, trademarks, service marks, etc. in this
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The publisher, the authors and the editors are safe to assume that the advice and information in
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This Springer imprint is published by the registered company Springer Nature Switzerland AG
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
This book series is dedicated to my wife Phullara
and our children Sourav and Devleena
Chittaranjan Kole
Preface to the Series
Genome sequencing has emerged as the leading discipline in the plant sci-
ences coinciding with the start of the new century. For much of the twentieth
century, plant geneticists were only successful in delineating putative chro-
mosomal location, function, and changes in genes indirectly through the use
of a number of “markers” physically linked to them. These included visible
or morphological, cytological, protein, and molecular or DNA markers.
Among them, the first DNA marker, the RFLPs, introduced a revolutionary
change in plant genetics and breeding in the mid-1980s, mainly because
of their infinite number and thus potential to cover maximum chromosomal
regions, phenotypic neutrality, absence of epistasis, and codominant nature.
An array of other hybridization-based markers; PCR-based markers; and
markers based on both facilitated construction of genetic linkage maps,
mapping of genes controlling simply inherited traits, and even gene clusters
(QTLs) controlling polygenic traits in a large number of model and crop
plants. During this period, a number of new mapping populations beyond F2
were utilized and a number of computer programs were developed for map
construction, mapping of genes, and for mapping of polygenic clusters or
QTLs. Molecular markers were also used in the studies of evolution and
phylogenetic relationship, genetic diversity, DNA fingerprinting, and
map-based cloning. Markers tightly linked to the genes were used in crop
improvement employing the so-called marker-assisted selection. These
strategies of molecular genetic mapping and molecular breeding made a
spectacular impact during the last one and a half decades of the twentieth
century. But still they remained “indirect” approaches for elucidation and
utilization of plant genomes since much of the chromosomes remained
unknown and the complete chemical depiction of them was yet to be
unraveled.
Physical mapping of genomes was the obvious consequence that facili-
tated the development of the “genomic resources” including BAC and YAC
libraries to develop physical maps in some plant genomes. Subsequently,
integrated genetic–physical maps were also developed in many plants. This
led to the concept of structural genomics. Later on, emphasis was laid on
EST and transcriptome analysis to decipher the function of the active gene
sequences leading to another concept defined as functional genomics. The
advent of techniques of bacteriophage gene and DNA sequencing in the
1970s was extended to facilitate sequencing of these genomic resources in
the last decade of the twentieth century.
vii
viii Preface to the Series
As expected, sequencing of chromosomal regions would have led to too

much data to store, characterize, and utilize with the then-available computer
software could handle. But the development of information technology made
the life of biologists easier by leading to a swift and sweet marriage of
biology and informatics, and a new subject was born—bioinformatics.
Thus, the evolution of the concepts, strategies, and tools of sequencing
and bioinformatics reinforced the subject of genomics—structural and
functional. Today, genome sequencing has traveled much beyond biology
and involves biophysics, biochemistry, and bioinformatics!
Thanks to the efforts of both public and private agencies, genome
sequencing strategies are evolving very fast, leading to cheaper, quicker, and
automated techniques right from clone-by-clone and whole genome shotgun
approaches to a succession of second-generation sequencing methods. The
development of software of different generations facilitated this genome
sequencing. At the same time, newer concepts and strategies were emerging
to handle sequencing of the complex genomes, particularly the polyploids.
It became a reality to chemically—and so directly—define plant genomes,
popularly called whole genome sequencing or simply genome sequencing.
The history of plant genome sequencing will always cite the sequencing
of the genome of the model plant Arabidopsis thaliana in 2000 that was
followed by sequencing the genome of the crop and model plant rice in 2002.
Since then, the number of sequenced genomes of higher plants has been
increasing exponentially, mainly due to the development of cheaper and
quicker genomic techniques and, most importantly, the development of
collaborative platforms such as national and international consortia involving
partners from public and/or private agencies.
As I write this preface for the first volume of the new series “Compendium
of Plant Genomes,” a net search tells me that complete or nearly complete
whole genome sequencing of 45 crop plants, 8 crop and model plants, 8
model plants, 15 crop progenitors and relatives, and 3 basal plants is
accomplished, majority of which are in the public domain. This means that
we nowadays know many of our model and crop plants chemically, i.e.,
directly, and we may depict them and utilize them precisely better than ever.
Genome sequencing has covered all groups of crop plants. Hence, infor-
mation on the precise depiction of plant genomes and the scope of their
utilization are growing rapidly every day. However, the information is
scattered in research articles and review papers in journals and dedicated
Web pages of the consortia and databases. There is no compilation of plant
genomes and the opportunity of using the information in sequence-assisted
breeding or further genomic studies. This is the underlying rationale for
starting this book series, with each volume dedicated to a particular plant.
Plant genome science has emerged as an important subject in academia,
and the present compendium of plant genomes will be highly useful to both
students and teaching faculties. Most importantly, research scientists
involved in genomics research will have access to systematic deliberations on
the plant genomes of their interest. Elucidation of plant genomes is of interest
not only for the geneticists and breeders, but also for practitioners of an array
of plant science disciplines, such as taxonomy, evolution, cytology,
Preface to the Series ix
physiology, pathology, entomology, nematology, crop production, bio-

chemistry, and obviously bioinformatics. It must be mentioned that infor-
mation regarding each plant genome is ever-growing. The contents of the
volumes of this compendium are, therefore, focusing on the basic aspects
of the genomes and their utility. They include information on the academic
and/or economic importance of the plants, description of their genomes from
a molecular genetic and cytogenetic point of view, and the genomic resources
developed. Detailed deliberations focus on the background history of the
national and international genome initiatives, public and private partners
involved, strategies and genomic resources and tools utilized, enumeration on
the sequences and their assembly, repetitive sequences, gene annotation, and
genome duplication. In addition, synteny with other sequences, comparison
of gene families, and, most importantly, the potential of the genome sequence
information for gene pool characterization through genotyping by sequencing
(GBS) and genetic improvement of crop plants have been described. As
expected, there is a lot of variation of these topics in the volumes based on
the information available on the crop, model, or reference plants.
I must confess that as the series editor, it has been a daunting task for me
to work on such a huge and broad knowledge base that spans so many
diverse plant species. However, pioneering scientists with lifetime experience
and expertise on the particular crops did excellent jobs editing the respective
volumes. I myself have been a small science worker on plant genomes since
the mid-1980s and that provided me the opportunity to personally know
several stalwarts of plant genomics from all over the globe. Most, if not all,
of the volume editors are my longtime friends and colleagues. It has been
highly comfortable and enriching for me to work with them on this book
series. To be honest, while working on this series I have been and will remain
a student first, a science worker second, and a series editor last. And I must
express my gratitude to the volume editors and the chapter authors for pro-
viding me the opportunity to work with them on this compendium.
I also wish to mention here my thanks and gratitude to the Springer staff,
particularly Dr. Christina Eckey and Dr. Jutta Lindenborn for the earlier set
of volumes and presently Ing. Zuzana Bernhart for all their timely help and
support.
I always had to set aside additional hours to edit books beside my pro-
fessional and personal commitments—hours I could and should have given
to my wife, Phullara, and our kids, Sourav and Devleena. I must mention that
they not only allowed me the freedom to take away those hours from them
but also offered their support in the editing job itself. I am really not sure
whether my dedication of this compendium to them will suffice to do justice
to their sacrifices for the interest of science and the science community.
New Delhi, India Chittaranjan Kole

Foreword
Mango (Mangifera indica L.) is one of the most ancient fruits of the Indian
sub-continent grown since as early as 2000 BC and is designated as the
“King of Fruits” in the Tropical world owing to its unique quality and high
nutritive value and vast diversity in color, size, and aroma. Besides, several
value-added and novel processed products form the part of popular mango
industry. It is the fifth most important fruit commodity traded worldwide,
along with bananas, apples, grapes, and oranges. At present, the world
produces over 42 M tons of fresh mango fruits in over 100 countries, while
India, China, Thailand, Mexico, Indonesia, Pakistan, Brazil, Egypt, and
Bangladesh are the major growers. Its cultivation has spread to almost all the
continents of the globe except Antarctica. The global production of mango is
projected to reach 65 million ton by 2028, with annual increment of 2.1
percent for the next one decade. While the production from the leading
exporting countries from Latin America and the Caribbean—critically
Ecuador, Brazil, Guatemala, Colombia, Costa Rica, and Mexico—is expec-
ted to reach 34 million ton, due to expected import demand from the major
importing countries.
Mango is an allotetraploid (2n = 40), highly heterozygous, and
cross-pollinated fruit tree with a small genome size of 450 Mb. It is reported
to have over 70 species scattered in the region extending from Northeastern
India to Southeast Asia. Both conventional and non-conventional crop
improvement attempts have led to the development of over three dozen
hybrids globally, though the existence of enormous genetic diversity in
M. indica has led to the identification of over 1200 registered chance seed-
lings, superior clones, hybrids, and rootstocks.
xi
xii Foreword
The development of molecular tools in mango is extremely limited, and

thus its genes, genetics, and genomics remain scantly understood. The whole
genome sequencing and the development of genetic maps of this species are
important components in marker-assisted breeding and thereby targeted and
effective genetic improvement. The high heterozygosity in mango is a big
challenge in terms of whole genome sequencing-based SNP/polymorphism
discovery. Accordingly, there are several scientific groups/consortia, which
are involved in deciphering its complete genome information. Hence, com-
plete information on genetic resources including the development of large
numbers of SNP molecular genetic markers; development of genetic map of
mango; association of phenotypic traits to the genetic map to identify useful
unique markers for breeding; assessment of the genetic diversity in mango
germplasm collections; and sequencing, assembly, and annotation of the
mango genome are still to be achieved. The robust genetic resources will
facilitate identification of genetic components associated with useful traits for
hastening breeding efforts with precision. In this direction, next-generation
genomics tools, bioinformatics, and omics approaches could be used in
tandem to uncover large amount of genetic information. Advanced tech-
niques like RADSeq can be used for rapid marker discovery and genotyping
in crops like mango, which are highly heterozygous and out-breeding fruit
species. Further, allelic database of mango for varietal differentiation has
been reported though limited number of markers could not differentiate
genotypes. Such leads achieved globally are though limited in the form of
genomic resources in public domain which would thus be logically used as
research tool for mapping, QTL studies, and genome completion in near
future.
Considering the importance of the crop, i.e., mango the above book with
focus on genome and omics is a timely effort undertaken to compile and
present the up-to-date information in genomic science using state-of-the-art
tools on different aspects pertaining to mango. It has a wide diversity of
aspects like botany, germplasm and genetic resources, alternate flowering,
propagation, classical genetics and traditional breeding, in vitro regeneration
and genetic transformation, molecular mapping and breeding, genome
sequencing, organelle genome, functional genomics, genomic resources,
databases, etc. The effort made would go a long way in upgrading and
updating the available information, which is being added vigorously in
mango by the global scientific community. This is a monumental effort made
by Prof. Chittaranjan Kole on Mango—a crop very close to my heart. Prof.
Kole is an internationally reputed scientist with original contributions on crop
genomics and breeding including several horticultural crops made through
his researches in India and USA on fruit trees, vegetables, and medicinal and
aromatic plants. Out of his 126 already published books, 55 are directly on
horticultural crops and trees. “The Mango Genome” will remain as another
valuable contribution from him for the academic community. The informa-
tion compiled in this book would serve as a valuable reference source for
researchers, students, plant breeders, and other stakeholders alike interested
Foreword xiii
in high-end mango research. I personally congratulate the authors and the

entire team of dedicated scientists who have contributed their reviews,
research findings, and above all compiled up-to-date information in this
publication.
New Delhi, India K. L. Chadha

April 2020 Former Deputy Director General (Hort.)
Indian Council of Agricultural Research
Former ICAR National Professor (Hort.)
President, Indian Academy of Horticultural Sciences
Preface
Mango is one of the most ancient fruit trees of the world. This tree and its
parts, mainly leaves and fruits, have been cited profusely in the Sanskrit
literature. Its leaves and fruits were used in Hindu ceremonies and worships,
and the fruits had been a popular food for the masses. The mango fruit trees
are grown in India for at least the last 4000 years.
Scientific studies and mentions in literature by travelers suggest the
Indo-Burma region in the Indian Sub-continent to be the center of origin of
this crop. Presently, mango is grown as a popular fruit tree in the tropical or
subtropical regions of Asia and Africa. However, it was later introduced to
other continents and is grown now in pockets of some countries in North and
South America, Europe, and Australia. It is reportedly cultivated in 120
countries of the world; however, India, China, Thailand, Indonesia, and
Mexico contribute to the major share of production.
The mango fruit is not only a source of delicious food but also very rich in
the content of nutritional components and nutraceutical bioactives. Consid-
ering all these aspects, the mango fruit is rightly called as “the King of
fruits”! The mango tree caters to the needs of fuel for a large number of
families specifically in the rural and tribal areas of the developing countries.
In spite of such importance of mango tree, there is no book available that
presents a compilation on fundamental aspects such as basic botany, genetic
diversity, classical genetics, traditional breeding, and advanced research areas
including molecular genetics and breeding, genetic transformation, and
genomics. This book on “The Mango Genome” attempted to fill precisely
such a gap with 13 chapters. Chapter 1 presents a brief introduction on the
fruit tree with information on its ancient history, distribution, cultural sig-
nificance, nutritional and nutraceutical importance, and various usage.
Chapter 2 deliberates on the origin and distribution, taxonomy, morphology,
variability, phylogenetic relationships, and other botanical aspects such as
pollination, self-incompatibility, and polyembryony. Both sexual and asexual
means may be used for propagation in mango. However, the mode of
propagation depends on the existence of polyembryonic and monoembryonic
mango plants. Various vegetative propagation methods including cuttings, air
layering, and graftings are widely used in mango. Micropropagation has also
been practiced profusely. All these methods have been discussed in Chap. 3.
Genetic resources are highly useful in genetic improvement in an economic
plant species. Mango, Mangifera indica, has 69 wild allied species that serve
as the source of genes conferring mainly biotic and abiotic stresses. Some
xv
xvi Preface
of these allied species are also used as rootstocks for the same purpose.
Chapter 4 depicts these characteristics of the wild gene pool useful for wide
hybridization. In addition, this chapter describes different varieties and cul-
tivars, and presents details on collection, characterization, conservation, and
utilization of genetic resources of mango. The extent of genetic diversity in a
crop helps in planning the breeding strategies. Chapter 5 enumerates the
methods used in characterization of genetic diversity in mango. These
includes morphological observations, biochemical characterization, and
molecular analysis employing molecular markers. Chapter 6 deliberates on
alternate bearing in mango, a phenomenon in perennial fruit crops that
invokes for understanding of the underlying mechanisms for planning
profitable orcharding. Chapter 7 presents the classical genetic studies
including mode of inheritance of qualitative and quantitative traits, charac-
terization and cataloguing of varieties, and sources of resistance or tolerance
of stresses in mango. This chapter also enumerates the breeding objectives,
different methods of breeding practiced, and the achievements made in this
fruit crop. Various in vitro culture techniques including in vitro shoot
establishment and micropropagation, in vitro regeneration through organo-
genesis and somatic embryogenesis, encapsulation and cryopreservation, and
embryo culture practiced in mango have been discussed in Chap. 8. In
addition, it presented the outcome of the researches on genetic transformation
in this crop. Molecular mapping of genes and QTLs followed by
marker-assisted breeding are useful techniques in recent plant genetic
improvement. These techniques are much more important in mango because
traditional breeding is constrained with long juvenile phase, high heterozy-
gosity, alternate bearing, polyembryony, heavy fruitlet drop, etc. Molecular
mapping itself is also constrained because of heterozygosity and long juve-
nile period. However, a number of molecular genetic maps have been con-
structed for mango using several molecular markers such as RFLP, AFLP,
SLAP, SNP but mainly for F1 populations. A number of genes and QTLs
have also been mapped in mango. These information have facilitated
marker-assisted selection, association mapping, and genome-wide associa-
tion studies. Chapter 9 elucidates these techniques and achievements of
molecular mapping and breeding in mango. Chapter 10 presents mango
genome sequences of four varieties reported by four groups including
Amrapali from India, “Tomy Atkins” from USA, “Kensington Pride” from
Australia, and “Hong Jian Ha” and “Alphonso” from China. The chapter also
enumerated sequences of mango transcriptome and chloroplast genome.
Chapter 11 depicts the first draft genome of mango chloroplast of the
“Langra” cultivar and enumerates many new functional genes in mango.
Chapter 12 presents the status of functional genomics resources generated
through studies on transcriptomics, proteomics, and metabolomics in mango
and their applications in trait mapping as well as in breeding for specific
target traits. The last chapter, Chap. 13, deals with all available, viz., linkage
map-based, whole genome-based, transcriptome-based, and SNP
marker-based genomic resources and database available which can be further
used for variety of development programs as well as intellectual property
protection.
Preface xvii
The chapters of this book have been contributed by 47 authors precisely

39 scientists from 7 countries including Brazil, China, India, Malaysia,
Spain, Thailand, and USA. I express my thanks to them for their lucid and
resourceful deliberations. I am also grateful to Dr. K. L. Chadha, former
Deputy Director General (Horticulture), Indian Council of Agricultural
Research (ICAR), former ICAR National Professor (Horticulture) and pre-
sently the President of the Indian Academy of Horticultural Sciences for
writing the Foreword of this book. He is an authority on one of the leading
fruit crops of the tropics and subtropics.
I thank Dr. Zuzana Bernhart, the Executive Editor, Life Sciences of
Springer Nature and Mr. Praveen Anand Sachidanandam of the Production
Division of Springer Nature for their cooperation right from inception till
completion of this book project.
Hope this book becomes useful for the students, teachers, and scientists
interested in this fruit tree and the concepts and techniques dealt with.
New Delhi, India Chittaranjan Kole

July 2020
Contents
1 Mango: The King of Fruits . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Shailendra Rajan
2 Botany of Mango . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
M. Sankaran, M. R. Dinesh, K. Abirami, and C. Murugan
3 Mango Propagation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Victor Galán Saúco, Alberto Carlos de Queiroz Pinto,
Sisir Kumar Mitra, Fabio Gelape Faleiro,
and Francisco Ricardo Ferreira
4 Genetic Resources in Mango . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Shailendra Rajan, Manish Srivastav, and Heiplanmi Rymbai
5 Genetic Diversity Analysis of Mango . . . . . . . . . . . . . . . . . . . . 75
Xin Hua He, Shahril Ab Razak, and Cong Luo
6 Alternate Flowering in Mango . . . . . . . . . . . . . . . . . . . . . . . . . 95
Hutchappa Ravishankar, Nimisha Sharma, and V. K. Singh
7 Classical Genetics and Breeding . . . . . . . . . . . . . . . . . . . . . . . . 111
M. Sankaran, M. R. Dinesh, and K. V. Ravishankar
8 In Vitro Culture and Genetic Transformation in Mango . . . . 131
César Petri, Richard E. Litz, Sanjay K. Singh,
and José I. Hormaza
9 Molecular Mapping and Breeding in Mango . . . . . . . . . . . . . . 153
Pumipat Tongyoo, Janejira Duangjit, Nimisha Sharma,
and Julapark Chunwongse
10 The Genome Sequence and Transcriptome Studies in
Mango (Mangifera indica L.) . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Nagendra K. Singh, Ajay K. Mahato, and Pawan K. Jayaswal
11 The Mango Chloroplast Genome . . . . . . . . . . . . . . . . . . . . . . . 187
Manish Srivastav, Sanjay K. Singh, and Nimisha Sharma
xix
xx Contents
12 Mango Functional Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . 195

Anju Bajpai, M. Muthukumar, and Sandeep Kumar
13 Mango Genomic Resources and Databases . . . . . . . . . . . . . . . 219
Sarika Jaiswal, Mir Asif Iquebal, UB Angadi, Sunil Kumar,
Anil Rai, Nagendra K. Singh, and Dinesh Kumar
Contributors
K. Abirami ICAR-Central Island Agricultural Research Institute, Port Blair,

India
UB Angadi Centre for Agricultural Bioinformatics, ICAR-Indian Agricul-
tural Statistics Research Institute, New Delhi, India
Anju Bajpai Division of Crop Improvement and Biotechnology,
ICAR-Central Institute for Subtropical Horticulture, Lucknow, India
Julapark Chunwongse Department of Horticulture, Faculty of Agriculture
at KamphaengSaen, Kasetsart University, Nakhon Pathom, Thailand
Alberto Carlos de Queiroz Pinto Consultant on Tropical Fruits, Eng. Agr.
Ph.D. Researcher from Embrapa (Retired), Visitor Professor, University of
Brasilia-DF, Brasilia-DF, Brazil
M. R. Dinesh ICAR-Indian Institute of Horticultural Research, Bengaluru,
Karnataka, India
Janejira Duangjit Department of Horticulture, Faculty of Agriculture,
Kasetsart University, Bangkok, Thailand
Fabio Gelape Faleiro Eng. Agr. Dr. Researcher of Embrapa Cerrados,
Brasilia-DF, Brazil
Francisco Ricardo Ferreira Eng. Agr. Dr. Researcher of Embrapa Genetic
Resources and Biotechnology, Brasilia-DF, Brazil
Victor Galán Saúco Consultant on Tropical Fruits, Ing. Agr, Ph.D,
Research Professor (Retired), Instituto Canario de Investigaciones Agrarias,
Canary Islands, Spain
Xin Hua He State Key Laboratory for Conservation and Utilization of
Subtropical Agro-Bioresources, College of Agriculture, Guangxi University,
Nanning, People’s Republic of China
José I. Hormaza Departamento de Fruticultura Subtropical y Mediterránea,
Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM
La Mayora—UMA-CSIC), Algarrobo-Costa, Málaga, Spain
Mir Asif Iquebal Centre for Agricultural Bioinformatics, ICAR-Indian
Agricultural Statistics Research Institute, New Delhi, India
xxi
xxii Contributors
Sarika Jaiswal Centre for Agricultural Bioinformatics, ICAR-Indian

Pawan K. Jayaswal ICAR-National Institute for Plant Biotechnology, New
Delhi, India
Dinesh Kumar Centre for Agricultural Bioinformatics, ICAR-Indian
Sandeep Kumar Division of Crop Improvement and Biotechnology,
Sunil Kumar Centre for Agricultural Bioinformatics, ICAR-Indian Agri-
cultural Statistics Research Institute, New Delhi, India
Richard E. Litz Department of Horticultural Sciences, Tropical Research
and Education Center, University of Florida, Homestead, FL, USA
Cong Luo State Key Laboratory for Conservation and Utilization of Sub-
tropical Agro-Bioresources, College of Agriculture, Guangxi University,
Nanning, People’s Republic of China
Ajay K. Mahato ICAR-National Institute for Plant Biotechnology, New
Delhi, India
Sisir Kumar Mitra Board Member of International Society for Horticul-
tural Science (ISHS), Brasilia, Brazil
C. Murugan Botanical Survey of India, Regional Office, Coimbatore, India
M. Muthukumar Division of Crop Improvement and Biotechnology,
César Petri Departamento de Fruticultura Subtropical y Mediterránea,
Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM
La Mayora—UMA-CSIC), Algarrobo-Costa, Málaga, Spain
Anil Rai Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural
Statistics Research Institute, New Delhi, India
Shailendra Rajan ICAR- Central Institute for Subtropical Horticulture,
Lucknow, Uttar Pradesh, India
Hutchappa Ravishankar ICAR-Central Institute for Subtropical Horticul-
ture, Lucknow, UP, India
K. V. Ravishankar ICAR-Indian Institute of Horticultural Research, Ben-
galuru, Karnataka, India
Shahril Ab Razak Biotechnology and Nanotechnology Research Centre,
MARDI Headquarters, Selangor, Malaysia
Heiplanmi Rymbai Scientist, Division of Horticulture, ICAR Research
Complex for NEH Region, Umiam, Meghalaya, India
M. Sankaran ICAR-Indian Institute of Horticultural Research, Bengaluru,
India
Contributors xxiii
Nimisha Sharma Division of Fruits and Horticultural Technology, ICAR-

Indian Agricultural Research Institute, New Delhi, India
Nagendra K. Singh ICAR-National Institute for Plant Biotechnology, New
Delhi, India
Sanjay K. Singh Division of Fruits and Horticultural Technology, Indian
Agricultural Research Institute, New Delhi, India
V. K. Singh ICAR-Central Institute for Subtropical Horticulture, Lucknow,
UP, India
Manish Srivastav Division of Fruits and Horticultural Technology, ICAR-
Indian Agricultural Research Institute, New Delhi, India
Pumipat Tongyoo Center for Agricultural Biotechnology, Kasetsart
University, Nakhon Pathom, Thailand
Abbreviations
2,4-D 2,4-dichlorophenoxyacetic acid

2D-GE Two-dimensional gel electrophoresis
2iP N6-(2-isopentenyl)adenine
AB Alternate bearing
ABA Abscisic acid
ABI Alternate bearing index/intensity
ACC Aminocyclopropane-1-carboxylic acid
ACO Aminocyclopropane-1-carboxylate oxidase
ADB Asian Development Bank
AES (PARIA) Agricultural Experiment Station, Paria (Gujarat, India)
AFL2 Apple floricula/lfy (gene)
AFLP Amplified fragment length polymorphism
AGP Alpha-1,4 glucan phosphorylase
AM Association mapping
ANMG Australian National Mango Genebank
AP Apetala (gene)
APAU Andhra Pradesh Agricultural University (India)
B5 Gamborg B5 (medium)
BA 6-benzyladenine
BBI Biennial bearing index
BFT Brothers of FT
BP Barba and Pateña
BSSKVV Balasaheb Sawant Konkan Krishi Vishwavidyalaya
(India)
Cas9 CRISPR associated protein 9
cDNA Complementary-DNA
CH Carbohydrate
CiFT Citrus flowering locus T (gene)
CISH Central Institute for Subtropical Horticulture (ICAR,
India)
cM CentiMorgan
CO Constans (gene)
cpDNA Chloroplast DNA
cpgenome Chloroplast genome
CPLLs Combinatorial peptide ligand libraries
CR Chromosomal rearrangement
CRISPR Clustered regularly interspaced short palindromic repeats
xxv
xxvi Abbreviations
CW Coconut water
ddRAD Double digest restriction-site-associated DNA
DEGs Differentially expressed genes
DUS Distinctness, uniformity, and stability
EMS Ethylmethyl sulfonate
ERF ET-responsive transcription factor
EST Expressed sequence tag
ETS External transcribed spacer
FAO Food and Agriculture Organization
FAOSTAT FAO Corporate Statistical Database
FAP Full air porosity
FBD Fruit bud differentiation
FI Flower induction
FLC Flowering locus c (gene)
FRS Fruit Research Station, Sangareddy (Andhra Pradesh,
India)
FT FLOWERING LOCUS T (gene)
FUL Fruitful
GAs Gibberellins
GAU Gujarat Agricultural University (India)
GC Gas chromatography
GD Genetic distance
GDJ Jaccard’s coefficient
GDMR Modified Rogers’ distance
GDNL Nei and Li’s coefficient
GDSM Simple matching coefficient
GEA Global Environment Agency
GI Geographical indication
GLM Generalized linear model
GS Genetic similarity
GST Glutathione S-transferase
GUs Growth units
GWAS Genome-wide association studies
HB-1 Healthy bud stage
HB-2 Healthy panicle stage
HPLC High-performance liquid chromatography
HPP High-pressure processing
HSSR Highly variable SSR
IAA Indole-3-acetic acid
IARI Indian Agricultural Research Institute (ICAR, India)
IBA Indole-3 butyric acid
ICAR Indian Council of Agricultural Research
IIHR Indian Institute of Horticultural Research (ICAR, India)
INSDC International Nucleotide Sequence Database
Collaboration
IP Intellectual property
IPGRI International Plant Genetic Resources Institute
ISSR Inter-simple sequence repeat
Abbreviations xxvii
ITS Internal transcribed spacer

IU International unit
IUCN International Union for the Conservation of Nature
KEGG Kyoto Encyclopedia of Genes and Genomes
LB Luriabertani
LC Liquid chromatography
LFY Leafy (gene)
LINEs Long interspersed nuclear elements
lncRNA Long non-coding RNA
LRR Leucine rich repeat
LTR Long terminal repeat
MABI Modified alternate bearing index
MAF Minor allele frequency
MALDI Matrix-assisted laser desorption/ionization
MAS Marker-assisted selection
miRNA Micro-RNA
MLM Mixed linear model
MMD Mango malformation disease
MPKV Mahatma Phule Krishi Vishwavidyalaya (India)
mRNA Messenger-RNA
MS Mass-spectrometry/Murashige and Skoog (medium)
MTA Material Transfers Agreement
NAA Naphthalene-acetic acid
NCBI National Center for Biotechnology Information
ncRNA Non-coding RNA
NGS Next-generation sequencing
NMU N-nitroso-N-methyl urea
nptII Neomycin phosphotransferase
PAGE Polyacrylamide gel electrophoresis
PAL Phenylalanine ammonia-lyase
PCA Principal coordinate analysis
PCR Polymerase chain reaction
PDB Protein Data Bank
PEE Pulsed electric field
PEM Pro-embryonic mass
PGRC Plant Genetic Resources Center
PPO Polyphenol oxidase
PRJNA# BioProject accession
PVP Polyvinyl pyrrolidone
qPCR Quantitative PCR
qRT-PCR Quantitative reverse transcription PCR
QTL Quantitative trait locus
QTLs Quantitative trait loci
RACE Rapid amplification of cDNA ends
RAPD Random amplified polymorphic DNA
RDA Recommended daily allowance
RE Repetitive element
RFLP Restriction fragment length polymorphism
xxviii Abbreviations
RNA-Seq RNA-sequencing
ROS Reactive oxygen species
RT-PCR Reverse transcription PCR
RTS Ready-to-serve
SAM S-adenosyl methionine/shoot apical meristem
SCoT Start codon targeted
SDS Sodium dodecyl sulfate
SINEs Short interspersed nuclear elements
SLAF Specific locus-amplified fragment
SMRT Single molecule real time
SNP Single nucleotide polymorphism
SoC1 Suppressor of over expression of constants
SPL5 Squamosa promoter binding
SRA Sequence Read Archive
SRAP Sequence-related amplified polymorphism
SSR Simple sequence repeat
SVP Short vegetative phase
TDF Transcript derived fragment
TE Transposable element
TFL1 Terminal flower1 (gene)
TNAU Tamil Nadu Agricultural University (India)
TOF Time of flight
TPI Triosephosphate isomerase
TSS Total soluble solids
UPGMA Unweighted pair group method with arithmetic averages
VAD Vitamin A deficiency
VNTRs Variable number tandem repeats
WGD Whole genome duplication
WPM Woody plant medium
Mango: The King of Fruits
1
Shailendra Rajan
Abstract 1.1 Introduction

Mango, the “King of Fruits,” is an econom-
ically important fruit in various parts of the Mango is one of the most important fruits grown
world. In addition to its excellent tropical in the tropics and subtropics of the world. The
flavor, mangoes embody nutrition and make Mango tree is not merely revered as a religious
eating healthy and delightful sensory experi- object but also is valued owing to its enormous
ence. Though mango cultivation is reported economic potential as all its parts are considered
from more than 120 countries, merely 15 usable and are used for various purposes (Singh
countries have share of more than 1% in its 1960). It is a source of food, fuel, and fodder,
world production. More than 60% of world mostly in the traditional Asian countries. The
mango production comes from India, China, Mango fruit is a livelihood for millions of people
Thailand, Indonesia, and Mexico. Major por- across the globe banks. Apart from its numerous
tion of mango production is consumed as usages, it is a rich source of nutrients and several
fresh mangoes; however, dozens of its pro- rare bioactive compounds. Mango acts as a
cessed products are also being commercially source of vitamin A for millions of people living
produced. Mangoes are low in sodium while in different subtropical, semi-arid, and tropical
there is ample quantity of potassium, phos- regions of Africa and Asia. Mango also finds a
phorous, and calcium in the fruit. Apart from place in the high-tech commercial cultivation in
nutritional benefits for human health, mangi- Western hemisphere and is fast emerging as a
ferin and lupeol, native bioactive compounds super food fruit. The ripe mango fruit has a
in mango, have exhibited several distinctive combination of taste and flavor.
health-promoting characteristics including Realizing as a super fruit, the consumption and
antitumor-promoting activity. area under its cultivation are increasing inces-
santly. But the king of fruits is also facing several
challenges due to perennially changing climate
and emerging biotic stresses under varied agro-
ecologies. It is becoming an export crop com-
modity for several countries resulting in inter-
S. Rajan (&)
ICAR- Central Institute for Subtropical Horticulture,
national export market competition.
Rehmankhera, Kakori, Lucknow 226101,
Uttar Pradesh, India
e-mail: srajanlko@gmail.com; shailendra.
rajan@icar.gov.in
© Springer Nature Switzerland AG 2021 1

C. Kole (ed.), The Mango Genome, Compendium of Plant Genomes,
https://doi.org/10.1007/978-3-030-47829-2_1
2 S. Rajan
1.2 Voyages to Different Buddhist monks during the fourth-fifth centuries

Continents BC introduced mango to the Malaya Peninsula
and East Asia. Chinese explorer Hwen T’sang
The mango has a fascinating history of domes- introduced mango into China after his return
tication and distribution as the sea transportation from India to his native country during the sev-
was exceedingly important before the early enth century AD (Singh 1960). During the tenth
twentieth century. The common mango (Mangi- century AD, the Persians brought mango to East
fera indica) is believed to have been originated in Africa (Purseglove 1969) whereas Portuguese
the Indo-Burma region. Its wild types are still took them to West Africa and Brazil during the
existing at many places in the Indian subconti- sixteenth century AD (Singh 1960).
nent (Yadav and Rajan 1993; Rajan and Hude- In Americas, at the outset, mango was intro-
damani 2019). As an important consequence of duced and established in Brazil. Thereafter, it
its origin and domestication in Indian subconti- was bought in West Indies, first in Barbados (in
nent, mango has become a common fruit plant in mid of the eighteenth century) and later came to
India (Mukherjee 1951, 1953, 1972). Old his- Jamaica in around 1782. In the early nineteenth
torical works and its descriptions made by century, it arrived in Mexico from Philippines
ancient travelers took place earlier in Southeast and the West Indies. During 1862, mango came
Asia than Western hemisphere. The origin in the to Miami around the same time. About 40 types
Northeastern India indicated by many workers is of mangoes were transported from India and
explained by the prevalence of related Mangifera planted in North Queensland part of Australia in
species in the Indo-Burma region (Mukherjee 1875 (Morton 1987).
1997). The belief that mango might have been Buddhists and “Tamils” played an important
naturalized in India (Hooker 1876) has also been role in introducing mango from India to South-
substantiated by opinion of several researchers. east Asian countries. At an early stage, it was
“On the basis of taxonomic and recent molecular brought to Malay Peninsula by the “Tamils.”
studies results, there is now evidence that mango Introduction from Indochina Peninsula resulted
has developed in a vast area, including north- in spread of polyembryonic varieties in the
western Myanmar, Bangladesh and northeast Philippines. Perhaps Carabao and Pico varieties
India” (Mukherjee 1997). are the outcome of these introductions. Valmayor
The mango has been known in India since (1962) documented the introduction of mango in
time immemorial. De Candolle (1884) estimates Eastern and Western hemispheres. In Eastern
that it has been cultivated for the last 4000 years, hemisphere, it was introduced between thirteenth
a figure based on repeated reports of botanists; and twentieth centuries. Knight and Schnell
however, Hill (1952) views it to be 6000 years. (1992) documented the details of introduction in
On the basis of 60-million-year-old fossil the USA.
impressions of carbonized mango leaves in the Its travel from the Eastern hemisphere to the
Palaeocene sediments Meghalaya, Srivastava and Western hemisphere and acceptability as an
Mehrotra (2013) proposed the origin of Mangi- important fruit ensued its cultivation in many
fera in Indian subcontinent. This also supports countries and expanded newer area under its
the lineage of Mangifera in the Indian subcon- cultivation. In Western hemisphere, in some of
tinent often debated due to existing dozens of the developed countries, modern ways of culti-
wild relatives in Malay Archipelago (Ram and vation were adapted, mostly based on temperate
Rajan 2003). fruit production. Newer production technologies
Traders, travelers, and rulers were fascinated made it more important in the international
with Indian mangoes and their efforts during the market and established it as a commercial export
last 2,500 years established mango as a crop in crop in Latin American countries. Still, mango is
tropics and subtropics. Perhaps the efforts of traveling to different parts of the world where it
1 Mango: The King of Fruits 3
was not cultivated earlier and presently being Tamil term for mango suggests that it was
grown in about 140 countries. introduced from India to Peninsular Malaysia
and eastern Asia. Huien T’Snag (632-45), prob-
ably the first to document mango, puts the fruit to
1.2.1 Deeply Associated with Asian people’s attention outside India. Ibn Hankel
Culture (902-68), Ibn Batuta (1325-40), and Jordanus
(1330) were important foreigners who described
Prominence of mango in Indian mythology and mango in their works. Praise of this fruit reached
religious ceremonies forms part of the long his- its climax when a Turkman saint and poet, Amir
tory in the country. Ancient Hindus valued Khusroo (c.1330), admired mango in his verse.
mango highly not merely because of religious or The Ain-i Akbari, an encyclopedic treatise of the
sentimental considerations but also they fully Moghul emperor Akbar (c.1500-1600), gives a
realized its importance in the economic and lengthy account of mango and its varieties.
cultural life of the society (Singh 1960). The Akbar is famous for his creation of an enormous
Sanskrit word “Amra” (mango) implies that it is plantation of one lakh mango trees, the “Lakh
the fruit of masses. The Hindi word “Aam” Bhag” in Darbhanga, of which traces are still
means the masses or the populace. It has been surviving (Singh 1960). There are also numerous
intimately connected with Hindu religion and places where mangoes have been mentioned in
highly valued as fabled transformation of Pra- cultural and theological writings.
japati (God of creation). Inflorescence and leaves
are used by Hindus at various ceremonies and for
the worship of “Saraswati,” Goddess of Wisdom 1.2.2 Gaining Importance in the New
and Arts. The “pancha-pallava” or the bunch of World
five sprigs from the mango tree is used by Hin-
dus at various ceremonies (Singh 1960). Until the middle of the twentieth century, mango
The influence of mango on Indian culture is was considered as an important commercial crop
well known as in ancient India, man and women in the Asian countries. Later on mango cultiva-
linked their names with mango. The lady who tion expanded and still continues to extend in
presented mango grove to Lord Buddha was newer subtropical and tropical environments. It
herself known as “Amradarika.” In the epic has become an important export commodity in
Ramayana, Valmiki mentions gardens and even non-traditional mango-growing countries where
forests of mango trees. Name of ragas (scores of the considerable proportion of their fruit pro-
music) as Amra-takeswara and Amra-panchma duction is exported. Analysis of FAOSTAT,
are based on this fruit. It clearly states that in 2014 data indicates that Mexico is the highest
India, mango cultivation is nearly as old as exporter of mango with about 17% of the country
Indian civilization. Indian art also recognizes the production. Although Peru produces < 1% of the
supreme merit of mango. “Barhut Stupa” of 110 world production but its share in the export is
BC, “Ajanta,” and “Elora” bear testimony of its larger (27.5%). The production of Floridian
antiquity as being excellent examples of sculp- varieties of mangoes is adapted to wide range of
tures of that time (Singh 1960). agro-ecologies and responsible for the expansion
During the fifteenth century, traders and of newer production areas. Brazil is also an
Buddhist monks transported superior seedlings to important exporter of mango (8.08% of the
Southeast Asia. Important mango varieties of country’s production). Indubitably, when it
Thailand, Malaysia, Indonesia, Cambodia, Viet- comes to mango production, Asia has a major
nam, and Philippines are polyembryonic in nat- share. The top five countries producing mangoes
ure. This indicates the common origin are from Asia. Additionally, Bangladesh and
disseminated through seedlings to these coun- Philippines are in the list of top 10 countries.
tries. In Malaysia and Indonesia, the Sanskrit or America’s tropical countries, Nigeria, Brazil, and
4 S. Rajan
Mexico are representative of the top 10 mango among the people. Great Britain issued the
producers. Mango pulp export is one of the world’s first postage stamp “Penny Black” offi-
important export commodities for India. Pulp cially on May 6, 1840. Later on, the U.S. Post
export of about 100 m US$ from India takes Office Department issued its first postage stamps
place to more than 50 countries and Saudi Arab, on July 1, 1847. Not only Asian countries, where
Yemen Republic, Netherland, Kuwait, UK, and mango is important for centuries, Western
USA are the major importers (Anonymous hemisphere has also used stamps. Many Car-
2017). ibbean countries, like Anguilla, Aruba, British
The mango has become a crop grown in many Virgin Island, Curacao, Montserrat, Netherlands
warm subtropical areas and throughout the trop- Antilles, and Saint Maarten, have issued stamps
ics. Widely adaptable varieties have led to on mangoes. With the increasing importance of
widespread mango cultivation in differing agro- the fruit, Angola, Cameroon, Central African
ecologies in different countries. It is remarkable Republic, Comoros, Congo Republic, Gabon,
in Australia’s tropical and subtropical northern Gambia, Ghana, Guinea, Madagascar, Madeira
areas. The major development regions are Island, Mali, Mayotte, Senegal, South
Queensland, the North and Western Australia Africa/Venda, Sudan, Togo, Upper Volta
(Bally et al. 2000). Superior Indian cultivars have (Burkina Faso), and Kenya have also issued such
become common in Bangladesh particularly in stamps.
Rajshahi, Dinajpur, Kushtia, and new Satkhira
(Abedin and Quddus 1990) (Fig. 1.1).
Mango has gained a lot of importance in most 1.3 Changing Face of Cultivars
parts of the world due to its taste and economic in International Markets
value where it might not be grown as a com-
mercial crop but its importance is well recog- Red-peel cultivars dominate the international
nized. It is a source of livelihood for millions and mango export market because of their eye-appeal
has immense importance in the Asian continent but in Asian countries consumers select the fruits
and a few of them like India, Philippines, and on the basis of overall understanding of the
Pakistan have declared it as the national fruit. It variety. Naturally, this is because of populous
is the national tree of Bangladesh. Many coun- developed preferences for specific local yellow-
tries have issued postage stamps on mangoes on and green-colored varieties. The outstanding
account of its importance and wide adaptability local varieties are sold at a premium price but
Fig. 1.1 Area under cultivation in different countries

they don’t find place in the international market due to narrow adaptability (Ram and Rajan
because of their yellow or yellow green color 2003).
even at the ripe stage. Gradually, the scenario is
changing and yellow skin mangoes are also
recognized in the US market because of their 1.4 Nutritionally Rich Fruit
quality. “Ataulfo,” a yellow-colored variety has
gained increased interest of consumers in the US Mango fruit is rich in carbohydrates, minerals,
(Ledesma and Campbell 2019). At least this dietary fiber (pectin) (Bello-Pérez et al. 2007;
variety has played a role in breaking red-peel USDA 2020), vitamin C, and vitamin A (b-
variety preference in the market. This change carotene) (Saleem-Dar et al. 2016). Mango pulp
may help in opening way for the excellent Indian has an energy value between 60 and 190 kcal
varieties in the United States, not much preferred (250-795 kJ) for 100 g of the pulp (Tharanathan
because of their yellow or greenish peel. The et al. 2006). Several other phytochemicals of
scenario is also changing in India where people mango help to sustain good health (Masibo and
are now interested in the red-colored varieties. He 2009).
Many of the red-peel varieties might not be even Ripened mango fruit is a significant source of
sweet enough to match expectations of the Indian sugars (glucose, fructose, and sucrose) along
consumers but have firm pulp and longer shelf with other carbohydrates including starch and
life. Breeding programs for developing new pectins (Bello-Pérez et al. 2007). From a nutri-
mango varieties in India have red-peel color also, tional and flavor standpoint, these compounds
as one of the important objectives. Thus many of are essential for human health.
the newly developed varieties are red in color. The nutritional content of mango varies with
Although “Carabao,” “Manila,” “Nam Doc Mai,” variety, location, and maturity stage. The content
“Alphonso,” “Kesar,” “Totapuri,” “Edward,” of major constituents of pulp is hereunder.
“Osteen,” and “Palmer” are cultivars of minor
importance in US but now there is a growing Food value per 100 g of ripe mango pulp
interest for these varieties. Production of “Kent” Calories 62.1–63.7 Cal
has shown a significant increase in the recent past Moisture 78.9–82.8 g
due to its use as fresh fruit and products. Acreage Protein 0.36–0.40 g
under “Tommy Atkins” and “Haden,” the lead-
Fat 0.30–0.53 g
ing international cultivars, is declining in the
Carbohydrates 16.20–17.18 g
Western hemisphere due to less demand
(Campbell and Ledesma 2013). Fiber 0.85–1.06 g
The consumer in the conventional United Ash 0.34–0.52 g
States does not fully apprehend the use of Calcium 6.1–12.8 mg
mature-green mangos, but in recent past there has Phosphorus 5.5–17.9 mg
been considerable growth in demand in ethnic Iron 0.20–0.63 mg
markets for mature-green fruit (Campbell and Vit A (carotene) 0.135–1.872 mg
Ledesma 2013). Indian varieties like
Thiamine 0.020–0.073 mg
“Alphonso,” “Kesar,” and “Totapuri” have
Riboflavin 0.025–0.068 mg
received considerable attention in the United
States as a result of air shipment from India in the Niacin 0.025–0.707 mg
recent past. Commercial cultivation of Totapuri Ascorbic Acid 7.8–172.0 mg
in the Western hemisphere had little success. Trptophane 3–6 mg
Kesar is a new cultivar for masses and not much Methionine 4 mg
tried for cultivation in United States. Excellent Lysine 32–37 mg
Indian varieties like Alphonso have limitation
6 S. Rajan
Values based on Indian mango varieties Name Amount Unit Min Max
(Gopalan et al. 1977)
Lycopene 3 µg 0 6
Values based on analyses of Floridan cul-
Lutein + zeaxanthin 23 µg 6 63
tivars (Tommy Atkins, Keitt, Kent, and/or
Vitamin E (alpha- 0.9 Mg 0.79 1.02
Haden cultivars)
tocopherol)
Name Amount Unit Min Max

Source USDA https://fdc.nal.usda.gov/fdc-
Water 83.46 G 80.84 88.1
app.html#/food-details/169910/nutrients
Energy 60 Kcal During the preclimateric process, fructose is
Energy 250 kJ the main monosaccharide (Bernardes et al.
Protein 0.82 G 0.44 1.14 2008), while, in ripe mango fruit, sucrose is the
Total lipid (fat) 0.38 G 0.21 0.5 main sugar (Saleem-Dar et al. 2016). Significant
Ash 0.36 G 0.25 0.42 differences for carbohydrates (10.5 percent and
Carbohydrate, by 14.98 G 32.4 percent) were found in different African
difference mango cultivars (Othman and Mbogo 2009).
Fiber, total dietary 1.6 G 1.2 2.3 Starch is the most significant ingredient of unripe
Sugars, total 13.66 G
mango, which is hydrolyzed at a mature stage to
including NLEA glucose (Derese et al. 2017). Pectin, a structural
Sucrose 6.97 G 0.07 9.37 carbohydrate, is abundantly present at unripe
Glucose (dextrose) 2.01 G 0.66 5.97
stage in mango pulp and the molecular weight
decreases during ripening (Bello-Pérez et al.
Fructose 4.68 G 3.8 7.99
2007; Saleem-Dar et al. 2016) because of its
Calcium, Ca 11 Mg 7 16
hydrolysis (Prasanna et al. 2004).
Iron, Fe 0.16 Mg 0.09 0.41 Alike several other fruits, mango has low
Magnesium, Mg 10 Mg 8 19 content of protein and fat in the pulp. In Indian
Phosphorus, P 14 Mg 10 18 cultivars, the total protein in the pulp has been
Potassium, K 168 Mg 120 211 reported to be 0.5-1% (Saleem-Dar et al. 2016).
Sodium, Na 1 Mg 0 3 Fruit maturity and cultivars influence the amino
Vitamin C, total 36.4 Mg 13.2 92.8
acid content. Mango contains considerable
ascorbic acid amount of alanine, arginine, leucine, glycine,
Thiamin 0.028 Mg 0.014 0.041 isoleucine, and serine at ripe stage while others
are in trace amount (Tharanathan et al. 2006).
Riboflavin 0.038 Mg 0.02 0.072
Vitamin A is an essential nutrient in limited
Niacin 0.669 Mg 0.198 1.31
quantities necessary for good human health
Pantothenic acid 0.197 Mg 0.161 0.24 (FAO/WHO 2004). Mango acts as a source of
Vitamin B-6 0.119 Mg 0.053 0.164 vitamin A for millions living in the world’s
Folate, total 43 µg 20 69 various subtropical, semi-arid, and tropical
Folate, food 43 µg 20 69 regions, particularly in countries where vitamin
Folate, DFE 43 µg A deficiency (VAD) is prevalent (Thomas and
Choline, total 7.6 Mg Oke 1983) as carotene is an essential precursor of
vitamin A. In many countries, mango is dis-
Vitamin A, RAE 54 µg
tributed in abundance in rural areas of developed
Carotene, beta 640 µg 185 1680
nations. Dried mango pulp is also a good source
Carotene, alpha 9 µg 0 40 of carotenoids and can be stored for 4-6 months,
Cryptoxanthin, beta 10 µg 0 32 when fruits are out of season (Drammeh et al.
Vitamin A, IU 1082 IU 2002). Vitamin A content of mango fruit ranges
(continued) from 1,000 to 6,000 IU (Matheyambath et al.
2016). Extraordinarily, high plastoglobule con- leaves, heartwood, roots, and fruit, and have
tent in mango promotes high carotenoid bioac- antioxidant, anti-inflammatory, radioprotective,
cessibility (Jeffery et al. 2012; Mayne 1996). antitumor, immune-modulatory (Garcia et al.
Mango fruit pulp has very less lipid content 2003), anti-allergic, antidiabetic (Mustapha et al
and can be considered as fat free. Seeds are rich in 2014), antibone resorption, mono-amine oxidase
lipids and fatty acids’ composition is comparable inhibiting, antiviral (Guha et al. 1996; Amin et al.
with cocoa butter. Those fatty acids might play a 2019), antifungal (Kanwal et al. 2010), antibac-
role in the cosmetics, medicinal, and food sectors terial (Engels et al. 2011), antispasmodic,
(Sonwai et al. 2012; Jahurul et al. 2015). Promi- antidiarrheal, antiparasitic as well as lipolytic
nent fatty acids in the mango kernel include lig- (Yoshikawa et al. 2002), hepatoprotective, and
noceric, arachidic, linolenic, and behenic acids gastroprotective (Shah et al. 2010) properties. In
(Jahurul et al. 2015). Association between the spite of considerable progress in phytochemical
aroma intensity and taste depends on the ratio of and medicinal analysis of mango, more efforts
palmitic–palmitoleic acid in the maturing mango. are needed to explore its active components and
It also defines the aroma and flavor of mangoes their application in pharmaceutical industries.
(Gholap and Bandyopadhyay 1977). Such com- Mango fruits have various phenolics required
pounds play important part in mango flavoring for maintaining good human health. The pulp
biochemistry (Desphande et al. 2016). contains several polyphenolic compounds, such as
Acidity in mango fruit is mainly due to the mangiferin, gallotannins, quercetin, gallic acids,
citric and malic acid (Matheyambath et al. 2016). isoquercetin, ellagic acid, and b-glucogallin
The content of pyruvic, citric, succinic, oxalic, (Schieber et al. 2000). The peel also possesses
and malic acids is significant and the content mangiferin, quercetin, ellagic acid, kaempferol,
varies according to the variety (Shashirekha and and rhamnetin (Berardini et al. 2005a, b).
Patwardhan 1976; Kumar et al. 1993). As per the The compound, mangiferin (l,3,6,7-
United States National Research Council (1989) tetrahydroxyxanthone-C2-b-D-glucoside), a pre-
recommended Daily Allowance (RDA), mango dominant bioactive ingredient isolated from dif-
is a rich source of essential minerals such as ferent parts of mango tree has been extensively
calcium, iron, magnesium, phosphorus, potas- studied both in vivo and in vitro for pharmaco-
sium, zinc, copper, manganese, and selenium logical effects like antioxidant activity, antidia-
necessary for human health. The fruits are low in betic, antitumor, lipometabolism regulating,
sodium (Njiru et al. 2014). cardioprotective, antihyperuricemic, neuropro-
tective, antioxidant, anti-inflammatory, anti-
pyretic, analgesic, antibacterial, antiviral, and
1.4.1 Bioactive Compounds immunomodulatory effects (Du et al. 2018). It has
been shown that Zvnamite®, a mango leaf extract
Mango has been linked to many pharmacological rich in the natural polyphenol and mangiferin,
effects, including antidiabetic (Mustapha et al enhances sprint exercise performance when given
2014), antioxidant, antiviral (Amin et al. 2019), in combination with luteolin or quercetin
and anti-inflammatory. Various effects have also (Gelabert-Rebato et al. 2019a, b).
been documented, including antibacterial, anti- Lupeol, a natural pentacyclic triterpene present
fungal, anthelmintic, antiparasitic, anti-HIV, in mango fruit, has gained attention in recent past
antibone resorption, antispasmodic, antipyretic, which has shown strong anti-inflammatory, anti-
antidiarrheal, immunomodulation, hypolipi- arthritic, antimutagenic, and antimalarial action.
demic, antimicrobial, hepatoprotective, and gas- Lupeol has also been found to have antitumor-
troprotective (Shah et al. 2010). promoting activity in mouse skin tumorigenesis
Components of mango are recurrently used as (Saleem et al. 2004; Saleem 2009) and an effect
a traditional medicine to cure numerous ailments. on the oxidative stress caused by dimethylolbu-
Active constituents are present in stem bark, tanoic acid in liver (Prasad et al. 2008).
8 S. Rajan
1.5 Usage yogurts, soups, meat, fish curry, spices, etc.

Large variation in mango pickles can be attrib-
Quality, nutrients, and bioactive compounds in uted to the recipes used in different parts of the
mango fruit are affected by genotype and ripen- world. In India, several varieties, specific to
ing stage at harvest and growing environment. region, are known for making specialized pick-
Mango is widely used in food, cosmetics, and les. Appimedi pickle famous from Western Ghats
pharmaceutical industries, right from root to the of Karnataka is made of tender mango mainly
top of the tree (Singh 1960). The fruit is used in grown in forests and also on the riversides.
all stages of development. Premature fruit is used Mango pulp and pickles are the most exported
for extraction of tannins and in the preparation of commodities from India (Vasugi et al. 2012).
other astringent products, viz., chutneys, curries, With the advancement of processing technol-
cold drinks, pickles, etc. while ripe fruits are ogy, research on innovative processing of mango
utilized for puree, squash, nectar, drinks, mango has taken place in the recent years. Research on
leather, fruit bars, canned and frozen mango sli- high-pressure processing (HPP), pulsed electric
ces, and candies (Ram and Rajan 2003). Mango field (PEF) processing, Holmic heating, micro-
stones are used for raising seedlings, oil, fiber, wave heating, radio frequency heating, ultravio-
and as animal feed. The kernel is a rich source of let (UV) light, ionizing radiation, pulse light
carbohydrates, calcium, and fat, and starch can technology, ultrasound, and ozone treatments has
be produced for industrial purposes. Goats and been undertaken (Ahmed and Ozadali 2012;
cattle are fond of eating mango leaves while Ahemad 2017). Non-thermal processing tech-
branches and wood are utilized for fuel, timber niques for retaining nutritional and sensory
besides use of bark for extraction of tannins and properties have been used. These innovative
gums (Singh 1960). technologies are at development stages and
commercialization in near future will ensure
better utilization of the mangoes.
1.5.1 Processed Mango Products
In terms of the variety of processed items, mango 1.6 Concluding Remark and Future
is a special crop, used for processing at raw and Prospects
mature crop stage. At an early stage of fruit,
sweet or sour chutney (mango sauce) and whole Tropical and subtropical mango production con-
fruit pickle are prepared. While when reached the tinues to face both abiotic and biotic threats.
stone hardening stage, products like “amchoor,” Rising demands of mango fresh fruit and value-
pickles, and green mango beverages prepared. added products are related to customer’s choice.
The mature fruit is distinguished by a distinctive Being a climate stress-sensitive plant, the task for
flavor and taste. The technique has been devel- the breeders is to create robust plants as per the
oped for various products, viz., canned and fro- need of the fresh fruit and finished product
zen slices, pulp, jelly, squash, tea, nectar and industries. With increasing export and changing
ready-to-serve (RTS) beverages, mango cereal consumer demand, the cultivar need of different
flakes, concentrates, dehydrated products, mango regions is going to change. Traditional mango
fruit bars, and mango toffee. breeding is time taking and may become difficult
There are a large number of traditional mango due to the requirement of large human and other
products processed at home or cottage industry resources for developing sufficient breeding
level. Indian National Mango Database details population. Mango is vulnerable to many new
about 230 recipes based on mango (Rajan et al. disease, insect-pest, and climate change prob-
2020). Mangoes are used for several hundred lems, and wild relatives, as a source of genes for
dishes and are used with pulses, buttermilk, biotic and abiotic stress resistance, may be
utilized as gene donors. Useful mango germplasm (Mangifera indica L.) cv. ‘Tommy Atkins’ peels.
identified for many horticultural traits and iden- Chem Sci 60(7): 801–4
Bernardes SAP, do Nascimento JRO, Lajolo FM, Corde-
tification of favorable alleles and quantitative trait nunsi BR (2008) Starch mobilization and sucrose
loci (QTLs) for marker-assisted selection will accumulation in the pulp of keitt mangoes during
help in reducing the time taken in breeding vari- postharvest ripening. J Food Biochem 32(3):384–395.
eties. Molecular biology has added to the scope of https://doi.org/10.1111/j.1745-4514.2008.00175.x
Campbell RJ, Ledesma N (2013) The changing face of
mango breeding providing an option to manipu- cultivars for the Western Hemisphere. Acta Hort
late plant expressions in efficient manner. 992:55–58
Researchers will have to strive to combine the De Candolle A (1884) Origin of cultivated plants. Hanfer,
best conventional and modern molecular Kengan Paul, Trench, London, UK
Derese S, Guantai EM, Souaibou Y, Kuete V (2017)
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London, pp 451–483. https://doi.org/10.1016/B978-0-
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Botany of Mango
2
M. Sankaran, M. R. Dinesh, K. Abirami,
and C. Murugan
Abstract M.sylvatica, M.odorata, M.zeylanica and M.

nicobarica are reported to occur in India.
Mango (Mangifera indica L.), the king of
Huge variability has been recorded in M.
fruits, belongs to the family Anacardiaceae. indica due to its inherent characteristics such
Myanmar, Thailand, Indo-China, and Malaya as cross-pollination, heterozygosity, incom-
during the Eocene or an earlier period in the
patibility and polyembryony. The molecular-
Cretaceous were assumed to be the origin of based phylogenetic tree generated among the
genus Mangifera. Later, the genus spread to different species of Mangifera showed their
India, to Sri Lanka in the west, to Eastern
genetic relatedness based on amplification of
Malaysia and to the Philippines in the East. chloroplast DNA (cpDNA) and ITS genomic
Southeast Asia is said to be the centre of regions.
diversity of genus Mangifera with existence of
maximum diversity in Peninsular Malaysia.
Presently, maximum number of Mangifera 2.1 Introduction
species is found in Borneo, Sumatra, Java and
Malay Peninsula. 69 species of Mangifera Mango (Mangifera indica L.), popularly known
exist worldwide based on morphological as ‘King of fruits’, is the most important among
characterization which are classified into two the tropical fruits. The fruit is rich in vitamins,
sub-genera Mangifera and Limus with several minerals and other phytochemical compounds.
sections. Out of 69 species, M.andamanica, Since time immemorial, mango is cultivated and
M. griffithii, M.khasiana, M.camptosperma, consumed in India. This is evidenced by ancient
Indian literature and scripts. Mango is highly
associated with socio-cultural and economic life
of the people. Due to invasions, mango wealth is
M. Sankaran (&) M. R. Dinesh
enriched in India by introduction of superior
ICAR-Indian Institute of Horticultural Research,
Hesaraghatta Lakepost, Bengaluru 560089, India quality germplasm. Among the different inva-
e-mail: kmsankaran@gmail.com; m. sions, Muslim kings, Nawabs were mainly
sankaran@icar.gov.in involved in conservation of best varieties of
K. Abirami mango. The fruits of mango play a significant role
ICAR-Central Island Agricultural Research Institute, in both nutritional and livelihood security of the
Garacharma Post, Port Blair 744101, India
society by providing essential nutrients to con-
C. Murugan sumers. A drink made from boiled unripe mango
Botanical Survey of India, Regional Office, TNAU
with salt is a wonderful remedy for heat stroke.
Campus, Coimbatore 641003, India

https://doi.org/10.1007/978-3-030-47829-2_2
14 M. Sankaran et al.
Mango juice is a restorative tonic; it should be regions, evidenced by local names, Sanskrit
taken throughout the season to stay healthy. names, taxonomy and recent molecular findings.
Mango bark is used in the treatment of Jaundice. After many controversies, the recent findings
Dried leaf powder is used in dental care. Stones of firmly state that both origin and maximum
mango are also used with leaf powder in pow- diversity of the genus Mangifera exist in
dered form. Oil extracted from stones is used for Southeast Asia (Mukherjee 1997; Bompard and
industrial purposes. Traditional users use it as hair Schnell 1997). As per Indian History, mango
tonic. It stops premature greying. Fresh mango originated in India and from there it was spread
bark with warm water is recommended for the to other regions like Southeast Asia, New World
patients having Gonorrhea. Mangoes are also a and Africa, as Northeastern India is at the
good source of antioxidants. The phenolic com- northernmost edge for distribution of the Man-
pounds ranged from 48.40 mg/100 g in the cv. gifera species (Mukherjee 1997). The Sudanic
Haden to 208.70 mg/100 g in the cv. Ubá. The origin of the genus Mangifera was reported by
beta-carotene content in the cv. Ubá was found to Bompard and Schnell (1997) based on the exis-
be 2220 mg/100 g and 77.71 mg/100 g of ted diversity in Malay Peninsula, Borneo and
ascorbic acid was also observed (Rebeiro et al. Sumatra. Apart from this, region between
2007). Myanmar and Indo-China is one of the main
centres of diversification, as wide range of spe-
cies belonging to the section Euantherae (viz. M.
2.2 Origin and Distribution caloneura, M. cochinchinensis and M. pentan-
dra) exists here. In addition, M. indica apparently
Eastern India, Assam to Burma or the Malayan originated in region on Western border of the
region is believed to be the origin of the culti- secondary centre of diversification mentioned
vated mango (Mangifera indica L.). Hooker above. Wildly grown common mango trees have
(1876) reported that mango might have origi- been reported in Bangladesh (Chittagong Hills),
nated naturally in India as wild. Originally, the Northeastern India (Assam Valley), Andaman
cultivated mango was an alloploid (Popenoe and Nicobar Islands and Myanmar. The forests of
1920). However, Indo-Burma was also reported Indian subcontinent are enriched with semi-wild
as the centre of origin of mango (Vavilov 1926). trees of mango. Maximum species diversity of
The historical records, related species and genus the genus Mangifera exists in Northeast India, in
distribution, fossil remains and the presence of peninsular Malaya, Borneo and Sumatra (Ara
innumerable varieties and many indigenous wild et al. 2005). Seedling variations of primitive
species show enormous evidence for India to be characters like polyembryony and dwarf growth
the geographical origin for mango. Based on the habit with species richness are found in forests of
fossil remains of leaf imprints, it was established Borneo, Malay Peninsula, Indonesian archipe-
that Assam was origin of M. pentandra (Seward lago, Thailand, Indo-China and Philippines. It is
1912). With respect to origin of mango, there now evidently clear that the genus Mangifera
were many reports by different researchers. The evolves in a large geographical area of Burma,
origin of genus Mangifera was probably Burma, Siam, Indo-China and the Malay Peninsula as the
Siam, Indo-China and the Malay Peninsula centre of origin, with maximum diversity in
according to Mukherjee (1951). However, he Southeast Asia (Popenoe 1920; Mukherjee 1951;
also reported that cultivated mango originated Iyer and Subramanian 1989). The maximum
from Assam–Burma region rather than the Malay concentrations of different Mangifera species in
and during Quaternary period. In controversy, De major geographical regions are in Malay Penin-
Candolle in 1884 stated that ‘if mango is not sula (19), Sunda Islands (16), Eastern Peninsula
originated from South Asia or the Malay Archi- (14) including M. indica and its allied species
pelago, it is impossible to find the wide vari- such as M. sylvatica, M. pentandra, M. calo-
ability among the cultivars found in these neura, M. caesia, M. foetida and M. odorata
2 Botany of Mango 15
(Mukherjee 1949a). Wild M. indica which are The genus Mangifera is mainly distributed in
botanically similar to M. sylvatica, M. caloneura, the Tropical Asia with maximum species diver-
M. zeylanica, and M. pentendra and other Man- sity in Malay Peninsula, Sumatra, Java and
gifera species studied so have chromosome Borneo (Western Malaysia). The primary centre
number of 2n = 2 x = 40 (Mukherjee 1950; Roy of origin of the genus Mangifera is Myanmar
and Visweswariya 1951; Sharma 1987; Mustaffa (Burma)-Siam-Indochina or Malay Archipelago,
1993; Mitra 2001). whereas Sunda Islands (Java, Sumatra, Borneo),
the Philippines and Celebes-Banda-Timor group
is considered to be the secondary centre of origin
2.3 Taxonomy of the genus Mukherjee (1985).
The species diversity of the Mangifera spreads
Mango belongs to the genus Mangifera which from Malaysia to other parts of the world. One
comes under the family Anacardiaceae and order species spreads to Pacific area, nine species to
Sapindales. The family Anacardiaceae comprises India and three species to Srilanka (Kostermans
73 genera and 850 species mostly tropical origin, and Bompard 1993). Four species were found
which also include some crops of temperate endemic in Andaman and Nicobar Islands. The
regions. The other relatives of Mangifera are indigenous species of mango in Philippines are
cashew (Anacardium occidentale), gandaria M. merrilli and M. monandra. The species M.
(Bouea gandaria), pistachio (Pistacia vera), altissima is specifically found distributed in Cel-
marula (Sclerocarya birrea), ambarella (Spon- ebes Island (Kostermans and Bompard 1993).
dias cytherea), yellow mombin (Spondias mom- The genus Mangifera L. is divided into two
bin), red mombin (Spondias purpurea), imbu sub-genera, namely, Mangifera and Limus
(Spondias tuberosa), dragon plums (Dracon- (Marchand) Kosterm. These two sub-genera do
tomelum spp.) kaffir plum (Harpepbyllum caf- not have common base and reported to be orig-
frum), etc. which are mainly distributed in Malay inated from two different ancestors. Though this
Peninsula stretching from south of the Kangar- fact is established, the ancestors of the two sub-
Pattani line to the Bismarck archipelago east of genera and species of Mangifera are still a misery
New Guinea (Whitemore 1975). The family (Kostermans and Bompard 1993). The mango
Anacardiaceae consists of species that yield species distributed in India are M.indica L. M.
various products like wood, gums and resins, sylvatica Roxb., M. khasiana, M. andamanica
wax and varnishes and tanning materials other and M. camptosperma, M. griffithi and M. nico-
than edible fruits. The resinous sap of some barica. The cultivated mango, M. indica L., is
members of the family Anacardiaceae causes related to M. longipes Griff. However, wide
allergic reactions like dermal irritation including variability exists in distributed populations of M.
some Mangifera spp. sylvatica Roxb. These species have adaptability
to specific regions of precise climatic require-
Mangifera species ments. Therefore, it is very essential to conserve
Cultivated mango comes under the family these species either in situ or ex situ, where
Anacardiaceae and order Sapindales. The similar climate prevails.
botanical classification of mango is as follows: Mangifera indica L. belonging to the sub-
Division: Magnoliophyta genus Mangifera have four sections, namely,
Class: Magnoliopsida (i) Marchandora Pierre with types M. gedebe Miq;
SubClass: Rosidae (ii) Euantherae Pierre with types M. duperreana
Order: Sapindales Pierre (M. caloneura Kurz.) and species like M.
Family: Anacardiaceae cochinchinesis Engler and M. pentandra Hooker
Genus: Mangifera f.; (iii) Rawa Kosterm with types M. griffithii
Species: indica Hooker f. and species like M. andamanica King,
M. gracilipes Hooker f., M. parvifolia, M. merrillii M. dongnaiensis and M. orophila that exists
Mukherjee, M. microphylla, M. nicobarica Kos- 1000 m above MSL and rarely up to 1500–
term and M. minutifolia and (iv) Mangifera with 1700 m above mean sea level. M. caloneura, M.
types M. indica L. and 12 species are included in collina, M. timorensis and M. zeylanica are
this section. Sub-genus Limus (Marchand) Kos- adapted to grow in seasonal dry climatic region
term of genus Mangifera L. consists of six sec- like deciduous or semideciduous forests. Wild
tions, viz. (i) Marchand Revis. with types M. types of M. indica and M. sylvatica are dis-
foetida Lour.; (ii) Manga Marchnad with types M. tributed at altitudes 600–1900 m MSL in specific
leschenaultii; (iii) Eudiscus Pierre with types M. regions of South China and Northeast India.
superba Hooker f.; (iv) Microdiscus Pierre with Out of 69 reported species, only few of them
types M. caesia Jack; (v) Deciduae Kosterm with are edible and rest of them are non-edible
types M. caesia Jack including species like M. (Table 2.1). According to Iyer (1991), the spe-
kemanga, M. pajang, M. superba and M. caesia cies must fulfill two criteria such as it should
Jack and (vi) Perini’s Kosterm., sect. nov. with have edible fruits and must possess
types M. foetida Lour including species like M. resistant/tolerant to biotic/abiotic stresses to uti-
foetida Lour., M. leschenaultii, M. macrocarpa, lize in the breeding programme to introgress
M. odorata and perhaps M. lagenifera. The certain trait/traits in the cultivated variety back-
ancestral origin of these two sub-genera is differ- ground (Tables 2.2 and 2.3).
ent (Kostermans and Bompard 1993). Wide
diversity is reported in terms of intra-specific
Table 2.1 Mangifera species with edible fruits
variability in the species M. zeylanica, which is
known in the local name Etamba at Sri Lanka. M. altissima M. longipes
A total of 69 species of Mangifera are M. caesia M.macrocarpa
reported worldwide. The diversity of the Man- M. cochinchinensis M. odorata
gifera species is found naturally distributed M. foedita M. pajang
between 27o latitude North to Caroline Islands at M. griffithii M. pentandra
East (Bompard and Schnell 1997). Wild mango
M. indica M. sylvatica
species are distributed in different parts of the
M. lagenifera M. zeylanica
world like India, Sri Lanka, Bangladesh,
Myanmar, Thailand, Kampuchea, Vietnam, Iyer (1991)
Laos, Southern China, Malaysia, Singapore,
Indonesia, Brunei, the Philippines, Papua New
Table 2.2 Species close to cultivated Mangifea indica
Guinea, and the Solomon and Caroline Islands.
28 species of the genus Mangifera are known to 1. M. indica complex 11. M. odorata complex
occur in Malayan region and reported as maxi- 2. M. andamanica King 12. M.caesia Jack
mum diversity. The altitudinal distribution of the 3. M. caloneura Kurz 13. M. kemanga Jack casesia
Mangifera mostly occurs below 300 m MSL. var.kemanga
However, there are also reports that few Mangi- 4. M. camptosperma 14. M. foetida Lour.
Pierre
fera species may be distributed at 600–1900 m
above MSL. The tropical lowland rain forests 5. M. indica L. 15. M. lagenifera Griff.
enrich more diversity of Mangifera. Areas with 6. M. longipes Griff. 16. M. macrocarpa Blume
well-drained soils show maximum distribution of 7. M. minor Blume 17. M. odorata Griff.
Mangifera species (44), about 9 species in floo- 8. M. siamensis Warb. 18. M. pajang Kosterm.
ded region. Mangifera species like M. gedebe, M. ex Craib
griffithii and M. parvifolia are found distributed 9. M. sylvatica Roxb. 19. M. superba Hook.f.
in particular type of swamp forest regions. 10. M. zeylanica
(Blume) Hook.f.
Someao Mangifera species distributed in sub-
Mukherjee (1985)
montane forests include Mangifera bompardii,
Table 2.3 Mangifera species as donors

Sl.No Species Traits Region of
occurrence
1 M. caesia Jack. Pulp is aromatic, sweet and white in colour East Borneo,
Karangan reserve
2 M. decandra Ding Hou Survives in water-logged condition. Hence may be Sumatra,
exploited as rootstock Pakambarue
3 M. gedebe Miq. Survives in water-logged condition. Hence may be C.E. Borneo
exploited as rootstock
4 M. indica var. Multi-season fruiting Saigon
mekongensis
5 M. inocarpoides Merr. & Survives in water-logged condition. Hence may be Papua, Morehead
L.M. Perry exploited as rootstock
6 M. pajang Kosterm. Fruits may be peeled like banana Sarawak, Kapit
District
7 M. similis Blume Free stone mangoes Borneo
Iyer (1991)
Though there is a growing awareness about 3. Rare: M. andamanica

conservation and sustainable utilization of wild M. camptosperma
relatives of cultivated species, yet little efforts
M. gedebe
have been made to conserve Mangifera species
except M. odorata, M. laurina and M. zeylanica.
In fact, the basic data on cytology, crossability Efforts must be made among the Southeast
with the cultivated and prevalence of apomixis in Asian countries to conserve and utilize the
the wild species are lacking to initiate any Mangifera species. The incorporation certain
meaningful breeding programme. traits these wild relatives are very important
Though enormous diversity exists in the genus considering the impact of global climate change
Mangifera, threats also exists in the distribution phenomenon.
of different species. Mukherjee (1985) has The genetic diversity and utilization of wild
reported mango species under threat which are as species in perennial crops play a major role in
follows and they are also listed in the red data both rootstock and scion breeding. In the genera
book published by IUCN (International Union for Mangifera, wide species diversity exists with
conservation of Nature and Natural Resources). various utilities. However, very less work is done
to collect, characterize and the possibility of
1. Endangered: M. cochinchinensis
crossing wild species with cultivated species.
Pest and disease occurrence is a major threat for
M. flava
commercial cultivation of mango that results in
M. lagenifera
yield loss. So, exploiting the wild species for
M. pentandra biotic resistance is a major need. However, the
M. reba main issue is the conservation and regeneration
M. superba of wild species in regions other than their origi-
2. Vulnerable: M. duperreana nal habitat. This may be due to difficulty in
M. inocarpoides adaptation and acclimatization of the species in
M. monandra
other habitats. Hence, it is very much essential
for in situ conservation of wild and threatened
M. timorensis
species of mango in their original habitats or in
M. zeylanica
regions where similar climatic condition prevails.
(continued)
2.3.1 Description of the Mangifera 2.3.2 Botanical Descriptions

Spp of Mangifera Species
in India
The genus Mangifera has evergreen trees/shrubs
with aerid or resinous juice. Leaves are simple, Based on the IPGRI descriptors, some Mangifera
alternate, rarely entire, petiolate; stipules 0. sp. such as Mangifera Odorata, Mangifera,
Inflorescence is terminal or axillary panicles, Camptosperma, Mangifera zeylanica, Mangi-
often crowded at the apices of twigs. Flowers are fera griffithii and Mangifera andamanica are
small, male and bisexual (polygamous), 4–5 characterized morphologically and the results
merous; bracts caducous. Calyx is 4–5 lobed showed wide variation among the species with
with imbricate. Petals are 4–5 in numbers, free respect to leaf, fruit, tree and stone (Sankaran
and imbricate. Disc is fleshy, usually 4–5 lobed, et al. 2018).
sometimes obsolete in male flowers. Stamens are
(i) Mangifera andamanica King (J. As. Soc.
usually 5, rarely 10–12, usually 1–2 fertile, the
Bengal 65: 470. 1896; Parkinson, For. Fl.
others imperfect or sterile, much smaller, rarely
Andaman IsIs. 139. 1923; Chandra and
all 5 fertile. Ovary sessile, superior, 1 loculed, 1
Mukherjee 2000).
ovuled; style excentric or lateral; stigma simple.
Fruit is usually a fleshy drupe.
Trees are 9–12 m tall. Leaves are elliptic-
KEY to the Six Indian Species oblong, 9–23 4–6.5 cm, thinly coriaceous,
base cuneate, apex notched and petioles are 1–
1a Flowers 4 merous 2 2 cm long. Panicles are 10–12 cm long, terminal.
B Flowers 5 merous 3
Bisexual flowers are 4 mm across; pedicel 3 mm
long. Sepals are 4, ca 3 1 mm and petals are 4,
2a leaves up to 27 3 cm,; M. andamanica
Sepals ovate; petals ca 4 1.8 mm, with 4–5 prominent ridges,
broadly ovate-lanceolate confluent at base. Disc is four-lobed, cupular,
B leaves up to 15 15 cm; M.nicobarica fleshy, 1.5 mm in diameter. Stamens are 4, 1
sepals triangulate; petals fertile, 2.5 mm long, rest 3 short, teeth-like, and
spathulate sterile. Ovary is 1 mm in diameter, 1 loculed, and
3a Drupes distinctly flat M.camptosperma 1 ovuled. Drupes ovate, 2.5 1.7 cm, apex
B Drupes only slightly 4 subacuate and is in distributed in India (Assam
compressed and Andaman Islands).
4a Drupes acute or obtuse at M.indica
tip (ii) Mangifera camptosperma Pierre (Fl.
b Drupes acuminate, with 5 Cochinch. t. 363A. 1897. Thothathri &
protruded tip Balakr. in Bull. Bot. Surv. India 24: 175.
5a Leaves 25–30 5–7 cm; M.sylvatica 1982; D Chandra & S.K. Mukherjee in Fl.
panicles peduncled, India 5: 466.2000)
pyramidal, 20–30 cm or
more; petals lanceolate,
tip reflexed Large trees up to 30 m tall. Leaves are
b Leaves 7–13 2–3 cm; M.khasiana oblong, 14–45 4–8 cm, glabrous, cuneate at
petals ovate-oblong, tips base, entire at margin, apex acuminate to cau-
not reflexed panicles date; lateral nerves are 15–20 pairs; petioles are
sessile with fascicles of
1.5–2.8 cm, glabrous, pulvinate. Panicles up to
branches at the base, 5–
10 cm long 30 cm long, pubescent. Fruits are flat, elliptic, 6–
9 6–8 cm, green when unripe and yellow
when ripe; epicarp is thin; mesocarp is fibrous, number with 1 fertile stamen of length 3 mm.
0.8–3 cm thick and endocarp is woody. Seeds Rest of the stamens are teeth-like staminodes.
reniform, 5 3 cm, filling most of the cavity of Disc is fleshy, erect, ca 0.7 1 mm, with 5
the stone. Distributed in India (Andaman and ridges and furrows. Ovary ca 1 mm in diameter,
Nicobar Islands), Myanmar, Vietnam and conical; style is lateral, ca 2 mm long. Fruits not
Thailand. seen. Distributed in India (Sikkim and Megha-
laya). Tree is endemic.
(iii) Mangifera indica L. (Sp. Pl. 1: 200. 1753;
Hook.f., Fl. Brit. India 2: 13. 1876; D (v) Mangifera nicobarica Kosterm. (in Kos-
Chandra & S.K. Mukherjee in Fl. India 5: term. & Bompard, The Mangoes 52. 1993; D
466.2000) Chandra & S.K. Mukherjee in Fl. India 5:
469.2000)
Variability exists in tree height ranging from
20 m to 45 m. All parts of the tree are glabrous Trees are up to 20 m tall; branches reddish-
except the inflorescence. Shape of the leaf is brown. Leaves are oblong or elliptic-
oblong-lanceolate, 15 to 30 3.5–6.5 cm, thinly oblanceolate, ca 15 5 cm, gradually tapering
coriaceous, base cuneate, margin entire, acute- and decurrent at base apex acute-shortly acumi-
acuminate apex; petioles are 1.5–6 cm long. nate; lateral nerves are 8–12 pairs; petioles up to
Length of panicles is 15–35 cm, terminal, rarely 2.5 cm long. Inflorescence is pseudo-terminal
axillary. Hermaphrodite and male flowers are panicles, fascicled; peduncles are pseudo-
5 mm in width and length of pedicel is 1.5– racemoid, 9–15 cm long. Flowers are white or
3 mm. Calyx is 5 lobed; lobes ca 2 1 mm, yellowish, 4 merous. Sepals are triangulate, up to
tomentose. Petals are elliptic, 5, ca 3 1.2 mm, 1.25 mm long. Petals are spathulate, ca 1.5 mm
with branched ridges and reflexed tips. Stamens long. Distributed in India (South Nicobar). Tree
are 5 in number with 1 fertile stamen and length is endemic. The species is closely allied to M.
2.5 mm. Rest of the stamens are sterile, small, andamanica and M. quadrifida, but differs from
teeth like; Disc ca 1.5 mm in diam., distinctly 5 them in leaf characteristics, and in case of latter
lobed. Ovary ca 1 mm in diam and obliquely in floral details as well.
ovoid, 1 loculed, 1 ovuled; styles ca 2 mm long,
lateral. The shape of drupes is oblong or sub- (vi) Mangifera sylvatica Roxb. (Fl. Ind. 2: 644.
reniform with sweet juicy pulp. Distributed in 1824; D Chandra & S.K. Mukherjee in Fl.
India (cultivated almost in all states), Nepal, India 5: 469.2000. (Common name: Asm:
Bangladesh, Myanmar and Malesia. Ban-am, Lakshmi am; Chittagong: Basam,
Kosam; Lep: Katur; Nep: Chuchi-am;
(iv) Mangifera khasiana Pierre (Fl. Cochinch. Sans.: Kosamra; Tipp.: Haibamin)
t. 364C. 1897. Mukherjee in Lloydia 12: 97.
1949; D Chandra & S.K. Mukherjee in Fl. Trees are 30–40 m tall. Leaves are lanceolate,
India 5: 468.2000) 25–30 5–7 cm, thinly coriaceous. Apex is
acuminate; petioles are 5 cm or more. Panicles
Leaves of the tress are lanceolate, 7.5– are 30–40 cm, terminal, glabrous, laxly flowered.
13 1.8–3 cm, thinly coriaceous, apex acumi- Flowers are ca 4 mm across; pedicel is ca 3 mm
nate; petioles are 0.8–2 cm long and slender. long. Calyx is 5 lobed, ca 1.5 0.5 mm, glab-
Panicles are 5–10 cm long, terminal and glabrous. Petals are 5, linear-lanceolate, ca
rous. Flowers are ca 4 mm across; pedicel 2– 4 0.8 mm, with 3 longitudinal swellings.
3 mm long. Calyx 5 lobed; lobes ovate, ca. Stamens are 5, 1 fertile, 3 mm long and rest
2 1 mm glabrous. Petals are 5, ca. teeth-like staminodes. Disc is ca 1 0.8 mm,
3.5 1.3 mm, concave, with 3 prominent erect, with 5 ridges and furrows. Ovary globose,
swellings, non-reflexive tips. Stamens are 5 in ca 2 mm in diam., style sub-terminal. Drupes are
M.andamanica M.camptosperma M.grifithii
M.indica M.odorata
M.zeylanica
Fig. 2.1 Fruits of different Mangifera species
4.5–6 2.5–3 cm, obliquely acuminate, beak seedling trees may get enough canopy space and
much drawn out; flesh is thin, white, slimy, hence exhibits vigorous growth. In contrast to
without any fibres. It is distributed in India this, the orchard grown trees will be of less
(Sikkim, Assam, Arunachal Pradesh, Meghalaya, vigour due to the reduced canopy space. There
and Andaman and Nicobar Islands), Nepal, are also few cultivars like Latra and Creeping
Bangladesh and Myanmar (Fig. 2.1). which are of spreading in growth habit and can
be trained as creeper without utilization of any
canopy space unlike other mango varieties. The
2.3.3 Detailed Description Indian origin mango cultivars also show wide
of Mangifera Indica L variation in canopy characteristics like com-
pactness of the canopy, branching pattern and
2.3.3.1 Tree Canopy leaf component. The variation in canopy char-
The trees from seedling origin are of vigorous acteristics was observed based on ecogeograph-
types with strong tap root and straight bole. The ical distribution of mango cultivars. The
seedling origin tree shows sympodial growth longevity of seedling origin trees is more than
which is known as Scarrone’s model. However, 100 years. However, the grafted mango trees
grafted trees are comparatively dwarf with have comparatively lower longevity and may
spreading branches. The canopy shape depends survive up to 80 years or less. In India, it is
on the availability of space, edaphic factor and reported that a largest mango tree is observed in
climatic influence. Naturally grown isolated Chandigarh with a wide trunk diameter of 3.5 m
and branches of 75 cm diameter. The canopy leaf also shows variations like wavy, entire,
space occupied by the tree is about 2250 m2. The undulated, twisted or folded. Leaf apex is
yield of the tree is about 16000 fruits in peak acuminate or rounded. The leaves are simple,
bearing years even after the tree age of 100 years exstipulate with alternate arrangement and
(Singh 1960a). The largest trees are also found in groove on upper side. The petiole has a swollen
various parts of the world. One such seedling tree base and the length varies from 1 to 12 cm. The
is reported (Popenoe 1920) from Brazil which leaves appear whorled as they are very closely
has a canopy spread of 125 ft and a girth of 25 ft.. arranged at the tips. Based on the growing con-
In general, the trees of Mangifera indica are dition and region, leaf size shows variation in
medium to large in stature with height ranging both length and breadth. The range of length
from 10 to 40 m. The trees are evergreen with varies from 12 to 45 cm and breadth ranges from
round canopy. The canopy shape varies among 2 to 12 cm. Fibres are present in leaves, which
the different cultivars ranging rom low and dense becomes brittle after drying and crackles when
to upright and open. The bark of the tree is crushed. Prominent secondary veins ranges from
usually rough and dark grey brown to black 18 to 30 pairs. The leaf’s lower surface is glab-
coloured, cracked outside or sometimes incon- rous and light green in colour whereas the upper
spicuously fissured. Presence of resinous canals surface is shiny and dark green in colour. The
is the characteristic feature of all members of new leaves emerge in flushes and are flaccid and
Anacardiaceae and the bark exudate is dark yel- pendulous while young. Varietal difference exists
lowish brown in colour and comprises resin in the colour of young leaves and is tan-red, pink
mixed with gum. On drying, the exudate changes or yellow brown in colour depending on the
colour to brown. Tannic acid, 78% resin and variety. The colour of the leaf changes to dark
15% gum are present in the bark. green when fully matured. In some varieties,
Lanceolate acute bud scales envelop the small turpentine smell is observed and few varieties are
terminal which appears during the initial stage of without any odour. Xanthones, mainly the man-
flowering. The twigs on the tree branches are giferin, are present in leaves. If cattle are exces-
thick, glabrous and dark green in colour with sively fed with mango leaves, they die due to
smooth and glossy appearance. The root system xanthones.
of the mango tree is strong with both tap root and
feeder roots. The tap root is long which grow 2.3.3.3 Inflorescence
deeper into the soil and is unbranched. The Both the new leaf sprout and inflorescence
length of the tap root ranges from 6 to 8 m or emerge from the bud and they are pseudo-
more. The feeder roots are highly dense and are terminal. However, there are a few cultivars
developed at the base of the trunk or little deeper. which have laterally positioned inflorescence.
The feeder roots are very important as anchor The shape of inflorescence is narrow at the tip
roots are produced by these feeder roots. The and broad at the base with a conical shape and
presence of good water table enhances the pro- the length is about 45 cm; however, the length of
duction of feeder roots and more feeder roots are the inflorescence varies depending on the culti-
produced above the water table. The root system var. Lanceolate acute bud scales envelop the
of an 18-year-old tree grows to a depth of 1.2 m small terminal which appears during the initial
and spread to an area of 7.5 m laterally (Bojappa stage of flowering. Many cultivars have
and Singh 1974). inflorescence with bracts and a very few are
ebracteate. The shape of the bract if present is
2.3.3.2 Leaves elliptical, concave and leafy. The inflorescence
Wide variation exists in the appearance of mango has panicles with yellowish green colour or light
leaves like oval-lanceolate, lanceolate, oblong, green with crimson-coloured patches. The
linear-oblong, ovate, obovate-lanceolate or inflorescence is pubescent but rarely glabrous in
roundish-oblong (Singh 1960b). Margin of the few cultivars. Tertiary and sometimes quaternary
Fig. 2.2 Types of shoots and inflorescence in mango (Davenport 2007)
branching of inflorescence called cymose exists reflexed upper half that are thin. Slightly dark
in the species (Singh 1960a, b). The number of ridges are found in petals. The petal colour
flowers per panicle varies between cultivars and changes to pink on drying. Five-lobed disc is
usually ranges from 500 to 6000 flowers. 70% of found in between corolla and androecium (Singh
flowers are bisexual and remaining 30% are male 1960a, b; Kostermans and Bompard 1993).
flowers. However, the ratio of bisexual and male Together, five staminodes and stamens are found
flowers depends on the varieties and also vary in androecium, of which one would be fertile and
due to the temperature variations existing during rarely two. Rest of them are sterile. The fertile
floral development (Fig. 2.2). stamens have longer length when compared to
staminodes and equal to the length of the pistil.
2.3.3.4 Flower Few variations observed in the structure of
Both male and hermaphrodite flowers exist in the androecium like cultivar Pico have three fertile
same panicle with more proportion of male stamens (Juliano and Cuevas 1932). A rare
flowers when compared with hermaphrodite variation is found in few other members of the
flowers. The male and hermaphrodite flowers are genus, where ten stamens in the form of pri-
small in size and ranges from 6 to 8 mm in mordia only are present (Maheshwari 1934). The
diameter. Flowers are aromatic, subsessile and stamens are attached on the inner margin of the
pedicellate rarely. Pedicels are usually absent and disc. Stamen and pistil are distributed and par-
very short if present. Panicle branch diameter is allel or oblique position to each other (Naik and
same as pedicel and is of articulate nature, and Gangolly 1950). Generally, the anthers are pink
hence sometimes assumed as pedicel (Barfod coloured and turn into purple colour during
1988). Calyx has five sepals with ovate-oblong flower shed. The ovary is slightly compressed
and concave lobes. The corolla is double the laterally and is sessile, oblique shaped. The disc
length of calyx with five petals (rarely four to has the ovary. In few genotypes, three carpels
eight), which are yellow coloured and three to develop into a flower. The ovule shows one-
five ridges on the ventral side. At bud stage, sided growth, which is anatropous and pendulous
petals are imbricated and are contorted. The nature. The style ends in stigma which arises
petals are free at base with irregular and non- from the edge of the ovary (Singh 1960a, b). The
Fig. 2.3 Filament

attachment in the anther sacs
of different Mangifera spp
Fig. 2.4 Pollen grain size

and shape of different
Mangifera spp
size of pollen grains varies among different the two poles. The pollen of the species M. odor-
varieties and ranges from 20 to 35 micron ata is zono-tricolporate shaped with endoapertu-
(Mukherjee 1950; Singh 1954a). The pollen raten pores arranged in 3 colpi. M. odorata has
grains are in variable shapes like spheroidal to semi tectate exine with striato-reticulate orna-
prolate spheroidal, radially symmetrical, suban- mentation. The length of polar axis is 40–45 µm
gular in polar view, isopolar, and have few big and breadth is 15–20 µm with perprolate shape.
triploid grains with size up to 50 micron. Man- The pollen grains are oblong shaped in the species
gifera indica usually produces pollen grain in M. camptosperma. Endoaperture is absent in M.
small quantity and they are 3-monocolporate and camptosperma pollen and hence is called as zono-
goniotreme. The sides of pollen grain are tricolpate type. The structure of exine is semi-
convex-subprolate with equidistant apertures and ectate type with reticulate sculpturing. The length
the external aperture (colpus) extends like a slit of polar axis is 25–30 µm and breadth is 5–20 µm
between the two poles. with perprolate shape (Sankaran et al. 2018)
(Figs. 2.3 and 2.4).
2.3.4 Pollen Characteristics 2.3.4.1 Floral Biology

The inflorescence is generally terminal in all the
The shape of the pollen grains in all species is species of the genus Mangifera; however, mul-
elliptic to oblong. The pollen of Mangifera indica tiple and axillary panicle from axillary buds is
is elliptic to oblong shaped with poles slightly also observed. Both male and hermaphrodite
flattened. The pollen of Mangifera indica has the flowers are seen in same panicle. The number of
presence of three colpi along the polar axis with an flowers per panicle varies among different spe-
inner porate aperture. The structure of exine is cies and varieties and the range is usually 1,000–
semi-tectate and the tectum is perforate with stri- 6,000 (Mukherjee 1953). The fruit set at initial
ato-microreticulate sculpturing. The length of the stage is determined by the proportion of bisexual
polar axis (P) is 35–40 µm and breadth is 15– flowers (Iyer et al. 1989). Hence, for economic
20 µm with prolate shape. The pollen of M. fruit set, the distribution of perfect flowers is an
odorata is elliptic in shape and is tapering towards important factor and when the percentage of
perfect flowers is less than 1%, fruit set will be the genus Mangifera and also among different
critical. Variation is observed among the different varieties of Mangifera indica. The fruit shape
species of Mangifera for anthesis. Flower usually varies from round to ovate-oblong among dif-
starts opening in the early morning hours in the ferent varieties with length ranging from 2.5 cm
genus Mangifera and continues up to noon in to 30 cm. The peel colour of the fruit at maturity
sunny situations. Between 9 and 10 a.m. maxi- also shows wide variation and colours exhibited
mum flower opening is observed in many vari- green, yellow and red shades. The peel is smooth
eties of the genus Mangifera. After anthesis, or rough with dotted glands. Both the fruits and
stigma shows maximum receptivity up to 6 h; fruit stalk have some acrid juice with turpentine
however, it extends up to 72 h in some varieties. smell due to the presence of myrcene and oci-
There are reports that in few varieties’ stigma mene in some varieties and is called as chenp in
receptivity initiates before flower opening (Singh Hindi. The acrid juice causes irritation to the
1960a, b). The pollination and fruit set depend on tongue and is due to the presence of chemical
both the factors such as pollen viability and called urushiol, 5-heptadecenylreorcinol.
stigma receptivity. About 1.5 h is required for
germination of pollen grain in Mangifera (Sen
et al. 1946: Singh 1954b; Spencer and Kennard 2.4 Pollination in Mango
1955). Under proper controlled condition, the
pollen viability could be retained for a long The genus Mangifera is highly heterozygous and
period of time. It is reported that pollen grains of cross-pollinated. However, there are also reports
Mangifera are viable even after 11 months of that self-pollination occurs in mango (Dijkman
storage with 98% viability under controlled and Soule 1951). Wide range of pollinators are
storage conditions at 7 °C and 25% RH. At reported as pollinating agents including wind,
decreased storage temperature, the viability of gravity and insects. Among the insects, honey
pollen grains can still be prolonged and stored up bees, house fly and thrips are major pollinating
to 24 months at 0○C and 25% RH (Singh and agents (Popenoe 1917; Maheshwari 1934; Malik
Singh 1952). 1951). Less than 50% of flowers get pollinated
when there is poor distribution of pollinating
2.3.4.2 Fruit Characters agents.
Botanically the fruit of Mangifera is fleshy drupe
with compressed nature. Variability occurs in
shape, size, colour, aroma, fibre content, flavour, 2.4.1 Incompatibility
taste and biochemical composition among the
different varieties and species of Mangifera. The Self incompatibility is reported in the genus
presence of beak (a small conical projection Mangifera by several workers (Singh et al. 1962a,
develops at proximal end of fruit) is also an b; Mukherjee et al 1968 and Sharma et al. 1972).
important characteristic feature of the fruits of Sporophytic self-incompatibility is reported in
Mangifera. However, variation occurs in the mango. However, cross-incompatibility also
appearance of beak among different genotypes. occurs in mango (Ram et al. 1976). The existence
Above the beak, a sinus is present in the fruits. of self-sterility was also doubted in genus Man-
The base of the fruit is elevated or depressed or gifera (Dijkman and Soule 1951). Based on the
intermediate to both depending on the variety. At eembryological studies, it was observed that
the base of beak, nak is present which is the 15 days after pollination, degeneration of endo-
pistillate area of the fruit. The fruit shape is not sperms occurs after self-pollination in spite of
uniform and it varies among different species of normal fertilization (Mukherjee et al. 1968).
2.4.2 Polyembryony preference as edible varieties. Hence, the

monoembryonic cultivars are of commercial
Both monoembryonic and polyembryonic modes importance in India, Florida, South America and
of reproduction are reported in the genus Man- Africa due to the superior fruit quality parame-
gifera. The seedling per seed is single in ters. The polyembryonic mango cultivars are
monoembryonic type of germination and more valued in countries like Southeast Asia, Central
than one seedling per stone are produced in America, Haiti, Hawaii, Australia and South
polyembryonic types. The polyembryonic seed- Africa due to their utility in crop improvement
lings arise from both the zygotic tissue and the (Singh 1960; Shukla et al. 2004). Classification
nucellar tissue which are surrounding the embryo of mango cultivars based on their embryo type
sac. The seedlings originated from the nucellar and geographical origin was done by RAPD
tissue are true to type. However, the monoem- molecular characterization (Lopez-Valenzuela
bryonic seedlings are variable as they are of et al. 1997). The genetic diversity analysis of
zygotic origin. In polyembryonic mango vari- both polyembryonic and monoembryonic vari-
eties, the nucellar seedlings will be vigorous and eties by RAPD markers, total genomic DNA and
the zygotic seedlings will degenerate. One chloroplast DNA RFLP (Ravishankar et al. 2004;
exception is observed in the variety Pico from Abirami et al. 2008) showed that polyembryonic
Philippines where both nucellar and zygotic and monoembryonic varieties have different
seedings remain after seed germination. The genetic base.
embryological study by Maheshwari and Ran-
gaswamy (1958) showed the presence of thick
and dense cytoplasm and starch content in 2.5 Variability in Mangifera indica
adventitious embryos originated from nucellar
cells. The adventitious embryos thus formed in The total number of cultivars reported in Man-
the nucellar region are slowly pushed into the gifera indica was 1595 in 1998 by Pandey.
cavity of embryo sac and they further divide and However, the list was revised as 1663 in 2010
differentiate into embryos. The occurrence of (Pandey and Dinesh 2010) and updated checklist
polyembryony in mango is determined geneti- was reported as 1682. The recently updated
cally. Polyembryony in mango is governed by cultivars/varieties are Ambika, Arunika, Pusa
recessive genes and is controlled by single pair of Pratibha, Pusa Shreshth, Pusa Lalima, Pusa
genes (Leroy 1947 and Sturrock 1968). How- Peetamber, Arka Neelachal Kesari, Arka Ravi,
ever, an exception in this is that an Indian Pant Chandra, Pant Sinduri, Mankurad Aldona,
monoembryonic cultivar Malgoa (Mulgoba) Paiyur-1, Vanlaxmi, Rajrani, Parish, Suvarna,
showed polyembryonic nature when grown in Sai Sugandha, Martmanbhog and Khirma. There
Florida (USA). Popular polyembryonic mango is a huge variability, which occurs among the
cultivars reported are Bappakai, Chandrakaran, cultivated and wild genotypes of mango (Pandey
Kurukkan, Mazagaon, Mylepalium, Muvandan, and Dinesh 2010). Seven hot spots of mango
Nekkare, Nileswar Dwarf, Olour and Peach, diversity reported in India are (i) humid sub-
from India. Polyembryonic genotypes are repor- tropical region (Manipur, Tripura, Mizoram and
ted to be introduced in India from Southeast Asia south Assam); (ii) Chhota Nagpur Plateau (tri-
(Ravishankar et al. 2004). Cambodiana, Carabao, junction of Madhya Pradesh, Odisha and Bihar);
Corazon, Edward, Palo, 13-1, Pahutan, Pico, (iii) Santhal Paragana; (iv) Southern Madhya
Senora, Starch, Strawberry and Florigon are the Pradesh (tribal area) adjoining Odisha and
polyembryonic cultivars reported from other Andhra Pradesh; (v) Dhar Plateau of Madhya
countries. Occurrence of polyembryony is Pradesh adjoining South Rajasthan and Gujarat,
reported more from coastal regions of India. The (vi) humid tropical southern peninsular India and
polyembryonic mango cultivars are highly (vii) Andaman and Nicobar group of islands
fibrous and are of inferior quality with less (Yadav and Rajan 1993). In addition to this
biodiversity hot spots of mango, Gangetic Plains, Africa; Bourbon of Brazil; Golden Brooks,
eastern peninsular region, Eastern and Western Florigon, Davis Haden, Zrifin, Glenn and Van
Ghats and Deccan plateau of India also show Dyke of Florida; Kensington of Australia; Nam
diversity richness. The genes controlling specific Doc Mai, Nuwun Chan, Namtal and Pak-Kra
traits like dwarfness, fruit size, red-peel colour, Bok of Thailand; and Tahar and Naomi of Israel
high pulp content, high content of total soluble come under the classification category of large
solids, long shelf life of fruit, regularity in fruit fruit size group. Among the Indian varieties, very
bearing, earliness and lateness in fruit maturity large fruit-bearing cultivars are Sufed Mulgoa
and good processing quality are enriched in the (1813 g), Himam Pasand (536 g), Anardana
mango cultivars reported worldwide (Pandey and (717 g), Balakondapari (647 g), Tenneru
Dinesh 2010). Some of the cultivars are also used (944 g), Cowasji Patel (713 g), Sora (1166 g),
as a source of genes for both biotic and abiotic Gaddemar (713 g), Hathijhool, Pansera and
resistances. The commercial and export quality Fazli. The cultivars which are categorized in very
mango varieties listed worldwide are good large-sized fruits from other countries are Man-
source for high-yield and good-quality fruits zanillo Nunez of Mexico, Osteen, Keitt, Ander-
(Pandey and Dinesh 2010). Characterization son and Haden of Florida and R2E2 of Australia.
based on IPGRI descriptors for 151 mango cul- Other very large fruited varieties are Nymath
tivars is catalogued (Dinesh and Vasugi 2002). (1328 g) and Rebello (627 g). The Indian vari-
The classification of nomenclature of South eties which are classified under fruit size of very
Indian mangoes was earlier reported by Naik and small group are Bhowani (50 g) and Chowras
Gangolly (1950) and Pandey (1984) in mono- (70 g). Indian cultivars like Amrapali (130 g)
graph of mango. Recently, DNA barcodes are and Rataul (107 g) are classified under small fruit
developed for 223 mango cultivars based on size group (Anon. 2014; Pandey 1984). In USA,
molecular characterization and biodiversity 19 varieties among the reported 61 varieties are
international descriptors (Dinesh et al. 2012). classified into large and very large fruit size
Characterization of polyembryonic and pickle- group (Brooks and Olmo 1972). Though thou-
making varieties from Western Ghats showed sands of mango varieties are reported worldwide,
wide variation in physico-chemical attributes the consumer acceptance is based mainly on fruit
(Dinesh et al. 2012). Based on the size of fruits, quality. A wide variation is observed in the
the mango varieties are classified into different physico-chemical attributes of mango varieties
groups as very small (99 g and below), small and hybrids based on their geographical location
(100–149 g), medium large (150–299 g), large and genetic base. Hence, there are about only less
(300–500 g) and very large (more than 500 g) than 100 varieties which are commercially
for ease in grading and marketing (Pandey and acceptable and grown worldwide. Among the
Dinesh 2010). The commercial and most popular noticeable commercial mango varieties, export
mango varieties like Dusehri Aman or Dashehari, quality varieties prevalent worldwide are
Alphonso Bombay, Pairi, Langra, Pusa Arunima, Alphonso, Dashehari, Banganpalli and Kesar of
Himsagar, Totapari, Sukul, Rumani, Neelesh- India; Bourbon, Carlota and Haden of Brazil;
wari, Rajapuri, Neelum, Suvarnarekha, Ambika, Mabrouka of Egypt; Madame Frances of Haiti;
Zardalu, Bombay Green, Arka Puneet, Arka Haden and Maya of Israel; Apple, Borino and
Anmol of India, Tommy Atkins, Eldon and Ngowe of Kenya; Haden, Keittoand Manila of
Sensation of Florida, Aroumanus and Golek of Mexico; Anwar Rataul, Samerbehist chowsa and
Indonesia, Kyo Savoy and Okrong of Thailand, Fazli Khan of Pakistan; Carabao of the Philip-
Vallenato of Colombia and Momi-K (Momi pines; Haden, Keitt and Zill of South Africa;
Kinney) of Hawaii belong to the category of Hindi Be Sennar and Kitchener of Sudan;
medium large-sized fruits. Varieties like Arka Okrong of Thailand; and Julie of Trinidad and
Aruna, Mallika, Alfazli, Manjeera, Mulgoa, Venezuela (Pandey and Dinesh 2010). Based on
Samarbehist Chowsa from India; Amelie of West the quality attributes, the mango varieties can be
utilized for various purposes like table purpose studying the phylogenetic relationships at genus
and processing into various value-added prod- and species level (Jasper et al. 2008; Shaw et al.
ucts. Based on the recovery and quality attributes 2005). Among the different molecular techniques,
the Indian cultivars have been classified for uti- the non-coding chloroplast regions are more
lization in processing of mango into different informative in generating the phylogenetic rela-
value-added products. Ramkela, Pulian, Chan- tionships among the different species (Shaw et al.
drakaran, Karanjio, Aswina and Sandersha are 2013). The phylogenetic relationship among the
grouped at pickling cultivars. Amrapali, Gautjit wild mango species distributed in Andaman and
and Jauhari Safeda are highly suitable for pro- Nicobar Islands and Northeast India, viz.
cessing into beverages. Quality mango nectar is M. indica, M. griffithii, M. camptosperma,
produced from Amrapali, Dashehari and Saheb M. odorata and M. andamanica, was studied
Pasand. Processing of mango into pulp is one of using chloroplast markers like petB-petD inter-
the major sectors for commercialization as the genic spacer, rps16 gene, trnL-trnF intergenic
fruit is made available throughout the year. spacer and nuclear marker—External Transcribed
Bangalora or Totapuri is the variety which is Spacer (ETS). The results showed that the culti-
mainly used for production of mango pulp on vated mango, Mangifera indica, was grouped
commercial scale as the production per tree is with M. griffithii and M. camptosperma showing
high with high pulp content and the cost of the their closed relatedness and all these three species
fruits are also less. Mango varieties identified for belong to the sub-genus Mangifera. The wild
juice making are Sukul, Mithuwa Ghazipur, species, M. odorata, was grouped separately
Neelphanso and Safeda Lucknow. Mallika, syrup along with M. andamanica and it belonged to the
of varieties of Dashehari, Banganpalli and Nazuk sub-genus Limus. Also, the study indicated that
Pasand are highly suited to produce mango slices the endemic species of Andaman and Nicobar
on commercial scale. Due to the presence of Islands, M. andamanica. is closely related with
variation in quality of the mango varieties, the Bouea oppositifolia as analysed from both ITS
juice of Amrapali and Nisar Pasand is blended and psbAtrnH rDNA analyses and therefore the
with fruits of inferior quality to produce mango taxonomic position of M. andamanica may be
beverages. Canned mangoes are one of the major reconsidered (Sankaran et al. 2018).
commercial value-added products in mango and
the varieties suitable for this are Alampur
Baneshan, Mallika, Nazuk Pasand, Dashehari 2.7 Conclusion
and Alphonso.
Study of taxonomy of Mangifera species is
essential to know the inter- and intra-species
2.6 Phylogenetic Analysis diversity. The wide diversity of species existing in
of Mangifera Species the genus Mangifera has more utility in breeding
programme of cultivated mango. The species
Molecular markers like genomic restriction frag- diversity can be utilized in two different ways:
ment length polymorphisms (RFLPs) and ampli- (i) utilizing the better fruit quality parameters for
fication of chloroplast DNA (cpDNA) were used improvement of cultivated mango and (ii) may act
to study the genetic relationship among the dif- as donor for specific traits like resistant to insect
ferent species of the genus Mangifera and the pest and diseases (Iyer 1991). The different spe-
phylogenetic trees were constructed (Eiadthong cies of Mangifera are vital gene source for biotic
et al. 1999). The phylogeny of different species of and abiotic stress resistances, which may be uti-
Mangifera was also studied using the sequence lized for developing resistant varieties and root-
analysis of External Transcribed Spacer stocks. However, for crop improvement
(ETS) (Vavilov et al. 1996). Non-coding chloro- programme, the information on possibility of
plast regions are successfully employed for crossability among different species needs to be
developed for production of superior genotypes Davenport TL (2007) Review: reproductive physiology of
through gene transfer. Both wild and cultivated mango. Braz J Plant Physiol 19(4):363–376
Dijkman NJ, Soule MJ (1951) A tentative method of
mango species having same chromosome number mango selection. Proc FL State Hortic Soc 64:257
(2n = 40) show the possibility of inter- and intra- Dinesh MR, Vasugi, CS (2002) Catalogue of mango
specific crossing. Mukherjee (1950) reported that germplasm. Indian Institute of Horticultural Research,
crossability exists between the different mango Hesseraghatta Lake PO, Bangalore 560089, pp 160
Dinesh MR, Vasugi C, Ravishankar KV, Reddy YTN
species like M.indica L., M. odorata, M. zeylan- (2012) Mango Catalogue, ICAR-IIHR, pp 468
ica, M. caloneura, M. sylvatica, M. foetida and M. Dinesh MR, Ravishankar KV, Nischita P, Sandya BS,
caesia. It has already been proved that M.odorata Padmakar B, Ganeshan S, Chithiraichelvan R,
and M.camptosperma are compatible with M. Sharma TVRS (2015) Exploration, characterization
and phylogenetic studies in wild Mangifera indica
indica. Further, in the recent past, global warming relatives. Am J Plant Sci 6:2151–2160
and urbanization have been a great threat to the Dinesh MR, Rajan S, Singh SK, Singh IP, Ravis-
habitats of Mangifera spp and several species are hankar KV, Reddy BMC, Parthasarathy VA,
under threatened conditions. Survey, collection, Sthapit B, Ramanatha Rao V, Sandya BS (2015)
Heirloom/seedling mango varieties of India – poten-
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goes and semi-cultivated forms/types have to be Eiadthong W, Yonemori K, Sugiura A, Utsunomiya N,
done. Major emphasis must be given for in situ as Subhadrabandhu S (1999) Analysis of Phylogenetic
well as ex situ conservation of threatened and Relationships in Mangifera by Restriction Site Anal-
ysis of an Amplified Region of cpDNA. Sci Hortic
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British India, vol 2. Dehra Dun, India, pp 13–20
indica background in order to capture the market
Iyer CPA (1991) Recent advances in varietal improve-
demand in the coming years. ment in mango. Acta Hortic 291:109–132
Iyer CPA, Subbaiah MC, Subramanyam MD, Rao GSP
(1989) Screening of germplasm and correlation among
certain characters in mango. Acta Hortic 231:83–88
Iyer CPA, Subramanian TR (1989) Genetic resources
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Mango Propagation
3
Victor Galán Saúco, Alberto Carlos de Queiroz Pinto,
Sisir Kumar Mitra, Fabio Gelape Faleiro,
and Francisco Ricardo Ferreira
Abstract polyembryonic mangoes as rootstocks.

Despite the existence of mango nurseries
Mango trees can be propagated both by sexual
where all the operations from sowing to
and asexual ways, but the existence of grafting are done directly in the soil without
polyembryonic and monoembryonic mango using any close structure, even without irriga-
plants conditionates its way of propagation.
tion, modern mango production is realized in
Air layering, cuttings, and even micropropa- nurseries with all seedling establishment, from
gation can be used for mangoes, however, sowing to grafting of plant, made in soil
practically all commercial mango plantings are
substrate in propagation beds and polyethylene
established nowadays from mangoes propa- bags under modern protected environment and
gated by grafting or budding procedures using automatic ferti-irrigation systems. The most
common grafting techniques as well as other
techniques for vegetative propagation are
V. Galán Saúco (&) described. The procedures for careful selection
Consultant on Tropical Fruits, Ing. Agr, Ph.D,
of mango seedlings for rootstock use, scion
Research Professor (Retired), Instituto Canario de
Investigaciones Agrarias, Canary Islands, Spain preparation, packing, and transport of bud-
e-mail: vgalan46@gmail.com wood as well as the regulations for exchange
A. C. de Queiroz Pinto of seeds and grafting material between coun-
Consultant on Tropical Fruits, Eng. Agr. Ph.D. tries are also indicated in this chapter.
Researcher from Embrapa (Retired), Visitor
Professor, University of Brasilia-DF, Brasilia-DF,
Brazil 3.1 Introduction
e-mail: alcapi@terra.com.br
S. K. Mitra The mango is commercially cultivated in all the
Board Member of International Society for
continents both in the tropics and subtropics from
Horticultural Science (ISHS), Brasilia, Brazil
e-mail: sisirm55@gmail.com 37º north till 33º south latitude. According to the
FAO statistics, mango is actually produced in
F. G. Faleiro
Eng. Agr. Dr. Researcher of Embrapa Cerrados, more than 100 countries (www.fao.org). Despite
Brasília-DF, Brazil the number of mango producing countries has
e-mail: fabio.faleiro@embrapa.br stabilized in the last decade, world mango pro-
F. R. Ferreira duction has increased considerably, 15.7 106
Eng. Agr. Dr. Researcher of Embrapa Genetic tons in 1990; 25.0 106 tons in 2000; 38.0 106
Resources and Biotechnology, Brasilia-DF, Brazil
tons in 2010, 50.6 106 tons in 2017. This
e-mail: francisco.ferreira@embrapa.br

https://doi.org/10.1007/978-3-030-47829-2_3
32 V. Galán Saúco et al.
continuous increase in production has been pos- traditional irrigation systems, or even without
sible in great part due to planting or top working of irrigation still exist in rural areas in many
more productive cultivars for which sound meth- underdeveloped countries. However, modern
ods of propagation are required. mango nurseries made all seedling establishment,
Mango trees can be propagated both by sexual from sowing to grafting of plant, in soil substrate
and asexual ways, but as can be seen below the in propagation beds and polyethylene bags under
existence of polyembryonic and monoembryonic modern protected environment and automatic
mango plants conditionates its way of ferti-irrigation systems.
propagation. Different propagation structures for modern
mango production such as polyhouses with
forced ventilation and evaporative cooling sys-
3.2 Mango Nurseries: Structure tem, shade nets (Fig. 3.1), and net houses as well
and Organization as mist propagation units were described in a
recent paper on mango propagation by de
Nurseries for mango propagation have different Queiroz Pinto et al. (2017). These modern
possibilities where all the operations from sow- propagation structures are also useful for propa-
ing to grafting are done directly in the soil gation of other tropical fruit trees and it will be
without using any close structure, using redundant to describe them again here.
Fig. 3.1 Shade Net structure used in modern commercial mango propagation nurseries
3 Mango Propagation 33
3.3 Substrates for Mango 3.4 Monoembryonic Versus

Propagation Polyembrionic Cultivars
Substrate quality has marked influence on mango Seeds of monoembryonic mango cultivars give
propagation. As indicated by de Queiroz Pinto rise to plants from sexual embryo and due to its
et al. (2017), a good nursery substrate should heterozygotic character will not develop uniform
have the following characteristics: plants and are not valid for true-to-the-type
(1) Light weight to facilitate transport but hold propagation of these cultivars. On the other
the plants firmly mainly around the root hand, polyembryonic cultivars propagated by
system. seeds, which are originated from nucellar
(2) Able to retain water but also allowing drai- embryos produce true-to-type progenies identical
nage and aeration. to the mother plant and, therefore, they can be
(3) It should have necessary nutrients for proper used either for propagating polyembryonic cul-
growth and development of mango and tivars or to establish mango rootstocks for
should be also easily available to the plants. grafting on them the desired monoembryonic
(4) It should be free from weed seeds, toxic cultivar. It should be noticed, however, that the
chemicals, and soil-borne fungus, bacteria, guaranty of homogeneity is not total, even if we
and pests. eliminate the potentially viable sexual embryo
(5) Sterilization should not change the charac- produced from open-pollination which may
teristics of the substrate. originate the development of a seedling distinct
from the mother plant. Generally the sexual
Sanitation of substrate is one of the most embryo is less vigorous than the nucellar embryo
important factors for the success of high-quality which makes selection of the most vigorous
graft mango, and this can be done either by pas- seedling a safe practice to ensure uniformity, but
teurization, solarization, or by chemical fumiga- it is not always the case- some polyembryonic
tion. In the first case, a temperature of about 70 °C rootstock can even produce tetraploid progenies
for 30 min is considered sufficient to kill almost all (Galán Saúco et al. 2002)—and it may be nec-
disease-producing organisms (Sahdu 2005). essary to complement selection at least by careful
Fumigation is most useful for destroying harmful observation of morphological characteristics to
bacteria, fungi, and nematodes in a relatively small eliminate off-types. With these precautions graf-
quantity of soil that is used for propagation of ted trees on polyembryonic rootstocks guarantee
plants. Methyl bromide was the most widely used homogeneity and, also, favor early or precocious
soil fumigant for mango for many years, but its use bearing because of the stress effect of the bud or
is nowadays prohibited in most countries. graft itself. It has been indicated, in some cases
A chemical alternative to eliminate pathogens particularly to reduce the initial cost in high-
from the medium that can be applied even when density plantings or to reduce the time for
the plant is growing in the media consists of reaching full productivity in the subtropics the
drenching the medium with certain fungicides convenience of direct field planting of polyem-
such as Captan or Fytolan at a dosage of 1 g/liter of bryonic rootstocks or simply polyembryonic
water (de Queiroz Pinto et al. 2017) seeds for posterior in situ grafting (Galán Saúco
Besides the use of clean and sterile medium, 2008; Oosthuyse 2017). However, the potential
all other parts and tools of the nursery must also loss of homogeneity derived from using root-
be disinfected to avoid recontamination of the stocks not 100% polyembryonic or from not
medium. General recommendations to achieve carefully managed makes this practice not always
this purpose include the use of 2% formaldehyde, recommendable (Galán Saúco 2018). Therefore,
chlorinated water, and alcohol or even boiling mango propagation by budding, and mainly by
water. grafting method, is the most common method
used for commercial mango production in most namely, M. lalijiwa and M.kasturi compatible
of the producing countries. with mango are also used as rootstocks in Hawaii
and Indonesia. The explanation for the use of
monoembryonic rootstocks in the area of origin
3.5 Seed Selection, Preparation, of mangoes in South East Asia may be that the
and Sowing majority of plantings are of old orchards with
low-density system where uniformity of the
Mango seed selection and preparation procedures rootstock is not as important as in modern
have been clearly described by several authors plantings and are also only used in some parts of
(Castro Neto et al. 2002; Galán Saúco 2008; Ram China and in Hawaii when polyembryonic seeds
and Litz 2009. Donovan et al. 2016; de Queiroz are not available (Galán Saúco 2017b).
Pinto et al. 2017). The fruits, whose seeds will be collected for
The seeds for mango propagation used as propagation, should be fully mature, but not
rootstocks should be free of pests and diseases overripe, to avoid germination inside the fruit or
and collected from healthy and productive rotten. They should be as large as possible to get
polyembryonic selected trees. According to the a strong rootstock, since there is a direct and
review made by Galán Saúco (2019) salinity and positive relation between seed size and vigor of
dwarfism are the main characteristics desired in the seedlings (Giri and Chaudhri 1966). In
most counties for a rootstock, although the latest countries, where seed weevil (Sternochetus
is not necessary in the subtropics due to the mangiferae) is present, special care should be
slower growth of trees under subtropical condi- taken to eliminate any seed affected by this
tions (Galán Saúco 2017a).and, with the advent insect. It is also recommended to avoid the fruits
and success of modern mango pruning tech- for seed purposes mainly from countries where
niques, it is possible to keep trees at a manageable temperatures are below 15 °C during fruit set and
size without losing productivity which explain beginning of the fruit growth because of the
why in countries like Brazil the dwarf character common occurrence of embryo abortion. Gen-
has been put as secondary aim in the mango erally, these fruits are of small size (Galán Saúco
breeding program (A.C. de Queiroz Pinto 2020, 2008), although some of them can reach com-
Personal communication). Other characteristics mercial size, but having almost no seed or seed
demanded for a rootstock include good compati- with no viable embryo.
bility with the cultivars, good ability to absorb The preparation of the seeds includes the
nutrients, particularly iron and calcium, tolerance following successive steps:
to flooding, tolerance to dry conditions, and (1) Extraction from the fruits.
favoring fruit quality. It should, of course, not be (2) Washing and elimination of all rest of pulp.
detrimental to yield or, even better, it should (3) Drying either in the shade for 1–2 days or
improve yield and/or yield efficiency (yield by with the help of an adequate ventilation
canopy unit area). However, in the majority of system.
countries, rootstocks are selected by the facility of (4) Removal of the endocarp with a pruning
obtaining seeds choosing local and well-adapted scissor or a sharpened knife avoiding dam-
polyembryonic trees exhibiting heavy and uni- aging the cotyledons, which may decrease
form production annually and long before intro- germination success.
duced in the area. A few exceptions to this are the
case of Israel where the main rootstock used is de Queiroz Pinto et al. (2017) indicate that the
13/1, also polyembryonic, but selected especially removal or not removal of the thin tissue cover-
for salt tolerance (Gazit and Kadman 1980) or in ing the cotyledons has not been noticed to have
India, Pakistan, Bangladesh, Oman, China, and influence on the germination success. de Queiroz
Hawaii where monoembryonic seedlings are also Pinto and de Carvalho Genú (1996) also report
used as rootstocks. Some Mangifera spp., the existence of a tool named Endocarp Remover
Fig. 3.2 Endocarp remover may help to pull out mango cotyledon free of injury from inside the endocarp. Figure inside
the circle: Final thin part of 13 mm like a duck beak. Translation for the Spanish legend: Enough for 3–4 medium fingers
which facilitates the operation to remove the Campbell 1994) say that mango seed retains
endocarp (Fig. 3.2). Although there are reports viability for only a short time and seeds older
indicating that seed viability can extend till than a couple of weeks frequently will not ger-
84 days by placing them in sterile cotton minate. Because of this short viability period it is
impregnated with deionized water (Ram 1997) or strongly recommended that seeds are sown as
up to 70 days by placing the mango seeds in soon as possible after fruit harvest. Warm tem-
charcoal dust in a desiccator set at 50% relative peratures above 30 °C should be avoided during
humidity (Caines 2020), the University of Flor- storing because they will provoke a quick ger-
ida Cooperative Extension Service (Sauls and mination (Parisot 1988). For sending seeds to
have a full air porosity (FAP) value between 15

and 20%.
Transplanting from the seedling beds to the
plastic bags where the seedlings are later grafted
should be done soon after germination which
occurs normally 2–3 weeks after sowing. To
avoid deformities in the area of the union of root
and stem due to the emergence of various seed-
lings from polyembryonic seeds it is advisable to
select as quick as possible the best seedlings
(erect and without deformity) eliminating all the
rest by cutting them at the stem base.
The size of the bag depends on the time they
will be maintained in the nursery before planting
and/or selling, but usually they have a size
between 300–350 mm length, 200–222 mm of
diameter and 0.15–0.20 mm thick dimensions.
These plastics bags should have lateral and bot-
tom holes to avoid flooding substrate. However,
in the subtropics where, by climate reasons, the
grafted plants may stay in the nursery a longer
period, polyethylene bags should better have a
Fig. 3.3 Placing the seed in the bag minimum diameter of 250 mm, a length of
400 mm, and the same thickness as above (Castro
distant places it has been recommended to place Neto et al. 2002; Galán Saúco 2008; de Queiroz
them between layers of vegetal charcoal (Singh Pinto et al. 2019). To avoid problems, some
1960), humid layers of newspaper or any other nurseries use open bottom bags placed in a type of
isolated material (Galán Saúco 2008). railing structure allowing good substrate aeration
Mango seeds should be planted by burying the and facilitating pruning of the taproot with the
ventral part (concavity portion) of the cotyledon consequent developing of a better secondary and
into the soil substrate and then cover the convex tertiary root system which improves rootstock
portion with the soil substrate (Fig. 3.3) and vigor. Mckenzie (1994) also recommends chem-
immediately irrigate with water preferably added ical application of cupric products in the interior
with an appropriate fungicide solution faces of the plastic bags for pruning the taproot.
In modern mango nurseries, seeds are sown Continuous seedling selection must be prac-
directly into an appropriate substrate in nursery ticed removing all of them showing abnormali-
beds of around 25 cm depth of light soil substrate ties like yellow leaves, short and compact
or be sown—this is the more appropriate method internodes, small and twisted leaves in the apex,
– into substrate inside of plastic bags. The seeds root deformations, or those which flowers pre-
should be buried into the substrate and covered cociously in the nursery.
with a substrate layer of maximum 1.5 cm in the Fertigation alone or combined with direct
appropriate position discussed above. These two incorporation of granulate and slow releasing
methods may avoid problems of damage in the fertilizers into the soil substrate of seedling-beds
root system which promotes losing of plants or polyethylene bags is usually applied in mod-
during transplanting from the nursery to the field ern nurseries. However, it is not recommending
found in traditional mango nurseries. Mckenzie the exclusive use of slow releasing fertilizer
(1994) indicates that a good soil substrate must when hot temperatures exist to avoid a faster
release of nutrients not desirable for seedling dwarfing or semi-dwarfing habit (Galán Saúco
development. Seedlings should be ready for 2017b). Other important aspects for a mango
grafting when reaching 400–500 mm height with rootstock include vigor, high yield potential,
a stem thickness of 8–12 mm at the middle of the good compatibility with scion variety, environ-
height, which normally occurs in modern nurs- mental adaptability, and resistance to pests and
eries between 8 and 12 months after sowing (de diseases.
Queiroz Pinto et al. 2018). Despite the noticeable impact on the growth,
yield, tolerance to salinity, nutrient absorption as
well as fruit quality of mango cultivars, rootstock
3.6 Propagation Methods studies and its relationship with the selected
scion cultivars are perhaps the most important,
Air layering, cuttings, and even micropropaga- field of research lacking on mango. This fact may
tion can be used for mangoes, however, practi- partially explain why polyembryonic rootstocks
cally all commercial mango plantings are long time introduced in the countries (named
established nowadays from mangoes propagated Criollo type varieties in the Latin-American
by grafting or budding procedures using countries) are generally used for mango propa-
polyembryonic mangoes as rootstocks. gation in the tropics since they are more adapted
Several types of grafting have been used for to the different areas where they are found. These
long time from approach grafting (inarching) and seedlings are widespread and found easily in
different buddings types to the most common, tropical regions and, for mango growers, they are
splice veneer, cleft, softwood, and side grafting. a source of selected homogeneous seedlings with
They are well described in Ram and Litz (2008), a more regular bearing condition and they will
Galán Saúco (2008), Donovan et al. (2016), and de probably continue to be the only option as root-
Queiroz Pinto et al. (2018), and, essentially, they stock until new specific studies be developed on
do not differ from grafting procedures for other each region (Galán Saúco 2019).
subtropical trees, but the most common in modern
mango propagation will be again described below.
As indicated by de Queiroz Pinto et al. (2018) 3.6.2 Scion Preparation
there are five steps to do correct grafting which, at Mother-Plant, Packing
slightly modified by us, can be seen below: and Transport
(1) Selection of plants and seeds for the estab-
lishment of seedlings to be used as rootstocks. As well explained by de Queiroz Pinto et al.
(2) Selection of plants of the desired cultivar (2018), the scions usually used for grafting
(mother plant) from which scions should be should have a size between 8 and 12 cm which
taken. roughly correspond to terminal shoots of about
(3) Picking, packing, and transport of scions to 4–6 months old under tropical conditions.
the nursery. According to Donovan et al. (2016), the scions
(4) Grafting in the nursery. should have at least 3 buds and be about 10 cm
(5) Maintenance of the grafted plant until long and the same diameter as the rootstock and
planting. those with swollen buds just before bursting are
the most suitable for grafting.
Before grafting all the leaves should be
removed and the petioles cut. It has been strongly
3.6.1 Selection of Mango Seedlings recommended to do this operation 1 week before
for Rootstock Use cutting the scions from the branch in order to
promote the swelling of the scion buds which
The two main aspects considered nowadays for a will improve the grafting success (Castro Neto
good rootstock are tolerance to salinity and et al., 2002). It is also possible to obtain a good
success in grafting by cutting the petioles exchange of germplasm started to be practiced

immediately after severing the scion from the with restrictions. Several international and
branch as it is usually done in the Canary Islands national laws have been established to regulate
(V. Galán Saúco 2020, Personal the exchange of genetic resources or material for
communication). the propagation of plant species, mainly the laws
In case of transport of the grafts to other and rules that consider bio-security to prevent
places then prolonging time between cutting and entry of new pests in the country. One of the
grafting, scions should be protected from desic- decisions taken after this Convention was the
cation, which can be done by different ways requirement for a document called Material
(Galán Saúco 2008; de Queiroz Pinto et al. 2017) Transfer Agreement (MTA), which allows the
like: exchange of genetic material. Therefore, in order
(1) Immersion of the bottom of the scions to import or export mango propagating material,
(around 2.5 cm) into a parafilm liquid solu- seeds, cuttings, and scions (grafts), the donor and
tion at about 51 °C. the recipient of the mango propagulum must sign
(2) Packing and tying several scions together in the MTA document, which sets out the rules for
toilet paper and then spray with tapwater. using this exchange material. In addition, the
(3) Wrapping them individually with a non- propagation material of mango must be attached
sticky adherent (cellofim or similar) and to a Phytosanitary Certificate issued by the donor
place them into a Styrofoam box. country according to the requirements of the
recipient country and should be subjected to
Scions prepared by any of the mentioned quarantine after arrival to avoid undesirable
methods can be kept in the lower portion of a introduction of pests, diseases, or weeds. To
house refrigerator (at 5 °C) in a sealed and complicate more the process there are, in most
labeled plastic bag where they can be conserved countries, a whole set of general laws, rules
without losing its freshness by around 1 month regulations and even taxes related to importation
(Donovan et al. 2016). of goods which delay the whole process of
transfer of plant material between countries
which the consequence in many cases of losing
3.6.3 Regulations for Exchange of the plant material (Ferreira et al. 2019).
of Seeds and Grafting
Material Between
Countries 3.6.4 Common Grafting Techniques
Until the early 1970s, germplasm was considered 3.6.4.1 Splice or Whip and Tongue
a human good with no restriction existing for its Grafting
transfer and exchange of plant material from one This widely used grafting technique is perhaps the
country to another and even between different easiest method of grafting. This is usually done on
parts of the same country including grafting 1–2 years-old rootstocks with a diameter of 0.6–
materials either for commercial purpose or for 1.0 cm. They are pruned at 10–20 cm above the
scientific research. However, germplasm soil making a slant cut of 3–4 cm long at the top
exchange it is subjected nowadays to a whole set part of the rootstock. A similar diagonal cut is
of legal and bureaucratic regulations. After made in the scion, which should be of the same
advent of the Biodiversity Convention, devel- diameter than the rootstock. Both exposed sur-
oped in Rio de Janeiro in 1972, and especially faces are then tied together with grafting tape
after its implementation in 1992, germplasm (Fig. 3.4a–c). About 90% of success can be
became the property of the country where it obtained with this technique, but the method has
occurs, and as such, based on this premise, the also proven useful with seedlings 3–9 months old.
a b c
Fig. 3.4 a Cutting the scion in two. b Insertion of the scion into a. c Wrapping the scion and rotstock with a plastic band
3.6.4.2 Veneer Grafting slipped into the split part of the stock providing
Several authors, cited by Ram and Litz (1997), that the thicker border of the cleft is placed
indicated that this is the most successful type of towards the external part of the rootstock and
grafting. It has been done using rootstocks of securing that the back of it meet firmly with the
different age from 3 months to 2 years which are scion. Another scion is inserted diametrically
prepared by making first a slanting cut of around opposed to the first scion. Once this is done, the
5 cm long. A second oblique cut is later made at wooden wedge is removed and the cut surfaces
the base of the first cut which permits the removal sealed with grafting wax.
of a piece of wood with bark. 3–6-month-old
scions shoots of 1.0–1.5 cm of diameter which 3.6.4.4 Softwood Grafting
are defoliated 3–15 days before grafting leaving It is done by direct insertion of a scion into the
the petioles attached are used. For doing grafting bronze colored stem of a rootstock in such a way
the base of the scion wood is fitted into the that the cut surfaces should adjust perfectly by
rootstock in such a way that the cambium layers practicing an appropriate cut on both scion and
of both scion and rootstock are in close contact rootstock. About 100% of success is obtained in
tying finally both securely with grafting tape. many cases especially if the leaves are not
removed below the grafting union. Softwood
3.6.4.3 Cleft Grafting grafting has been recommended in dry hot
This technique can be used for rootstocks of weather and places with low precipitation.
greater diameter and even for top working. It is
normally done with 5–7 cm or more rootstocks 3.6.4.5 Side Grafting
which are cut back to around 45 cm above the It is normally practiced with 1.0–1.5 cm diameter
ground and then split to a depth of about 5 cm rootstocks using around 10 cm long scions
long in the center of the stem with the help of a defoliated about one week prior to grafting which
knife and a mallet keeping the cut open, if nec- are inserted into the wedge of the rootstock and
essary, by inserting a hard wooden wedge. A 15– then tied with grafting tape. The top part of the
20 cm long scion coming from terminal shoots rootstock should be removed after the graft union
older than 3 months is wedged securely to a between stock and scion has occurred. It has
depth of 6–7 cm with the cleft of the scion been reported to be useful for humid coastal
areas of India and also for mild weather in

absence of strong winds, heat, and heavy rain.
It should be however mentioned that all these
grafting techniques can be more successful in
modern nurseries with environmental control
conditions than in open-air nurseries with low or
without a good environmental control.
3.6.5 Care and Maintenance

of the Grafted Plant Until
Planting
For improving success of mango grafting it is

advisable to cover, immediately after grafting,
the graft and the scion with a plastic bag about
200 mm long, 40 mm wide, and 0.01 mm thick
or similar tied just below the graft union to pre-
vent desiccation of the scion (Fig. 3.5). In case
that the grafted plants were exposed directly to
the sun the plastic bag should be covered with a
Fig. 3.6 Mango graft after removal of protection
white paper bag to reduce heat stress. All the

shoots and branches that eventually grow out
from rootstock must be removed. Both plastic
and paper bags should be eliminated after the
scion start to grow 1–2 cm which usually takes
between 15 and 30 days (Fig. 3.6). After this
grafted plant should remain in the nursery for at
least two periods of growth for proper hardening,
after which will be ready for planting in the field
(Fig. 3.7).
In order to keep identified the grafting point
for longer time some nurseries paint this area.
Normal nursery practices of watering, fertilizing,
root-pruning, etc. should be carried out during
the time the plants remain in the nursery. Har-
dening, which involves exposing the plant to
regular sunlight, and reducing the frequency of
watering, must be practised before leaving the
nursery for field planting. For doing it the grafted
plants should be gradually exposed during a few
weeks to full sunlight to ensure a good response
Fig. 3.5 Covering the grafting union to protect it to the changing environmental conditions, but
hard plastic (about 80 mm long 60 mm width)

in which the names of the orchard and the root-
stock and scion variety besides the date of
grafting must be written on the label.
3.6.6 Other Techniques

for Vegetative
Propagation
Mango can be also propagated through cuttings

and air layers. Although there are some reports
indicating 100% of success for cuttings (Ram
1997; Reuveni and Castoriano 1997) and up to
70% for air layers using growth regulators
(Chhonkar and Singh 1972), these techniques are
not generally used for commercial mango prop-
agation. It may however be useful in case of the
need of using a monoembryonic rootstock
because of its resistance or tolerance to biotic or
abiotic stresses. Although this circumstance has
not yet be occurred in mango since no such tol-
erance or resistance has been detected in any
monoembryonic rootstock it may be useful in the
future because of the possibility of using other
Mangifera species showing tolerance to flooding,
cold conditions, or even resistance to anthracnose
(Bompard and Schnell 1997), some of which are
graft and sexually compatible with mango
(Campbell 2004; Ledesma et al. 2017).
Information about different methods of root-
ing can be also found in Ram and Litz (2008) but
the main recommendations for rooting cuttings
Fig. 3.7 A high-quality commercial graft
as summarized by Galán Saúco (2008) from lit-
erature review are as follows:
care should be taken during hardening to avoid (1) Use preferably hardwood etiolated cuttings
putting plants directly on the ground outside, of around 15 cm length and 1.2–1.8 cm of
where they could, particularly under subtropical diameter with 3–5 buds keeping 1–2 leaves
conditions, experience damaging low or high in the apex,
temperatures. Hardening is, obviously, more (2) Use substrates of low pH (4.5–7) and
important when the plants have been grown incorporate rooting hormones like indole
under modern environmental conditions than butyric acid or naphthalene acetic acid at
when the nursery is established in open-air dosages between 5,000 and 15,000 ppm and
nurseries. slow-release fertilizers.
Labeling the graft plant is a very important (3) Use nebulization and bottom heat (best
final step and this is done with a hard paper or temperature between 25 and 30 °C).
3.6.7 Micropropagation through direct somatic embryogenesis. The con-

version of somatic embryos to plants occurred
Although a high homogeneity of planting mate- 4 weeks after inoculation of somatic embryos in
rial is achieved from conventional propagation culture medium.
on a polyembryonic pattern, micropropagation There is an advance in technological knowl-
may have a special interest either to clonally edge about mango tissue cultures, however, there
propagate monoembryonic patterns (Thomas is still no optimized protocol for micropropaga-
1999) and even to propagate cultivars (Hussain tion and its practical use is still incipient.
et al. 2000; Kidwai et al. 2009; Mishra et al. Therefore, further basic studies are still necessary
2010; Bimal and Singh 2017). to establish the proper culture medium for tissue
Micropropagation is a technique that can be culture, besides the methodologies to reduce
used to obtain plants with phytosanitary quality, costs and somaclonal variations that might occur.
positively related with fruit quality and produc- The scientific advances obtained in the areas of
tivity. Additionally, micropropagation and tissue micropropagation, organogenesis, and somatic
culture can allow the rapid multiplication of embryogenesis open important perspectives for
genotypes of interest from a small number of biotechnological breeding and for the economic
explants obtained at any time of the year process to micropropagation of different mango
(Andrade et al. 2005). These micropropagation cultivars in a high scale and with high genetic
possibilities are also important to support genetic and phytosanitary quality.
improvement programs based on conventional
and biotechnological methods, which requires
the development of an efficient plant regeneration
References
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The potential of tissue culture of mango to
Al-Busaidi KT, Shukl M, Al-Burashdi AH, Al-Blushi GS,
produce a large number of somatic embryos of Al-Jabri MH, Al-Kalbani BS, Al-Hasani HD (2016) In
both mono and polyembryonic mango cultivars vitro regeneration of mango (Mangifera indica L.) cv.
has been documented (Bimal and Singh 2017). Baramasi through nucellar embryogenesis. J Hort
Forest 8:37–43
There have been several references concerning
Andrade SEM, de Queiroz Pinto, AC, Faleiro FG,
the micropropagation of many mango cultivars Cordeiro, MCR, Ramos VHV, Teixeira JB (2005)
using different types of explants and culture Desenvolvimento e avaliação de protocolos para
medium (Litz 1986; Litz and Lavi 1997; Thomas descontaminação de explantes de MangueiraVisando
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Genetic Resources in Mango
4
Shailendra Rajan, Manish Srivastav,
and Heiplanmi Rymbai
Abstract and introgressing genes through hybridization

for evolving new varieties. Mango is subject to
Mango (Mangifera indica L.) is an important
various production constraints, both biotic and
fruit crop of the world and predominantly abiotic. Some of these are global in nature,
grown in tropics and subtropics of Asia, while others are of national or local impor-
Africa, and America. Apart from thousands
tance. Genetic resources need to be screened as
of varieties in Asia, there are 69 species of donor for resistance genes against stresses.
Mangifera in wild gene pools. In India, the Probability of getting new varieties through
primary centre of diversity, mango cultivation
seedling selections is becoming meager as the
commenced a few thousand years ago and newer orchards are being planted using grafted
seedling propagation for several centuries and plants.
out-crossing emanated the valuable gene pool.
Characterization and evaluation of mango
germplasm is an imperative step for its 4.1 Introduction
utilization in breeding programs being under-
taken in different parts of the world. Genetic Genetic resources can be defined as all materials
resources have been effectively used for con- that are available for improvement of a cultivated
ventional breeding mainly seedling selection plant species (Haussmann et al. 2004). Mango
genetic resources constitute all the diverse
genetic material having value as a resource for
present and future generations of human being. It
S. Rajan (&)
ICAR- Central Institute for Subtropical Horticulture, includes total pool of genetic variability that
Rehmankhera, Kakori, Lucknow 226101, exists in the species or within species with which
Uttar Pradesh, India the crop plant is sexually compatible (Holden
e-mail: srajanlko@gmail.com
et al. 1993). There have been many factors which
M. Srivastav have led to an increased realization of the
Division of Fruits and Horticultural Technology,
importance and conservation of indigenous as
ICAR- Indian Agricultural Research Institute,
New Delhi 110012, India well as exotic genetic resources. It is more per-
e-mail: msrivastav@iari.res.in tinent with respect to the ‘King of fruit’ mango
H. Rymbai since out of the 70 plus Mangifera species hardly
Scientist, Division of Horticulture, ICAR Research one dozen is under cultivation globally, while
Complex for NEH Region, Umiam 793103, many are under the constant threat of extinction
Meghalaya, India
in their regions of origin due to wrath of natural
e-mail: rymbaihort@gmail.com

https://doi.org/10.1007/978-3-030-47829-2_4
46 S. Rajan et al.
calamities, climate changes, etc. before they are characters, mostly related with fruits, and less
actually collected, studied, documented, and emphasis has been given to flower and vegetative
conserved for immediate or long-term use by the characters. Large variation exists in tree vigour,
mankind. Wild relatives are genetically much fruit size (50-2000 g), fruit shape (more than 15
more diverse than related cultivated types. Wild types of shapes have been recorded) (Ram and
gene pools and thousands of mango varieties Rajan 2003).
extend ambit for characterization, evaluation, Based on polyembryony, cultivated diversity
conservation, and utilization. India as the primary in mango can be classified into two major
centre of diversity and secondary gene pools in groups: (i) subtropical with monoembryonic
other parts of the world exists. The characteri- varieties (Indian types) (ii) tropical with
zation and assessment of mango germplasm has polyembryonic varieties (Southeast Asian types).
been carried out in different areas of the world. Polyembryonic cultivars spread along the west-
For traditional breeding, primary and secondary ern coast of India may have been introduced
gene pool has been used for the development of from Southeast Asia into Goa, either from their
new varieties. Mangoes are subject to different Malacca colonies in the Malay Peninsula or from
biotic and abiotic production constraints. For Timor in the Indonesian Archipelago (Mukherjee
many production problems, genetic resources can 1997).
be exploited to search for genes. The Malay Peninsula, the Indonesian Archi-
pelago, Thailand, Indo-China, and the Philip-
pines are the places of greatest diversity in wild
4.2 Diversity and Distribution relatives of mango (Mukherjee 1985; Bompard
1989; Kostermans and Bompard 1993). Many
India, together with several other Southeast mango wild relatives have small fruits with hard,
Asian countries is growing mangoes for thou- acidic pulp, large stones, plentiful fiber, and
sands of years thus have access to huge genetic resinous astringent substances that are found near
resources in Asia. Mango genetic resources play the fruit peel. Along with M. indica at least 26
an important role in developing newer varieties other species of the genus present in Southeast
as per the farmers need and it will become more Asia are grown to produce edible fruits (Gruezo
vital in near future. In mango, so far, natural 1992).
genetic variability has been exploited for The Indian subcontinent is considered as the
improving productivity as well as introducing most important centre of diversity for M. indica
new varieties with specific traits. Maintenance of and has a large array of cultivated varieties. M.
mango gene pool of cultivated and uncultivated indica is distributed in most of the tropical and
types is important in present day context and subtropical parts of India. M. indica occur as
more for future breeding programs because with wild in forests as well as in cultivated areas. In
the advent of new biotechnological tools, genetic India, wild mangoes are found almost all over the
manipulations techniques available, these tropical and subtropical hilly forests and ravines
resources might be used for desirable genes. of up to 1000 m and the Andaman Islands.
Enormous genetic diversity exists in primary Yadav and Rajan (1993) reported significant
and secondary centres of domestication of M. variability in wild mangoes in different parts of
indica in terms of tree performance, tree vigour, the country (Fig. 4.1).
flowering behavior, fruit quality, resistance to Seedling races originated from monoembry-
disease and pests, etc. However, limited efforts onic mango stones are the most important com-
have been made to quantify the genetic variation ponent of diversity present in India. Almost all
existing in nature. Moreover, most of the commercial mango cultivars have arisen as a
molecular studies are confined to ex situ germ- result of the selection from these seedlings.
plasm collections. Majority of the workers Seedling trees are generally hardy and can
described variability in terms of morphological withstand water stress (Yadav and Rajan 1993).
4 Genetic Resources in Mango 47
Fig. 4.1 Important zones of

variability in wild Mangifera
indica in India (Yadav and
Rajan 1993; Ram and Rajan
2003)
With the increasing awareness, vegetatively are particularly suited to humid districts from
propagated types (grafts) are replacing seedling Ratnagiri (Maharashtra) to Valsad and Surat
use for new plantation. (Gujarat) in the West Coast, wild types are found
M. indica grown in India has many best in Western Ghats particularly appimidi types
quality fruit-bearing varieties. There are three (Chadha 1996). In Goa, in addition to cultivars
major diversity centres where large number of like Mankurad, Hilari, and Fernandin, diversity
varieties evolved, viz., Lucknow-Saharanpur belt exists in the form of local cultivated types. In
of Uttar Pradesh, the Murshidabad area of Central India, particularly in Madhya Pradesh,
western Bengal, and the Hyderabad in Andhra commercial varieties of northern, southern, and
Pradesh. Large variations in cultivated forms are western India are grown. Moreover, apart from
still available in old orchards of these areas. the commercial varieties of other states, diversity
Planting of seedling trees was continued till mid in the form of local varieties like Dahiyar, Kar-
of last century (Rajan et al. 2016). Diversity in ela, Sunderja, and Madhu Kuppi is available. In
the form of over a thousand different cultivated some cultivars like Sunderja, variability within
varieties of mango are existing in India (Rajan cultivar also exists.
and Hudedamani 2019). In Indian market, about The southern region of India has rich diversity
30 cultivated varieties are playing major role. of mango in Andhra Pradesh, Karnataka, Tamil
Eco-geographical adaptation of commercial Nadu, and Kerala. In the coastal districts, diver-
varieties is one of the key factors for many cul- sity in the form of juicy varieties (Rasalu), viz,
tivars and regional consumer preference. Peddarasam, Chinnarasam, Cherukurasam, Pan-
In India, Uttar Pradesh has the greatest chadara Kalasa, Firangiludwa, and Kothapalli
diversity in cultivated types. In western region, Kobbari are available. In Tamil Nadu, along with
apart from important commercial varieties, which the popular varieties like Neelum, Mulgoa,
48 S. Rajan et al.
Kalepad, Bangalora, and Peter, substantial area Florida from the superior germplasm imported
under local varieties exists. Kerala has several from different mango areas has made it an
polyembryonic races of mango and some vari- important fruit of subtropics and tropics
eties obtained from other states have adopted (Mukherjee 1997).
well. In eastern states, Bihar, West Bengal, and
Odisha have rich diversity. Besides cultivated
types, wild types are also found in Odisha and 4.2.1 Primary and Secondary Gene
Bihar. In Odisha, varieties of Andhra Pradesh, Pools
e.g., Banganapalli, Neelum, Totapuri, and
Suvaranrekha are grown. However, the state Indian subcontinent is considered as the primary
represents the great diversity in seedling types. centre of origin for M. indica and later the mango
Several wild types are also common in this state. was distributed in other continents creating sec-
Mangoes are well distributed throughout ondary centres of variability. In India, mango
Bangladesh. It is one of the major tree species cultivation commenced a few thousand years ago
indicating its spread and popularity among the and seedling propagation for several centuries and
rural people (Abedin and Quddus 1990). Most of out-crossing emanated the valuable primary gene
the commercial cultivars are of Indian origin and pool. Creation of diversity coincided chronologi-
adapted in Bangladesh. In Bangladesh, seed cally with the dispersal of cultivated mango,
propagation has been continuing for many cen- starting with Southeast Asia, later to Africa,
turies resulting large variations. The variability Central and South America. In recent decades,
has been mostly created by natural cross- mango has become a common crop in most of the
pollination (Ram and Rajan 2003). tropics and subtropics, nevertheless, primary gene
In Indonesia, considerable diversity is avail- pool confines to Asia and particularly to Indian
able in M. indica and other edible Mangifera Subcontinent. Hundreds of varieties contribute
species because most growers in the villages are toward mango production in Asia which accounts
still maintaining even inferior cultivars around about 60% of the world production.
their houses (Kusumo 1996; Vasudeva et al. During late nineteenth and early twentieth
2015). Sizeable variability in M. indica is found century, dozens of mango varieties were evolved
in Thailand. Variability is available in the form in Florida establishing the western hemisphere
of three main types based on the stage of con- mango industry (Schnell et al. 2006). These
sumption, viz, green mango, ripe mango, and varieties are as per the preferences of the Western
dual-purpose mango. In Philippines, diversity in consumers’ taste, aroma, and red peel color.
M. indica is distributed throughout the country Breeding system of mango prefers out-crossing.
(Coronel 1996). Significant diversity in polyem- Availability of several genotypes from diverse
bryonic types is available in this country (Ram geographical locations resulted into the devel-
and Rajan 2003). In China, M. indica is dis- opment of secondary gene pool in Florida. This
tributed in Guangdong, Hainan, Yunnan, gene pool immensely contributed for the estab-
Guangxi, Fujian, Taiwan, and Southwest lishment of Florida mango industry, furthermore,
Sichuan. Sporadic cultivation is also found in the in western hemisphere.
south of Zhejiang (Mukherjee 1985; Shupei and Several molecular characterization studies
Yanqing 1996). results based on a considerable number of culti-
Nowadays, mango is commercially grown vars have also conceptualized various groups of
throughout the tropics and in many subtropical mango cultivars (Shamili et al. 2012; Dillon et al.
areas of the world (Rajan and Hudedamani 2013; Tsai et al. 2013; Sherman et al. 2015;
2019). It is cultivated in wide range of agro- Singh et al. 2016; Ajayi et al. 2019; Warschefsky
ecological conditions, at the equator and at lati- and von Wettberg 2020). This grouping is not
tude of 35-37 oN in southern Spain. Widespread only based on the chronology of their introduc-
distribution of seedling selections made at tion in different countries but also on the
molecular basis and genetic relatedness. In most 4.2.2 Wild Relatives of M. indica
of the countries, mango cultivar collections are
secondary collections. Cultivars were introduced Changing consumer preference and climate
from the country of origin indirectly to other change has confounded the need of developing
area. Mostly, this process has taken place for new mango varieties through the introduction of
evaluating suitability of cultivar for commercial novel existing genes from diverse available
production in mango-growing countries. In most sources. Germplasm collections in the field
of the mango-growing areas of western hemi- genebank and wild relatives are the major gene
sphere, seedlings are not used for planting new sources for developing the disease-resistant and
orchards, and therefore further evolution of the locally adapted varieties with several desirable
diversity could not take place. characteristics. During beginning of the twentieth
A good number of cultivars moved from one century, it has been realized that the wild rela-
country to another thus at most of the places tives can serve as an important genetic resources
diversity was not naturally created because in building breeding programs (Vavilov 1926;
grafting was used for multiplication. In general, Tanksleyj and McCouch 1997; Meilleur and
grouping of the diversity by molecular studies Hodgkin 2004). Compared to domesticated
was based on the grouping of country of origin. germplasm, crop wild relatives often exhibit
Phenotypic and genotypic analysis of the diver- better resistance to biotic and abiotic stress
sity has clearly indicated that the place of their (Hajjar and Hodgkin 2007). Although advanta-
origin is related with the group to which they geous traits from crop wild relatives have been
belong. Analysis of the primary and secondary used to improve major crops for more than eight
diversity based on molecular tools has also decades, the genetic diversity of mango wild
revealed almost similar grouping results. relatives remains unutilized.
Collections of mango cultivars have been In addition to the abundance in Malaysia’s
named as Indian, Floridian, Thai, Pakistani, peninsular area (Kostermans and Bompard
Filipino, Spanish, Colombian, etc. by researchers 1993), Mangifera genus comprising approxi-
working on diversity analysis by molecular mately 69 species are mainly found on the
markers. High variability has been reported in the islands of Borneo, Java, and Sumatra. M. khasi-
Thai accessions (Eiadthong et al. 2000). Most of ana Pierre, M. sylvatica Roxb, M. camptosperma
the Thai cultivars have polyembryony, thus it Pierre, M. andamanica King were recorded in
seems many of these varieties have given rise to various parts of northeastern India sub-
zygotic seedling variants, different from mother Himalayan tracts. M. sylvatica is known to
genotype, widening genetic variability. Genetic occur in East Sikkim, in West Bengal and in the
diversity in cultivated mango cultivars in Pak- islands of Meghalaya, Assam, and the Andaman
istan is similar to North Indian gene pool as most (Mukherjee 1949b; Agharkar and Roy 1951;
of the varieties were from India and being com- Yadav and Rajan 1993). Wild Mangifera gene
mercially cultivated. pool existing in natural habitat has been well
India, being primary centre of diversity, a lot of documented by Mukherjee (1985) and Koster-
variation exists among regionally established mans and Bompard (1993). Information on their
varieties. Rajan et al. (2013) reported similarity in occurrence, distribution, and utilization in Asia
climatic suitability of north and east Indian vari- has been accounted by Iyer (1991), Ram and
eties. Most of the Pakistan cultivars are from north Rajan (2003); Rajan and Hudedamani (2019).
and eastern mango gene pool. Being a part of India Most of the Mangifera species are useful as
and free exchange of germplasm, Pakistan mango sources of gene(s) for one or another desirable
industry is based on north and east Indian gene trait. These species can be utilized in crop
pool. At molecular level also the similar results improvement program or as rootstocks through
have been reported (Ahmad et al. 2008). proper exploitation of their special attributes.
50 S. Rajan et al.
Mangifera species useful for crop improve- (Iyer 1991, Kostermans and Bompard 1999, Ram
ment program fall into two categories; 1) species and Rajan 2003).
having edible fruits with other desirable charac- Several of the wild relatives in southeast Asian
ters, and 2) species that may not have edible countries are valued for their aromatic fruits uti-
fruits but serve as gene source for improvement lized for making various dishes. These wild rel-
of specific trait like resistance to anthracnose, atives are also rich in bioactive compounds like
tree decline, floral and vegetative malformation, mangiferin and lupeol which are considered
powdery mildew, hoppers, gall midge, etc. (Iyer important for human health. Clinical trials have
1991). The role of wild relatives of mango is demonstrated various health benefits of this
more important with respect to trait-specific native compound of Mangifera (Tangah et al.
breeding compared to varietal diversity present 2017). Wild species are also used for their
in Mangifera indica. Kosterman and Bompard medicinal value. Bark of M. zeylanica, a native
(1993) reported 69 Mangifera species with species to Sri Lanka, is being used in traditional
maximum species diversity available in penin- medicine for the treatment of cancer. Cytotoxicity
sular Malasyia. In India, six Mangifera species to the cancer cell lines has been reported (Ediri-
are available, of which few are under threat of weera et al. 2016). In some parts of the southeast
extinction, viz., M. griffithii, M. camptosperma, Asia, due to high rainfall, M. indica cannot grow
and M. zeylanica. Similarly, the diversity within successfully; however, M. odorata is being
Mangifera indica in terms of seedling origin grown successfully in these areas. M. casturi
varieties has also been eroded due to extensive Kosterm, a common species in South Kalimantan
infrastructural development across the India ter- and East and Central Kalimantan, with typical
ritory. Mangifera species and wild types have dark-colored fruits, deep orange pulp, unique
tremendous value in trait-specific mango breed- flavor, aroma and very tasty is also suited to ever
ing (Table 4.1). wet climates (Ram and Rajan 2003).
Not many attempts have been made to know
that wild species of the Mangifera genus can be
4.2.3 Use of Wild Relatives easily crossed with cultivars of M. indica for the
transfer of desirable alleles. So far, only limited
Under natural habitat, wild relatives of M. indica numbers of possible interspecific crosses were
are confined to the countries where extensive attempted. Initiatives at Florida to produce new
breeding program is presently not operating. The hybrids with reduced susceptibility to disease
introductions of these wild relatives to the field using wild relative’s, viz., M. lalijiwa, M.
gene banks in Florida, Australia, and India have quadrifida, M. rubropetala, with M. indica were
been made with limited utilization for breeding. successful. New hybrids between Mangifera
Iyer (1991) detailed several Mangifera wild spe- species and M. indica can provide the first step
cies producing edible fruits, viz., M. altissima, M. toward these goals (Ledesma et al. 2017). M.
longipes, M. caesia, M. macrocarpa, M. laurina was used as the pollen parent in a
cochinchinensis, M. odorata, M. foedita, M. breeding program with a M. indica hybrid in
pajang, M. griffithii, M. pentandra, M. indica, M. Australia resulting 60 successful hybrids (Bally
sylvatica, M. lagenifera, and M. zeylanica. et al. 2013).
A good number of wild relatives have been
identified with useful traits. M. caesia can be
utilized for its fragrance; M. gedebe, M. inocar- 4.2.4 Mangifera Species as Rootstock
poides, and M. decandra can be exploited as
rootstock for waterlogged conditions; M. pajang Mangifera species have also been used as root-
can be looked for varieties with peelable fruits, stock. There are reports of grafting experiments
whereas, M. similis has free stone mangoes between M. indica and M. foetida, M. odorata,
Table 4.1 Mangifera species having direct bearing on mango improvement

S. No. Species Special Characteristics Source
1 M. caesia Milky white soft pulp having sweet taste East Borneo, Karangan Reserves
and fragrance
2 M. decandra Tolerant to water-logged conditions and Sumatra, Borneo Pakambaru
can be used as rootstock (Indonesia)
3 M. gedebe Tolerant to water-logged conditions and Borneo, Pegu, Myanmar, Thailand,
can be used as rootstock Indo-China, Thailand
4 M. indica var. Fruits twice a year Saigon, Vietnam
mekongensis
5 M. Tolerant to water-logged conditions and Papua, Morehead
inocarpoides can be used as rootstock
6 M. paiang Fruits can be peeled like banana Borneo and Kapit Sarawak
(Malaysia)
7 M. similis Free stone fruits Kalimanthan (Borneo)
8 M. mangifica Fibreless Western Malaysia
9 M. rufocostat Off season bearing habit Sumatra, Borneo, and Malay
and M. Peninsula
swintonioides
10 M. foetida Sweeter, less fibrous pulp Sumatra, Kalimantan (Borneo) and
Java
11 M. odorata Fragrance, firmness, ability to grow under Philippines, Peninsular Thailand,
high rainfall, excessive humidity and sour- Western Malaysia, Vietnam
sweet taste
12 M. casturi Prolific bearer with small, black, and sweet South Kalimanta (Borneo)
fruits
13 M. altissima Tolerant to insects (hoppers, tip and seed Solomon Islands, New Britain, New
borers) Guinea, Moluccas, Sulawesi, Lesser
Sunda Islands and the Philippines
14 M. pentandra Prolific bearer due to high proportion of Northern Malay Peninsula
hermaphrodite flowers
15 M. laurina Immune to anthracnose West Java and tropical Malaysia
16 M. orophila Restricted to mountain forests and known Malay Peninsula and Sumatra
as mountain species
17 M. Restricted to mountain forests and also South Vietnam
dongnaiensis known as mango of mountain
Source Mukherjee (1985), Angeles (1991), Iyer (1991), Bompard (2009), Usman et al. (2001)
M. kemanga, M. caesia in Java (Ochse and fact that these two species have distinct bark
Bakhizen 1931), M. odorata on M. indica in growth and have remote affinity with common
Philippines (Wester 1920), M. indica on M. mango. From different experiments, it has been
zeylanica in Sri Lanka (Gunaratman 1946). postulated that closely related species of M.
Similarly, M. indica ‘Madu’ in Java and M. indica within a subgenus Mangifera have better
laurina in Sabah, Borneo have been used as scion and roostock compatibility. In the inun-
rootstocks for M. casturi. Grafting of M. caesia dated riverbanks of West Kalimantan (Borneo),
on M. indica (Wester 1920) and M. indica on M. M. laurina is occasionally used as rootstock for
kemanga or M. caesia (Ochse and Bakhuizen M. indica, and this has been tried by the
1931) were unsuccessful. This may be due to the Department of Agriculture in Sabah (Lamb
52 S. Rajan et al.
1987). Grafts of M. casturi, M. griffithii, M. permanently inundated areas, viz., M. gedebe, M.

laurina, M. odorata, M. pentandra, and M. quadrifida, M. griffithii. Other species of the
Zeylanica on M. indica showed high success section Rawa, viz., M.gracilipes, M. microphylla,
percentage (Campbell 2004). There are several M. paludosa, M. parvifolia can serve as potential
species of Mangifera growing well permanently rootstocks of mango on poorly drained soils or in
inundated areas, viz., M. decandra, M. gedebe, areas liable to prolonged flood (Bompard 2009).
M. quadrifida, M. griffithii, M.gracilipes, M.
microphylla, M. paludosa, M. parvifolia can
serve as potential rootstocks of mango on poorly 4.3 Varieties and Cultivars
drained soils or areas suffering from prolonged
flood (Bompard 2009). Mangifera species like Mango is very rich in terms of varietal diversity.
M. orophilla and M. dongnainsis may be used in There are more than a thousand varieties of
future as mango rootstocks for sub-mountainous mango growing across the world propagated
areas. either through seedling as well as vegetative
(Ram and Rajan 2003). However, most of them
have originated as a chance seedling and main-
4.2.5 Mangifera Species for Pest tained asexually (Singh 1960; Ram and Rajan
and Diseases Resistance 2003). Due to high level of heterozygosity in
mango, each and every seedling is unique in its
The most devastating disease which causes huge fruit characteristics. Use of mango seedlings for
economic loss to mango production is anthrac- planting new orchards was continued till the
nose. M. laurina a species having subglabrous middle of twenty-first century. Although later on,
and laxly flowered panicles is well adapted to at many places new orchards where planted using
area with perpetual wet climates and found to be grafts, even then the seedling orchards were
immune to anthracnose disease and can be used available in India. Multiplication through seed-
for imparting resistance in future bred varieties ling resulted in a large number of varieties in
(Bompard 1993). Sharma and Chaudhry (1976) India, Florida, and Southeast Asia. Cultivation
reported that wild type trees from Tripura state of for a long time over an extended area, reflecting
India were free from mango malformation. M. different selection criteria and genetic responses
altissima is another species which has to varied environmental influences are responsi-
resistance/tolerance to major insects and pests of ble for high degree of diversity represented by
mango like mango hopper, tip, seed borers, etc. mango varieties. Based on the mode of propa-
There is an urgent need to screen the Mangifera gation, M. indica germplasm can be classified
species for their reaction against major diseases into two groups.
and insect pests.
4.3.1 Seedling Races (Wild

4.2.6 Extension of Mango Cultivation and Cultivated)
in Non-traditional Areas
This group includes plants derived from both
Wild mango species reported from Malaysia and monoembryonic and polyembryonic mango
Vietnam like M.orophila and M. dongnaiensis stones. Almost all the mango cultivars are the
are restricted to mountain forests at 1,000 to result of selection from these seedlings. As
1,700 m above mean sea level. These species compared to cultivars this group exhibits wide
could be explored to extend the possibility of variability with regard to fruit and tree characters.
mango cultivation in temperate regions (Iyer and In India and other parts of the world, the seed-
Schnell 2009). Similarly, there are several spe- lings of monoembryonic cultivars are not much
cies of Mangifera that can be grown in cared, but in places where the polyembryonic
varieties are commercially grown, seedlings are parts of the world. There are approximately 30
important. A number of polyembryonic varieties commercial cultivars in India. Most of them are
have been reported in mango (Singh 1960) of limited adaptability and have a regional pref-
mostly from coastal areas. No commercial vari- erence for production, performance, and con-
ety in North India is polyembryonic (Ram and sumers (Yadav and Rajan 1993). In different
Rajan 2003). In about 20 polyembryonic vari- regions of India, however, the situation is slowly
eties (indigenous and exotic) available, except replaced by the standard cultivars ensuring
Kensington, most of them have inferior fruit higher returns. Mango varieties are categorized
quality (Yadav and Rajan 1993) with some into broad groups based on their place of origin;
exceptions of southeast Asian varieties. the Indian mango varieties and Indo-Chinese
group which originated in south East Asia (Evans
et al. 2017). However, another group of mango
4.3.2 Horticultural Varieties varieties having their origin from Florida, USA
(Vegetatively are commercially cultivated in central and south
Propagated) America, Europe, and Mexico. The present day
and Cultivars Floridian mango varieties have been originated
as open pollinated seedling of south Indian
The varieties of M. indica, which produce the variety Mulgoa and Sandersha (syn. Totapuri).
best quality fruits, are mostly of Indian origin. Important commercial mango varieties from dif-
About a thousand monoembryonic varieties ferent countries are summerized in Table 4.2.
occur in India and those from other regions of the The commercial cultivars in Bangladesh are
world are not more than 50 (Mukherjee 1949a). Gopal Bhog, Khirsapat, Himsagar, Langra, Fazli,
Significant clonal variations have been observed Mohon Bhog, Kohinoor, and Kua Pahari. Most
in the commercial varieties being grown in dif- of these were selected from superior chance
ferent tracts. In the same variety, there are clones seedlings in India and subsequently adapted in
with very big sized fruits whereas small sized Bangladesh. In China, about 130 cultivars are
fruits are also not unusual. Attempts have been available and originated from the following three
made to collect the variability in these clones sources: (i) Traditional local cultivars (ii) intro-
(Rao and Mukherjee 1982; Singh et al. 1986; ductions from southeast Asia, south Asia, Africa,
Chadha 1989). and Australia, and (iii) Novel germplasm selec-
Large-scale seedling population of mango ted by various mango producing provinces/
gave rise to several outstanding types but due to regions in China (Ram and Rajan 2003).
lack of grafting method till the early twentieth Almost all local mango cultivars in Philippines
century most of the promising seedlings could have polyembryonic seeds which enable them to
not be asexually multiplied. Promising seedling preserve their phenotypic identities for genera-
varieties were limited to the single tree and thus tions. About eight distinct varieties have been
could not attain the commercial status. Grafting recognized: ‘Carabao’, ‘Pico’, ‘Pahutan’, Mam-
enabled Indians to multiply outstanding seed- palang, ‘Digos’, ‘Binoboy’, ‘Dudul’, and
lings for planting orchards. The process gave rise ‘Senora’. Numerous mango varieties have been
to multiplication of hundreds of varieties through introduced from foreign countries. However,
grafting. Vegetative propagation helped in except for two varieties which are better con-
establishing seedling varieties as a cultivar. sumed at the green stage, none has surpassed the
In addition to various seedling varieties, over eating qualities of the ‘Carabao’ and ‘Pico’
one thousand vegetatively multiplied mango mangoes (Coronel 1996).
cultivars have been registered. Most of these In Sri Lanka, both monoembryonic and
were selected as chance seedlings and maintained polyembryonic cultivars are grown. Cultivars
asexually afterward. Most of such cultivars come Willard, Pandithasekera, Neelam, Chembatan,
from India, and numbers are limited to other Walamba, and Ambalavi are among
54 S. Rajan et al.
Table 4.2 Most important mango cultivars in major producing countries

Country Cultivars
Australia ‘Kensington Pride’, ‘Banana’, ‘Earlygold’, ‘Glenn’, ‘Haden’, ‘Irwin’, ‘Keitt’, ‘Kent’, ‘Zill’
Bangladesh ‘Aswina’, ‘Fazli’, ‘Gopal Bhog’, ‘Himsagar’,’Khirsapati’, ‘Langra’, ‘Kishan Bhog’,
‘Kohinoor’, ‘Kua Pahari’, ‘Mohan Bhog’
Brazil ‘Adams’, ‘Embrapa 141’, ‘Ametista’, ‘Apple’, ‘Ataulfo’, ‘Augustus’, ‘Bourbon’, ‘Brooks’,
‘Davis Haden’, ‘Delicioso’, ‘Espada’, ‘Extrema’, ‘Fernandeza’, ‘Florigon’, ‘Glenn’,
‘Haden’, ‘Iturbae’, ‘Kent’, ‘Palmer’, ‘Rosa’, ‘Santa Alexandrina’, ‘Santa Cruz’, ‘Sensation’,
‘Smith’, ‘Tommy Atkins’, ‘Vitoria’, ‘Zill’
China ‘Baiyu’, ‘Guixiang’, ‘Huangpi’, ‘Huangyu’, ‘Macheco’, ‘Sannian’, ‘Yuexi No. 1’
Costa Rica ‘Haden’, ‘Irwin’, ‘Keitt’, ‘Mora’, ‘Tommy Atkins’
Columbia ‘Albania’, ‘Bocado de Reina’, ‘Cauca’, ‘Chancleto’, ‘Haden’, ‘Irwin’, ‘Keitt’, ‘Kent’,
‘Lorito’, ‘Mango de Azúcar’, ‘Mango Manzanita’, ‘Magdalena River’, ‘Mariquita’,
‘Palmer’, ‘Tommy Atkins’, ‘Van Dyke’, ‘Vellenato’, ‘Zill’
Cuba ‘Bizcochuelo’, ‘Cecil’, ‘Delicioso’, ‘Filipino’, ‘Haden’, ‘Huevo de’, ‘La Paz’, ‘Kent’,
‘Macho’, ‘Manga Amarilla’, ‘Manga Blanca’, ‘San Diego’, ‘Smith’, ‘Toro’
Haiti ‘Francine’, ‘Madame Francis’, ‘Francis’, ‘Julie’
India ‘Alphonso’, ‘Banganapalli’, ‘Bombay’, ‘Bombay Green’, ‘Chausa’, ‘Dashehari’, ‘Rataul’,
‘Fazli’, ‘Fernandian’, ‘Himsagar’, ‘Kesar’, ‘Kishen Bhog’, ‘Langra’, ‘Mallika’, ‘Mankurad,
‘Mulgoa’, ‘Neelum’, ‘Pairi’, ‘Suvarnarekha’, ‘Totapuri’, ‘Vanraj’, ‘Zardalu’, ‘Amrapali’,
‘Bangalora’, ‘Gulabkhas’
Indonesia ‘Arumanis’, ‘Dodol’, ‘Gedong’, ‘Golek’, ‘Madu’, ‘Manalagi’, ‘Cengkir’, ‘Wangi’
Israel ‘Haden’,’Tommy Atkins’,’Keitt’, ‘Maya’, ‘Nimrod’, ‘Kent’, ‘Palmer’
Kenya ‘Apate’, ‘Apple’, ‘Batwawi’, ‘Boribo’, ‘Boubo’, ‘Dodo’, ‘Gleen’, ‘Haden’ ‘Irwin’, ‘Kent’,
‘Kimaji’, ‘Kisikio Punda’, ‘Ngowe’, ‘Zill’
Malaysia ‘Arumanis’, ‘Kuala Selangor 2’, ‘Golek’, ‘Apple Rumani’, ‘Malgoa’, ‘Apple Mango’,
‘Maha-65’, ‘Tok Boon’
Mexico ‘Agua’, ‘Ajo’, ‘Alcanfor’, ‘Alcanforado’, ‘Amate’, ‘Amatillo’, ‘Ataulfo’, ‘Canela’, ‘Chico’,
‘Coche’, ‘Cuero’, ‘Haden’, ‘Irwin’, ‘Jocote o Cachetico’, ‘Keitt’, ‘Kent’, ‘Manilila’,
‘Manilon’, ‘Manzana’, ‘Manzanillo’, ‘Melon’, ‘Ora’, ‘Palmer’, ‘Papaya’, ‘Pepino’, ‘Peter’,
‘Pija’, ‘Pina’, ‘Platano’, ‘Pomarrosa’, ‘Sensation’, ‘Sin nombre 1’, ‘Sin nombre 2’, ‘Sin
nombre 3’, ‘Tapanero’, ‘Tecolote’, ‘Tommy Atkins’, ‘Trinadad’, ‘Van Dyke’ and ‘Viejita’
Peurto Rico ‘Amini’, ‘Colombo Kidney’, ‘Divine’, ‘Blanco’, ‘Haden’, ‘Mangotino’, ‘Mayaguezano’ and
‘Tete Nene’
Myanmar ‘Aug Din’, ‘Ma Chit Su’, ‘Sein Ta Lone’, ‘Shwe Hin Tha’
Pakistan ‘Anwar Ratol’, ‘Chausa’, ‘Dashehari’, ‘Gulab Khas’, ‘Langra’, ‘Siroli’, ‘Sindhri’,
‘Suvarnarekha’, ‘Zafran’, ‘Baganapalli’
Philippines ‘Carabao’, ‘Manila Super’, ‘Pico’, ‘Binoboy’, ‘Carabao’, ‘Dudul’, ‘Pahutan’, ‘Senora’
Singapore ‘Apple Mango’, ‘Arumanis’, ‘Golek’, ‘Kaem Yao’, ‘Mangga Dadol’
South Africa ‘Brooks’, ‘Chené’, ‘Crimson Pride’, ‘Fascell’, ‘Glenco’, ‘Heidi’, ‘Joa’, ‘Keitt’, ‘Kent’,
‘Manzanillo’, ‘Neldica’, ‘Osteen’, ‘Peach’, ‘President’, ‘Saber’ ‘Sensation’, ‘Shelly’, ‘Smith
Seedling’, ‘Tommy Atkins’, ‘Zill’
Spain ‘Osteen’, ‘Tommy Atkins’, ‘Sensation’, ‘Glenn’, ‘Gomera-1’, ‘Gomera-3’, ‘Palmer’,
‘Lippens’, ‘Irwin’, and ‘Valencia’, ‘Pride’ and ‘Kensington Pride’
Sri Lanka Karutha Colomban, Willard, Vellai Colomban, Petti amba, Malwana amba, Parrot Mango
and Peter Pasand, Dapara, Hingurakgoda
Taiwan ‘Jin-hwung’, ‘Keitt’, ‘Tommy Atkins’, ‘Tainong No. 1’ and ‘Tsar Swain’
(continued)
Table 4.2 (continued)

Country Cultivars
Thailand ‘Nam Doc Mai’, ‘Ngar Charn’, ‘Okrong’, ‘Rad’, ‘Choke Anand’, ‘Kao Keaw’, ‘Keow
Savoey’, ‘Pimsenmum’
United States of ‘Adams’, ‘Anderson’, ‘Apple’, ‘Davis Haden’, ‘Dixon’, ‘Earlygold’, ‘Edward’, ‘Eldon’,
America ‘Fairchild’, ‘Florigon’, ‘Ford’, ‘Gibbons’, ‘Glenn’, ‘Haden’, ‘Irwin’, ‘Julie’, ‘Keitt’, ‘Kent’,
‘Lily’, ‘Lippens’, ‘Osteen’, ‘Palmer’, ‘Simmonds’, ‘Smith’, ‘Springfels’, ‘Tommy Atkins’,
‘Zill’
Vietnam ‘Combodiana’
Source Malo (1970); Pandey (1986); Ram and Rajan (2003); Human and Rheeder (2004); Durán-Zuazo et al. (2004);
Mukherjee and Litz (2009), Njuguna et al. (2009); Human et al. (2009); Galvez-Lopez et al. (2010); Pleguezuelo et al.
(2012); Rajan and Hudedamani (2019); http://Mangifera.res.in/varieties.php
monoembryonic ones, whereas Peterpasand, centre of diversity of M. indica in Florida.

Kohuamba, Karutha Colomban, Dampara, Parrot ‘Haden’ a seedling of Indian variety ‘Mulgoba’
and Vellaicolomban are polyembryonic (Ram gave rise to varieties like ‘Glenn’, ‘Lippens’,
and Rajan 2003). Medagoda and Herath (1984) ‘Osteen’, ‘Parvin’, ‘Smith’, ‘Springfels’,
reported that Petti Amba also produces polyem- ‘Tommy Atkins’, and ‘Zill’. ‘Saigon’ seedling
bryonic seed and the highest incidence of selections made from ‘Cambodiana’, and intro-
polyembryony is shown in Parrot mango. Similar ductions from Indo–China resulted into the cul-
to India, different cultivars do not perform in the tivars like ‘Alice’, ‘Herman’, and ‘Florigon’.
same way in different parts of the island. Vari- Compared to outstanding Indian cultivars, the
eties for different agro-ecological regions are Florida mango cultivars are highly adaptable to
identified and the recommendation of varieties many agro-ecological regions and are regular
for the dry zone, intermediate zone, and wet zone bearer. These cultivars are highly attractive and
are different. develop red blush at maturity, firm flesh, a high
In China, at present the germplasm which flesh to seed ratio and regular bearing habit are
have become the principal cultivated varieties in reasons for their increasing popularity. Florida
the provinces/regions in South China include cultivars, e.g., ‘Tommy Atkins’, ‘Keitt’, etc. are
Huangpi, Wupi, Neelum, Okrong, Nam Doc also moderately resistant to anthracnose, an added
Mai, Dashehari, Carabao, Baiyu, Dabaiyu, advantage during prolonged storage and export
Liuxiang, Macheso, Sannian, Zihua, Guixiang, (Knight 1993). In many countries, now cultiva-
Chuanmang, Yexi No.1, Guire No.10, Irwin, tion of Florida cultivars is well adopted, provid-
Keitt, Haden, Zill, Sensation, Caixuan, Tainong ing the base for international mango trading.
Nos.1 and 2, Chun Hwang, Honghua, etc. Vari- Therefore, only about six dozens cultivars are
eties Huangpi, Taoye, Honghua, and Sannian commercially grown in the world, of which the
have been widely used as rootstocks. Some export quality commercial cultivars are
germplasms have been used as breeding material. Alphonso, Dashehari, Banganpalli, Chausa, and
For example, crossing of Neelum with Golek at Kesar of India; Bourbon, Carlota, and Haden of
Guangxi University of Agriculture has resulted Brazil; Mabrouka of Egypt, Madame Frances of
in novel germplasm, such as Guixiang, Lupi, and Haiti; Haden and Maya of Israel; Apple, Borino,
Xiaotian. The SCCTC has also screened from and Ngowe of Kenya; Haden, Keittoand Manila
Neelum seedling tree a new selection Long- of Mexico; Anwar Rataul, Samerbehist Chowsa
jingda, which yields very large fruit. and Fazli of Pakistan; Carabao of the Philippines;
Introductions of polyembryonic varieties from Haden, Keitt and Zill of South Africa; Hindi Be
Southeast Asia (Philippines, Cambodia), India, Sennar and Kitchener of Sudan; nam Doc Mai
and other sources created an important secondary and Okrong of Thailand; Julie of Trinidad and
56 S. Rajan et al.
Venezuela (Pandey and Dinesh 2010; Rajan et al. Bombay state were classified by Burns and
2020). Prayag (1921) into three major classes on their
In India, the same variety is grown in different fruit shape basis as round-fruited, long-fruited,
regions and fruits produced in geographical and indefinite.
regions are recognized for quality due to specific Sturrock (1951) developed an artificial key
climate of the location. Alphonso of Konkan based on fruit characters for the identification of
region; Kesar from Gujarat; Banganpalli of mango varieties grown in Florida. Hartless
Vishakhapatnam region in Andhra Pradesh; (1913) for the first time used floral characters as
Dashehari of Malihabad, Mall, and Kakori; criteria for classification. Popenoe (1920) classi-
Appemidi of Shimoga and Chikmanglur distirict; fied 300 varieties, based on the descriptor list of
Kesar in Marathwada; Zardalu in Bhagalpur; the varieties from all parts of the world on the
Khirsapati (Himsagar), Laxman Bhog, Fazil of basis of fruit characters, coloration of panicle
Malda have been issued Geographical Indication axis, laterals and pubescence of the panicle
(Sharma and Rajan 2018). branches, and the number of embryo in the seed.
Naik and Gangolly (1950) described 335 south
4.3.2.1 Classification Indian varieties, based on system which seems to
and Characterization be natural (Singh 1960). Besides fruit characters,
of Varieties other characters were also given importance by
Maries (1902) made attempts to collect and Naik and Gangolly (1950). On the basis of pri-
describe Indian mango varieties scientifically on mary characters mentioned above, south Indian
the basis of fruit characters in the beginning of varieties are grouped in main groups. Secondary
the twentieth century. Other early attempt in characters were used to distinguish sub-group of
Puerto Rico and Hawaii were made to classify classes. Tertiary characters are used to distinguish
the varieties by Collins (1903) and Higgins varieties within each classes or sub-groups (Naik
(1906), but no definite system of classification and Gangolly 1950). On the basis of fruit shape,
could be evolved. Later, varieties of Bhagalpur varieties are categorized into six main groups or
(Bihar) were described by Woodhouse (1909) cohorts. Considering leaf tip and folding of leaf,
following system of classification mainly based each main group is further divided into four
on fruit characters. The varieties were classified classes giving rise to 24 classes.
in three broad groups: (i) round fruit, (ii) Bombay Majority of the attempts made to classify
type, and (iii) long oval or rectangular fruits, mango variety show that the fruit shape is the
longer than broad. In Florida, Rolfs (1915) most important and stable character for distin-
classified the mango varieties into nine main guishing varieties from each other. Various fruit
groups based on the fruit and stone characters shapes of mango have been described by Naik
and growth habit of the tree. The varieties were and Gangolly (1950) and Gangolly et al. (1957).
grouped into groups: (i) Turpentine, (ii) Elcanor The size of fruit is also of relative importance,
group, (iii) Pineapple, (iv) No.-11 group, fruit dimensions and weight are helpful in dis-
(v) Bombay group, (vi) Cambodiana group, tinguishing varieties. Among the fruit characters,
(vii) Sandersha group, (viii) Mulgoba group, the presence and form of beak is of prime
(ix) Gola group. Wester (1920) suggested mak- importance for the classification of mango vari-
ing the system of classification should be com- eties. Wide variation in the form of beak is pre-
prehensive and evolving the mango varieties not sent. It may be absent in some varieties and
only from India but also from the other mango- prominent with various shapes of the fruit. This
growing regions. Agreeing with this view, character is genotype specific and shows least
Wester (1920) described important mango vari- variation under various environments. Apart
eties of Philippines and a descriptive list of from the shape of the fruit, characters like fruit
Indian mango varieties was also given. Based on base, shoulder, sinus, apex, and cavity of stalk
the system of Woodhouse, 89 varieties of insertion are important characters. Variation in
these characters have been depicted in mono- mangoes was the prime objective of these col-
graphs of Naik and Gangolly (1950) and Gan- lections. Scientific approach for the collection of
golly et al. (1957). mango germplasm was made after the establish-
Illoh and Olorode (1990) used multivariate ment of Fruit Research Stations at Sabour,
methods for the grouping of varieties grown in Kodur, Saharanpur, Sangareddy, and Vengurla.
Nigeria. On the basis of flower and fruit charac- With the establishment of Indian Institute of
ters, they grouped the varieties in four groups. Horticultural Research, Bangalore, efforts were
Rajan et al. (1998 and 1999b) used hierarchical made to collect mango varieties of south and
approach for analyzing diversity in canopy west India (Chadha 1996). At the Central Insti-
characteristics of mango and classified important tute Subtropical Horticulture, Lucknow, a con-
varieties based on leaf component and diffuse certed effort was made to have a National
non-interceptance values of the tree canopy. collection of mango germplasm representing
Rajan et al. (1999c) applied multivariate analysis germplasm from different parts of the country.
of growth and yield performance of Dashehari Majority of the attempts made for the survey
scion on 24 varieties as rootstock. and collection of mango germplasm are limited
During last three decades, with the advance- to in situ evaluation for various characters with a
ment in molecular techniques, a good number of special emphasis on fruit quality. However,
studies have been undertaken for characterizing several reports on the survey and collection of
varieties. Initial studies on isozyme banding germplasm attempted in different parts of the
pattern (Degani et al. 1990), random amplified country are available (Patwardhan 1918; Burns
polymorphic DNA (RAPD) analysis (Schnell and Prayag 1921; Mukherjee 1948, 1949a, b;
et al. 1995), and DNA finger print information Gangolly and Singh 1950; Mukherjee 1950a, b;
(Adato et al. 1995) have been used for grouping Naik and Gangolly 1950; Singh and Singh 1957;
the cultivars and estimating gene diversity in Teotia and Srivastava 1961; Singh and Jawanda
different groups of the cultivars. Use of molec- 1962; Teaotia and Singh 1963; Kashyap and
ular markers as tools for analyzing the diversity Jyotshi 1969; Teaotia and Singh 1971; Dhaki
of mango has been well documented. 1972; Saha 1972; Bose et al. 1974; Sadhu and
Using group constellation, cultivars were Bose 1976; Sharma and Choudhary 1976; Das
grouped into three distinct clusters for selecting and Hota 1977; Hoda and Mandal 1979;
promising parents (Rajan et al. 2009). Mango Kulkarni 1979; Mukherjee et al. 1983; Tyagi
cultivars can be categorized into several groups 1986; Ramaswamy 1988; Yadav 1989; Gupta
on the basis of their suitability for different usage. et al. 1993; Lal and Gupta 1993; Choudhari et al.
The group may be as table and sucking types. 1993; Singh et al. 1993; Thimmaraju 1993.
Majority of the cultivar contain none to scanty Mukherjee (1948) collected and described 77
fiber and firm flesh make them suitable for table varieties of mango from Murshidabad. Saha
purpose, whereas varieties with high juice content (1972) and Mukherjee et al. (1983) conducted
and fiber are used for sucking purpose. Some of surveys for the collection of superior types in
the varieties are excellent sucking types with high West Bengal.
juice content but sucking types are mostly limited Very few systematic attempts have been made
to India and Bangladesh (Ram and Rajan 2003). to collect the large variability available in Bihar.
Das and Hota (1977) and Parida and Rao (1989)
studied diversity in mango gene pool in Odisha.
4.4 Germplasm Collection From the collection of 500 varieties from different
and Introduction districts of the state, 35 varieties were selected for
desirable characters. Expeditions were also made
Exploration and collection of mango germplasm by Sharma and Chaudhary (1976), Yadav (1989),
in India started in the sixteenth century (Singh Singh et al. (1993) to study the variability in
1960). The search for better fruit quality mango in North eastern region. Singh and
58 S. Rajan et al.
Jawanda (1962) studied the seedling populations Mango varieties from foreign countries were
of mango in Punjab for selection of superior perhaps first introduced into the Philippines
types. One-hundred-fifty mango varieties of during prehistoric times. Recorded introductions
Bihar and Uttar Pradesh were collected and were made in early 1900s when numerous vari-
described by Singh and Singh (1956). Teotia and eties were introduced from India. One of these
Singh (1963, 1971) and Teaotia and Srivastava Indian varieties, the ‘Katchamitha’, gained
(1961) collected and studied the variability in acceptance by the Filipinos. During Second
mangoes of eastern Uttar Pradesh. Mangoes of World War, several collections were destroyed.
south and central India have also attracted the However, in the mid 1970s, the Institute of Plant
attention for collection. Burn and Prayag (1921) Breeding in U.P. Los Banos was able to retrieve
collected the varieties of mango and described a few of these mango varieties, not from Lamao
them. Vanraj and Kesar were selected in Gujarat but from other nearby sources. The college of
and the later Kesar has become an important Agriculture of U.P. Los Banos collected mango
commercial variety in many mango-growing varieties from Hawaii and planted these around
areas (Chadha 1996). the university campus (Coronel 1996).
In Bangladesh, mango germplasm collection In Thailand, Ministry of Agriculture and Crop
started in 1946 and maintained at the Central Experiment Station, Sisaket Horticultural
Horticulture Station, Dhaka. At Regional Horti- Research Centre, Bangkok; Noi, Horticultural
culture Research Station, Nawabgonj, collection Research Station, Chachoengsao; Rubber
of known cultivars started in 1985. Many of the Research Centre, Surat; Thani Horticultural
superior clones/seedlings identified in the Research Centre, and Tachai Horticultural
National Mango Shows were collected and Research Station have made collections (Vangnai
planted (Hossain 1996). 1996). In Sri Lanka, Plant Genetic Resources
In Hainan (China), during 1959 to 1967 sur- Centre (PGRC) specially established for this
veys for mango genetic resources, collection, and purpose in 1989 leads the collection program
introduction of exotic germplasm were made. The (Medagoda and Jayawardena 1997).
South China Academy of Tropical Crops (now
CATAS) and other institutions or departments
also introduced germplasm subsequently from 4.5 Characterization
other countries through various channels. Vari-
eties introduced in between 1963 and 1980 from Morphological characterization is the easiest and
Cuba, Indonesia, Sri Lanka, and Thailand inclu- simple characterization process that allows study
ded Haden, Maden, Mecico, Emperado, Aru- of plant variation using visual attributes. The
manis, Golek, Okrong, Nam Doc Mai, Keaw morphological characters mainly help in identi-
Saweuy, Chaokun thip, Pemsenmun, No.811, fying elite mango varieties as well as superior
No. 814, etc. In Taiwan, five varieties including donor parents for different horticultural traits.
Haden, Irwin, Zill, Keitt, and Kent were intro- The fruit characters combined with several other
duced from the USA. Over 30 varieties from the traits were used in the classification of varieties
mango producing countries, 12 varieties from (Burns and Prayag 1921). Even primary, sec-
Costa Rica were collected. Nearly 100 genotypes ondary, and tertiary characters were utilized for
have been collected in Taiwan (Zhen 1989; Shu characterization (Singh and Singh 1956; Pandey
et al. 2000). 1984; Rajan et al. 1999a, b). The fruit characters
In Indonesia, efforts were made for the col- were used for grouping the cultivars based on
lection of genetic resources of mango at Cukur- their performance and their region of adaption
gondang and 224 accessions have been collected. (Rajan et al. 2013a, b).
In 1987, Purnomo collected 19 Mangifera spe- Before the development of the normative
cies from South Kalimantan and East Kalimantan DUS evaluation guide by a Task Force appointed
(Kusumo 1996). by the PPV&FR authority (PPV&FRA 2008),
IPGRI descriptors were used for visual charac- Rajan 1993); leaf area index (Rajan et al. 1999b);
terization of mango (IPGRI 2006; Pinto et al. fruit color (Iyer and Subramanayam 1991); pulp
2006). The biochemical markers (Subedi et al. content (Chadha 1996); TSS (Yadav et al.1987;
2004), morphological and molecular techniques Rameshwar et al. 1979); time of ripening (Iyer
combined (Mussane et al. 2011; Ramessur and and Subramaniam 1986), regularity in bearing
Ranghoo-Sanmukhiya 2011) were used for con- (Anon 1979); malformation (Prasad et al. 1965;
firming the phylogenetic relationship and geo- Mishra 2004) have been studied.
graphic distribution of different Mangifera Germplasm has been evaluated on the basis of
sp. (Eiadthong et al. 1999). anatomical and physiological parameters to cor-
DNA markers have been used for characteri- relate them with the tree vigour (Mukherjee and
zation of diversity in M. indica and wild Man- Das 1976; Srivastava et al. 1980; Singh et al.
gifera species (Eiadthong et al. 1999; Gonzalez 1986; Kurian and Iyer 1992; Srivastav et al.
et al. 2002; Weerarathne et al. 2005; Bajpai et al. 2009). Mango germplasm in India has been
2008; Shamili et al. 2012; Dillion et al. 2013; screened for varietal resistance against different
Dinesh et al. 2015). Adato et al. (1995) used diseases. Germplasm resistant/tolerant to leaf
variable number tandem repeats (VNTRs) blight, die back and bacterial canker has been
markers for DNA finger printing and genetic reported (Verma and Singh 1970; Shekhawat and
analysis of mango genotypes and hybrids. Vari- Patel 1975; Kishun and Chand 1986).
ous PCR approaches were used for the study of Other reports on the evaluation aspects from
genetic variation, parentage, and grouping (Sri- Dhaka (Ahmad 1973), Binodpur (Hossain 1974),
vastava et al. 2007). Studies on morphology and Chittagong (Ahmad et al. 1988), Hathazari
molecular characterization indicate almost simi- (Golder et al. 1992) are available. In Thailand,
lar pattern in grouping (Dinesh et al. 2015). critical evaluation of the germplasm is under-
The use of a good number of sequence-based taken using morphological and agronomical
molecular tools started with the advent of the characters, and certain biochemical patterns are
sequencing techniques and are also used to also being characterized. The National Research
classify mango germplasm for different objec- Council of Thailand had many projects on the
tives. The isolation of novel ripening cDNA development of molecular techniques for identi-
clones was based on gene cloning (Lycett et al. fication of mango varieties through application of
1997), while mRNA isolation and characteriza- DNA finger printing (Vangnai 1996).
tion were used during mixing of the mango to Characterization of mango germplasm in
classify differently expressed genes (Saiprasad Indonesia at Cukurgondang comprises a total of
et al. 2004). Latest studies on molecular charac- 224 accessions. Some cultivars have more than
terization focus mainly on identification of the one accession, such as Arumanis has five, Golek
candidate fruit color and ripening genes, genes has eight, and Manalagi has three. so that there
active in biosyntheses of phenylpropanoid/ are in all 181 cultivars. The cultivars were
anthocyanin, and specific isoforms (CISH planted and evaluated on cv. Madu as rootstock.
2015). The Mango Genome already published The characterization based on the morphological
would be a valuable source for mango genomics description of 181 cultivars was reported by
workers (Singh et al. 2016; Li et al. 2020; Wang Kusumo et al. (1975) and Kusumo and Suminto
et al. 2020). (1987).
Evaluation of mango cultivars in India for Purnomo et al. (1990) evaluated the acces-
different characters has been reported by several sions maintained at Cukurgondang (Indonesia).
workers: Juicy cultivars of south India by Twenty mango cultivars were evaluated for
Kulkarni (1979); sucking varieties of Uttar Pra- suitability as table fruit or processing based on
desh and Bihar (Teaotia and Singh 1963; Singh the taste, fiber, and water content (Suhardjo and
1972; Gupta et al. 1993); raw sweet and pickling Suhardi 1986). The results showed that cultivars,
varieties (Kulkarni 1979); dwarfing (Yadav and namely, Manalagi, Gedong, Alphonso, Danas
60 S. Rajan et al.
Madu, Kidang, Sengir, and Bangalora are good knowledge, ex situ field genebank and on-farm
for table purpose while the other 13 cultivars are conservation have contributed the most.
good for processing.
4.6.1 In Situ Conservation

4.5.1 Variability in M. indica
Kostermans and Bompard (1993) recommended
The list of 1595 cultivars of mango in world for both ex situ and in situ conservation of
(Pandey 1998) was revised with the names of Mangifera spp. Although, in situ conservation
1663 cultivars by Pandey and Dinesh (2010). has advantages, its big drawback is that the nat-
Mango has rich diversity in Gangetic Plains, ure reserves in Asia may not be secure. There is
Eastern Peninsular region, Eastern and Western an urgent need to conserve the diversity in the
Ghats and Deccan plateau of India. A list of the zone of natural variability. Wild seedling races
names of cultivars available in the world as are reported to occur almost throughout India in
probable gene sources for dwarfness, fruit size, the natural forests of Tripura, Orissa, Chota
red peel color, high pulp content, high content of Nagpur, and Western Ghat (Yadav and Rajan
total soluble solids, long shelf-life of fruit, reg- 1993). In the forest of the northeastern India,
ularity in fruit bearing, earliness and lateness in many of the seedlings still have a lot of primitive
fruit maturity and good processing quality have features such as polyembryony and dwarf habit.
been mentioned by Pandey and Dinesh (2010). Work with ecotypes in Manipur for wild mango
The sources of resistance to biotic and abiotic trees reveals that primitive characteristics persist
stresses are available at the cultivar level to the and out-crossing with commercial varieties has
limited extent. Commercial and export quality not taken place (Yadav and Rajan 1993).
mango cultivars of the world have been enlisted In India, in situ conservation of wild forms of
by Pandey (1998) and Pandey and Dinesh M. indica was suggested in the hill region of
(2010). These varieties are obviously excellent Orissa, Chhotanagpur, and the plateau adjoining
gene sources for high yield and fruit quality Madhya Pradesh, forests bordering Myanmar in
parameters. Dinesh and Vasugi (2002) cataloged Manipur valley and Western Ghat (Mukherjee
151 cultivars of mango. They have evaluated 1949b; Yadav and Rajan 1993). In situ conser-
cultivars for 54 characters as per the International vation efforts in Indonesia have been confined to
Plant Genetic Resources Institute (IPGRI) some protected forests and National Forest Parks
Descriptors. for the conservation of wild plants and animals
Dinesh et al. (2012) using Biodiversity Inter- but mango species were not given particular
national Descriptors had developed barcodes for attention (Kusumo 1996). In situ conservation of
the above-mentioned additional varieties through M. sylvatica Roxb. is possible in one or several
molecular characterization. These varieties areas of greater Chittagong Hill Tracts (Bangla-
include some polyembrynic varieties and 34 desh). It deserves urgent attention since forest is
pickle-making varieties known as Appemidi declining fast.
from Western Ghats.
4.6.1.1 On-Farm Conservation
‘The objective of on-farm conservation is to
4.6 Conservation allow natural genetic introgression between
domesticated crop and its wild relatives’ (Harlan
For crops, various germplasm conservation 1992) and to maintain crop evolu-tion in farmer’s
methods are followed such as field gene bank, fields, farms, home gardens, and landscapes
seed storage, in vitro storage and cryopreserva- (Bellon and Etten 2014). Considerable efforts
tion of shoot tips and pollen (Rajan and Hude- under the Asian Development Bank
damani 2019). In mango, with current available (ADB) sponsored initiative were made to
conserve the fruit genetic resources of ten encourage conservation. The diversity fairs also
countries, including India, China, Bangladesh, helped in recognizing the custodian farmers
Indonesia, Malaysia, Nepal, Philippines, Sri (Gajanana et al. 2015b).
Lanka, Thailand and Vietnam, under the 2010 The heirloom varieties have a significant
initiative ‘Conservation and Use of Native diversity and the study was undertaken in India
Tropical Fruit Species and Biodiversity in Asia’ under UNEP-GEF TFT project for their identi-
(Mal et al. 2011). fication and conservation. Such varieties may be
In India, a significant number of accessions directly used for commercial cultivation or as
were collected and conserved in ICAR institutes parents to add characteristics through breeding
under UNEP-Global Environment Agency (Rajan et al. 2014; Dinesh et al. 2015). Although
(GEF) funded by project in five States Amravati several edible Mangifera species, obsolete and
(Maharashtra) and Chittoor (Andhra Pradesh), old varieties are being maintained in home gar-
Malihabad (UP), Pusa (Bihar) and Sirsi (Kar- dens in mango-growing countries of Asia but
nataka) on the Mango (Gajanana et al. 2015a; scientific backup for on-farm conservation is
Sthapit et al. 2016). lacking. However, this program needs strength-
Custodian farmers played an important role in ening for the conservation of valuable diversity
in situ on-farm diversity conservation in mango. available in genus Mangifera. Since the conser-
Custodian farmers are the farmers actively sup- vation by this means require incentives to the
porting, adopting and promoting agricultural farmers, it should be supported through interna-
biodiversity and related knowledge over time, in tional organizations. It is important to be aware
the farms and communities (Dinesh et al. 2015; of the complementarity of the different tech-
Gajanana et al. 2015a; Sthapit et al. 2015; niques in the conservation of gene pool. Con-
Vasudeva et al. 2015; Rajan et al. 2016). servation in field gene banks should be used as a
In 36 rural communities of India, Indonesia, backup in case material is lost in situ (Husk
Malaysia, and Thailand, the identification and 1998). Nevertheless, farmers are still keeping
documentation of tropical fruit tree traditional inferior cultivars in their home gardens, espe-
knowledge was undertaken. There are several cially in the mango production centres because of
motivations to the farmers for on-farm diversity their use value (Vasudeva et al. 2015).
conservation. The analysis in India, Indonesia,
Malaysia, and Thailand showed that many
farmers conserve rich variation with few rare, 4.6.2 Ex Situ Conservation
special fruit tree species or varieties, motivated
mostly by conservation philosophy (Sthapit et al. 4.6.2.1 Field Gene Bank
2015). Personal, social, cultural/religious, natural Presently, establishment of field gene bank is the
and biological traits also played important role in most important way for the conservation of
motivating the farmers for conserving the mango mango germplasm. The plants are conserved in
diversity apart from economic factor (Gajanana the field as living inventory. It is easier to con-
et al. 2015a). ‘National Fruit Catalogue of serve in the field, characterize and use in breed-
Tropical Fruit Diversity’ was developed based on ing programs. However, field genebank may be
the identification of unique varieties along with subjected to pressure from land use, prevalent
details of custodian farmers (Dinesh et al. 2014). diseases and pests, which may result into germ-
For on-farm conservation of cultivated and plasm depletion.
wild germplasm of fruit trees, awareness is In India, few decades back, germplasm of M.
required on diversity conservation. Fruit Tree indica was collected and assembled as working
Diversity Fairs in India are being arranged for collection in the field genebank at different
general awareness about the diversity of fruit locations with major emphasis to the accessions
trees as a participatory method to recognize with desirable traits be exploited as variety or to
indigenous varieties with different traits and be used in breeding program (Table 4.3).
62 S. Rajan et al.
Table 4.3 Field genebank sites of mango in India

Northern India ICAR- Central Institute for Subtropical Horticulture, Lucknow
ICAR- Indian Agricultural Research Institute, New Delhi
Horticulture Experiment & Training Centre, Saharanpur (Uttar Pradesh)
Horticultural Experiment & Training, Centre, Basti (Uttar Pradesh)
G.B. Pant University of Agricultural Technology, Pantnagar (Uttarakhand)
Fruit Research Station, Rewa (Madhya Pradesh)
Western India Regional Fruit Research Station, Vengurla (Maharashtra)
Agricultural Experiment Station, Paria (Gujarat)
Gujrat Agricultural University, Navsari (Gujarat)
Mahatma Phule Agricultural University, Rahuri (Maharashtra)
Southern India ICAR- Indian Institute of Horticultural Research, Bengaluru (Karnataka)
University of Agriucultural Sciences, Dharwad (Karnataka)
Fruit Research Station, Sangareddy (Andhra Pradesh)
Fruit Research Station, Anatharajupet, Kodur (Andhra Pradesh)
Eastern India Central Horticultural Experiment Station, Ranchi, (Bihar)
Agricultural Research Institute, Sabour Bhagalpur (Bihar)
Regional Research Center, ICAR-CISH, Malda (West Bengal)
Fruit Research Station, Krishanagar (West Bengal)
A closer look to the accessions available in field bank. It had 52 mango varieties and four other
gene banks established at various places indi- Mangifera species (M. altissima, M. caesia, M.
cates that substantial diversity of cultivated M. foetida, and M. odorata). A duplicate collection
indica is conserved, but these collections do not of some 58 foreign mango varieties was estab-
contain any representative variability of other lished in 1981 at the campus of the Western
Mangifera species like M. sylvatica, M. Luzon Agricultural College in San Marcelino,
andamanica, M. gedebe and M. khasiana which Zambales. An independent collection of foreign
need to be collected from Manipur, Indo-Burma varieties was established at Davo National Crop
region and Andaman and Nicobar islands (Ram Research and Development Centre of the Bureau
and Rajan 2003). Mango germplasm in India is of Plant Industry in Bago Oshiro, Davao City.
safely duplicated at few centres because germ- Varieties not previously maintained at the Insti-
plasm of one region behaves differently in other tute of Plant Breeding were propagated and
region. planted at the National Collection Site in U.
In Thailand, the Department of Agriculture P. Los Banos (Coronel 1996).
(DOA) have established Tropical Fruit Germ- Live collections of the crops have long been
plasm Resources Centre at Khao Chong, Muang maintained by the Sri Lankan Department of
District of Trang Province. Besides, other col- Agriculture. However, attempts have been made
lections of mango are located at U-thong Field to systematically organize these collections into
Crop Experiment Station, Sisaket Horticultural field gene banks to conserve the variety of fruit
Research Centre, Bangkok; Horticultural crops that are multiplied vegetatively. The effort
Research Station, Chachoengsao; Rubber to collect and conserve local germplasm is not
Research Centre, Surat; Thani Horticultural given a high priority (Medagoda and Jayawar-
Research Centre, and Tachai Horticultural dena 1997).
Research Station. More than 80 varieties are The Bangladesh Society for Horticultural
being maintained and evaluated at Pakchong Science established a Fruit Plant Repository on a
Experiment Station of Kasetasrt University, 200 hectare of land at Madhupur, Tangail about
Nakhon Ratchasima province (Vangnai 1996) 120 km away from the capital city. However, ex
In Philippines, Department of Horticulture, at situ collections at the Research Stations at BARI,
U.P. Los Banos, had established a fruit gene Joydebpur; Fruit Research Station (FRS),
Binodpur; Regional Horticulture Research Sta- studies, Mukherjee (1948) described 72 varieties
tion (RHRS), Hathazari, Chittagong; Horticulture of Bengal.
Centre, Baluria, Natore and Horticulture Centre, In addition, local varieties have also been
Kallyanpur, Nawabgonj are maintained. documented from different regions (Teaotia and
Srivastava 1961; Teaotia and Singh 1963;
4.6.2.2 In Vitro Conservation Kashyap and Jyotishi 1969; Teaotia and Singh
Germplasm maintenance of mango in field gene 1971; Saha 1972; Bose et al. 1974; Sadhu and
banks has its own limitations because of large Bose 1976; Parida and Rao 1989).
land and other resource requirements. The other Sri Lanka Database management for PGR
possible way for the conservation of the gene activities for inventory as well as for utilization is
pool through in vitro conservation is still in fancy now operational at PGRC (Medagoda and
because till date tissue culture technique in Jayawardena 1997). At present registration work
mango is not available. Pollen storage of on mango is being continued. Hossain and
important mango varieties suggested by Iyer and Ahmed (1994) published a ‘Monograph on
Subramaniam (1989) and Dutta et al. (2013) may Mango Varieties of Bangladesh’. It contains
be used in hybridization program for gene detailed studies of 72 mango cultivars of Govt.
transfer. Pollen storage can reduce the lag period farms and private orchards of greater Rajshahi
which is required for grafted plants to attain district. The description of cultivars in Indonesia
flowering stage and pollen of desired parents was documented (Kusumo and Suminto 1987;
could be exchanged for breeding. Purnomo et al. 1990).
Documents prepared under the aegis of the
International Plant Genetic Resources Institute
4.7 Documentation (IPGRI) on eco-geographical study of known
Mangifera genetic resources (Mukherjee 1985)
In India, initial characterization consisted of are available. Another document by Kostermans
recording data on desirable characters by the and Bompard (1993), in the latest revision of the
users. First written evidence of evaluation and taxonomy of Mangifera was the consequence of
documentation of mango germplasm is available joint IBPGR-IUCN (International Union for the
from Ain-i-Akbari written in the sixteenth cen- Conservation of Nature)-WWF (World Wildlife
tury (Singh 1960). Burns and Prayag (1921) Fund) project initiated in 1985 on wild mangoes
documented the germplasm of mango from on the island of Borneo and in the Malay
central India. Description of 335 varieties was peninsula (Bompard 1989), the regions that held
documented and published by Naik and Gan- the highest concentrations of Mangifera species.
golly (1950) in ‘A Monograph on classification The detailed documentation of the recognized 69
and nomenclature of South Indian Mangoes’. species, many of which were collected during the
Singh and Singh (1956) described 150 mango course of this project has formed the basis of the
varieties of Uttar Pradesh and Bihar in a publi- future line of work on the genus’ status reports,
cation titled ‘A Monograph of the mangoes of compiled by IPGRI, on the genetic resources of
Uttar Pradesh’ published in two volumes. Gan- mango in Asia: South Asia (Bangladesh and
golly et al. (1957) also described 210 important India); Southeast Asia (Indonesia, Philippines,
varieties grown in the country from states of Thailand) and East Asia (China) and Sri Lanka
Punjab, Haryana, and Uttar Pradesh in North deal with the mango gene pool diversity in these
India; Andhra Pradesh and Tamil Nadu from important mango-growing countries (Ram and
South; Maharashtra and Gujarat from West; and Rajan 2003).
Bihar, Odisha and West Bengal from East India Based on characterization of mango germ-
and documented this in the form of a monograph, plasm under subtropical conditions, Rajan et al.
‘The Mango’. On the basis of comprehensive (1999a) catalogued 252 Indian mango varieties
64 S. Rajan et al.
using 56 descriptors. E-catalogue on 184 vari- in situ conservation for mango genetic resources.
eties of India was developed as open and Human habitat is expanding fast due to popula-
searchable offline database (Rajan et al. 2012). tion pressure leading to subsequent household
Documentation of status of genetic resources is fuel crisis and environmental hazards. Therefore,
important for their management, protection and there is an urgent need to manage the genetic
utilization. Documentation is also crucial for erosion of the mango genetic resources. Despite
germplasm exchange and sharing of benefits several advances in biotechnological approaches
also. Besides, the information on germplasm for the conservation of germplasm, presently,
published as reports, informal publication, field genebank is the only alternative for the
information supplements, books, journals and conservation of Mangifera genetic resources.
research papers is important. The electronic The genetic improvement of mango hitherto has
medium is making information more readily depended on the utilization of the genetic vari-
available enabling countries to know about ability found within a single species, i.e., M.
germplasm wealth (Rajan et al. 2020). indica thus Mukherjee (1985) stressed that ‘a
The data on field gene banks can tell us what concerted sampling strategy should be devised
else needs to be conserved and help to determine for ex situ samples to meet urgent needs for use
appropriate germplasm management needs. The in research for improvement of the crop through
exchange data availability is a measure of the breeding or as rootstocks. Sources of resistance
success of the documentation system of the gene to mango malformation, anthracnose, powdery
bank. IPGRI has advocated standard documen- mildew, gall midge are urgently needed’.
tation of genetic resource information with its
mandate to improve the conservation and use of
plant genetic resources. IPGRI has published 4.8 Genetic Erosion
descriptor lists in respect of many crops (Ram
and Rajan 2003). Consumer’s preferences are associated with
Through catalogues, the genetic variation of changing market needs for fresh fruit and value
mango is recorded and shared. A catalog of 252 added products thus making mango cultivation
mango cultivars (Rajan et al. 1999a, b) and two more or less commercial venture. Large-scale use
mango catalogs with information for 404 acces- of clonally multiplied mango cultivars has
sions (Dinesh et al. 2014) were published, while diminished the genetic variability and chances of
the Philippines released catalog on mangoes seedling selection, a method which resulted
(Rajan et al. 2014). development of countless varieties in western
The Mango Resources Information System and eastern Hemisphere. Climate change and
(www.mangifera.org) includes information about urbanization triggers the depletion of genetic
the 682 accessions with details of fruit, leaf and diversity in the wild gene pool. Many workers
other characteristics, as well as the 26 expressed have understood the value of biodiversity pro-
sequence tags (ESTs) and 285 nucleotide tection and its genetic potential. Several mango
sequences present in mangoes. This allows rapid populations are endangered by habitat loss
knowledge access and was used as a quick (Rajan and Hudedamani 2019). Several reports
method to retrieve data from a large collection of have indicated that four species of the common
information (Rajan et al. 2013a, b). National mango, viz., M. pajang, M. zeylanica, M. lalijiwa
Mango Database developed at ICAR-CISH has and M. odorata have been listed as endangered,
several modules on genetic resources of mango while, the Kalimantan mango (Mangifera cas-
including wild relatives, distribution, molecular turi) has been listed as extinct even in its wild
data, Field Gene Banks and IP issues and visited habitat (IUCN 1998a, b, c, d, e; Rhodes and
by millions of visitors (Rajan et al. 2020). Maxted 2016; IUCN 2017). Since, variability
In most of the countries, there is still no def- available in mango is still unexplored and many
inite and effective strategy/policy of ex situ and of the indigenous land races are threatened with
extinction, collection of this diversity was sug- threatened. M. laurina and M. monandra are
gested (Yadav and Rajan 1993). getting more rare (Coronel 1996).
Although mango is most important fruit in
Asia, there is a potential for competition between
the cultivated and non-commercial varieties for 4.9 Utilization of Genetic Resources
arable land. The largest mango producing coun-
tries including India have the most potential for Characterization and evaluation of mango
its cultivation to be displaced by other more germplasm is an imperative step for its utilization
profitable crops. India being a major centre of in breeding programs. Available germplasm has
diversity in mango, there is also significant ero- been considerably characterized to identify
sion of the gene pool owing to urbanization, desired traits mostly based on morphological and
industrialization and deforestation (Yadav and molecular markers. Moreover, germplasm con-
Rajan 1993). Other Mangifera spp. have their servation for future utilization also requires
centre of diversity and origin in Southeast Asia, a dependable information. Comprehensive details
region that has accomplished great economic of mango cultivars, characterization of desired
development in recent years at the cost of genetic traits or genes and evaluation information on
erosion in wild relatives (Ram and Rajan 2003). germplasm based on morphological as well as
In Thailand, M. indica has narrow base of molecular markers will lead to better utilization.
genetic variation which is the main cause of Mango germplasm is being extensively used
genetic erosion in mango cultivars. Few principal in breeding being conducted at different locations
commercial varieties are grown for commercial spread all over India. The main emphasis has
purpose. The introduction of selected clonal been to develop regular bearing, colored varieties
varieties to replace seedling varieties is also and to avoid the formation of spongy tissue in
causing genetic erosion in the cultivated mango cultivar Alphonso (an export variety). Cultivar
(Vangnai 1996). In Indonesia, genetic diversity is Neelum has been used to impart regular bearing
still maintained by the villagers in the form of habit, cv. Vanraj for colored skin character and
inferior cultivars around houses which is under cv. Banganapalli to avoid spongy tissue forma-
the threat of extinction due to the need to build tion. As a result of massive hybridization pro-
houses or clearing of land for growing other grams, more than 45 mango varieties have been
crops. In situ conservation efforts in Indonesia developed, including Amrapali (dwarf, regular
have been confined to some protected forests and bearing), Mallika (regular bearing, processing)
National Forest Parks for the conservation of and Ratna (regular bearing, free from spongy
wild plants and animals but mango species are tissue). Variety Sindhu is a recently developed
not given particular attention as yet. Neverthe- hybrid with papery and soft stone. Ambika
less, inferior cultivars in the home gardens of (regular bearer and red colored) and Arunika
farmers, especially in the mango production (dwarfer than Amrapali, regular bearer and red
centres such as Pasuruan, East Java and Indra- colored) developed from ICAR-CISH. Elaichi
mayu, West Java may be under threat (Kusumo has been used for incorporation of resistance
1996). against mango malformation (Rajan et al. 2005).
In Bangladesh, many of the elite varieties Few studies based on fruit traits have been con-
(which are not commercial varieties) are in ducted for selecting promising parents (Rajan
potential threat of erosion. The predominance of et al. 2009).
one major variety, the ‘Carabao’, is threatening Rootstocks response to soil salinity, a signif-
the existence of the minor varieties in Philip- icant abiotic stress, restricts mango production
pines. ‘Carabao’, ‘Pico’, ‘Pahutan’, ‘Binoboy’, worldwide. Salt resistant polyembryonic root-
‘Dudol’, ‘Senora’, ‘Digos’ and ‘Mampalang’ stock makes mango cultivation possible in salt
mangoes are the eight recognized local mango and problematic soils. Collection and screening
varieties. Mangifera species are also greatly of polyembryonic mango types from tsunami
66 S. Rajan et al.
affected areas of the South Andaman district Concerted studies are needed to identify
where trees are under natural selection pressure climate-resistant germplasm that can be used
for salt tolerance and screening of collections directly for cultivation or in breeding program. In
against high sodium in sodic soils ex situ the context of climate change, priorities must be
(Damodaran et al. 2013). The six accessions, reviewed and strategy must be prepared both for
viz., GPL-1, GPL-3, ML-3, ML-4, ML-2, and in situ and ex situ conservation. Duplication of the
GPL-4 exhibited the high-soil sodium and pH accessions in field gene banks increases the insti-
tolerances. Damodaran et al. (2018) studied the tution’s burden and therefore it is necessary to
field tolerance of sodium, potassium, antioxi- analyze and reduce duplication to simplify con-
dants, and biochemicals for polyembryonic servation efforts in addition to helping to identify
accessions in salt-impaired soil in relation to their low-cost techniques. Extensive surveys may be
dynamics. Study resulted in the identification of carried out in diversity-rich regions to identify and
two rootstocks (ML-2 and ML-6) suitable for collect trait-specific mango germplasm.
mango production in salt-affected soils. Studies can also strengthen attempts to mini-
Wild species are valuable source of resistance mize threats to wild populations by collection
genes for many of the common pathogens of and maintaining germplasm from rich areas of
cultivated mango. Wild relatives are reported genetic diversity. Extending opportunities to help
source of genes. Initiatives at Florida to produce local custodian farmers for on-farm conservation
new hybrids with reduced susceptibility to dis- efforts would provide safe livelihood choices for
ease using wild relatives, viz., M. lalijiwa, M. them. Climate change has also made it difficult
quadrifida, M. rubropetala with M. indica were for crops in areas to explore the idea of creating
developed. New hybrids between Mangifera conservation sites outside the current germplasm
species and M. indica can provide the first step distribution. In order to manage diverse genetic
toward these goals (Ledesma et al. 2017). M. trait-specific germplasm to achieve broad-based
laurina was used as the pollen parent in a performance, core and mini-core collections need
breeding program with a M. indica hybrid in to be produced and evaluated.
Australia resulting 60 successful hybrids (Bally
et al. 2013).
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pp 77–93
Genetic Diversity Analysis of Mango
5
Xin Hua He, Shahril Ab Razak,
and Cong Luo
Abstract diversity analysis. The current review pro-

vides essential details about genetic diversity
Genetic diversity is the foundation of plant
analysis of mango by morphological, bio-
breeding, and the importance of plant genetic chemical, and molecular markers. The statis-
diversity is increasingly being recognized as a tical tools used for assessing genetic diversity
specific field. The plant genetic diversity can
are briefly discussed, as it can promote the
be collected and preserved in the form of plant understanding of analysis tools and their
germplasm resources such as gene bank, DNA practicality to the researchers. This review
library, and so forth. Mango is one of the most
could benefit mango researchers and produc-
excellent and popular tropical and subtropical ers to employ the new methods and technolo-
fruit crops around the world. The study of gies for better and rapid evaluation, for
mango genetic diversity using multiple molec-
efficient utilization of germplasm from genetic
ular markers is an important strategy for resources to their applied breeding programs.
mango germplasm collection, conservation,
utilization, and new variety breeding. This
chapter comprehensively reviews two impor- 5.1 Introduction
tant areas: (i) enumeration of existing plant
genetic diversity by analytical methods; and With the growing population pressure, rapid
(ii) modern tools available for plant genetic development of urbanization and modernization,
biodiversity is getting threatened in both direct
and indirect ways. For example, land degradation,
X. H. He (&) C. Luo deforestation, urbanization, coastal development,
State Key Laboratory for Conservation and and environmental stress are collectively causing
Utilization of Subtropical Agro-Bioresources, mass extinction of plant species. Mango (Mangi-
College of Agriculture, Guangxi University,
fera indica L.) is one of the economically, nutri-
100 Daxue Road, Nanning 530004,
People’s Republic of China tionally, and admired woody fruit crops which are
e-mail: honest66222@163.com widely grown in tropical and subtropical areas of
C. Luo the world. It has been known that Mangifera
e-mail: 22003luocong@163.com species originated in Southeast Asia. Due to rapid
S. A. Razak economic development in Southeast Asia, the
Biotechnology and Nanotechnology Research agricultural expansion to feed the people or for
Centre, MARDI Headquarters, 43400 Selangor, harvesting valuable hardwood, a number of nat-
Malaysia
ural and wild mango germplasm resources or
e-mail: shahrilf@mardi.gov.my

https://doi.org/10.1007/978-3-030-47829-2_5
76 X. H. He et al.
plantations have been destroyed. Therefore, this such as plant height, growth pattern, flowering
has resulted in irreversible genetic loss of mango habit, inflorescence shape, young leaves color,
genetic resources (Kaur et al. 1980; Mukherjee fruit-bearing behavior, fruit shape, fruit color,
and Litz 2009; Sennhenn et al. 2014). The plant seeds type, and disease resistant (Bhat et al.
genetic diversity provides opportunity for plant 2010). It does not require expensive technology
breeders to develop new and improved cultivars but large tracts of land are often demanded for
with desirable characteristics (Govindaraj et al. these field experiments, making it possibly more
2015). Genetic diversity is the vital pillar of bio- expensive than biochemical or molecular
diversity and diversity within species, between assessment. These marker traits are often sus-
species, and of ecosystems. However, the prob- ceptible to phenotypic plasticity; conversely, this
lem is that modern mango cultivars, especially, allows diversity evaluation in the presence of
have been selected and bred mainly for high yield environmental variation which cannot be
potential under superior production conditions, neglected from the genotypic variation (Govin-
which led to narrowing the diversity of mango. daraj et al. 2015). These kinds of markers are still
The purpose of conservation genetics is to having their advantages and they are necessary
maintain genetic diversity at multiple levels. for distinguishing the adult plants from their
Conservation efforts and related research rarely genetic contamination in the field. The most
focus on individuals, but the genetic variation is important benefits of morphological assessment
always existing in individuals. Every individual are that descriptor lists are easily available for
is genetically different in nature. There are dif- most of the major fruit crops including mango.
ferences in genetic traits among different mango Description of mango germplasm using mor-
varieties, such as high or low yield, early or later phological indices is the important step which
maturity, high or poor fruit quality, resistant or must be carried out prior to biochemical or
not resistant to the pests and disease. It is extre- molecular characterization. IPGRI (2006) pub-
mely important to trace and utilize the mango lished the descriptors of mango, which consist of
genetic diversity and ultimately conserve the valuable passport data for the identification of
important germplasm of promising and threat- various accessions/cultivars, characterization of
ened mango varieties/cultivars to broaden the recorded traits and initial assessment at mor-
genetic resource repository (Litz 2004). The phological level. The mango descriptor list has
correct evaluation of genetic diversity within and further quickened the cultivar/varietal description
between plant populations is routinely performed and evaluation process. Morphological data are
by several techniques, such as (i) morphological obligatory in primary germplasm assessment as
observation, (ii) biochemical characterization they comprise tree, leaf, inflorescence, fruit, and
evaluation, and (iii) molecular (or DNA) marker seed characteristics (Knight et al. 2009;
analysis. Khan et al. (2015) has reviewed on Mukherjee and Litz 2009). Characterization is
morphological, biochemical, and molecular the essential factor which plays an important role
characterization of mango germplasm. This paper before exploring the genetic diversity through
will indicate analytical methods, tools, and biochemical or molecular markers (Litz 2004).
techniques in genetic diversity of mango which This fact cannot be denied that historically when
are made widely available for utilization. molecular markers were not available, people
often used morphological characteristics to dis-
tinguish mango cultivars or species. Because
5.2 Morphological Diversity some experts have reviewed mango morpholog-
Analysis ical diversity in detail (Khan et al. 2015), we only
accumulate some important literatures in
Morphological markers are those key features Table 5.1, which can be used successfully for
that can be identified and measured visually by identification, evaluation, and diversity analysis
naked eye and based on the botanic characters, of mango genetic resources.
5 Genetic Diversity Analysis of Mango 77
Table 5.1 Morphological diversities of mango

Character Work done References
Tree The mango botany, cultivation, and uses Singh (1968)
Introduction, botany, and importance Mukherjee (1997)
Origin, history, and distribution Ahmed (2004)
Production areas Human (2008)
Leaf A study of the distinguishing vegetative, floral, and fruit characteristics of Ibrahim (1952)
Punjab mangoes
Relation of growth to fruit bearing in mangoes Khan (1960)
A numerical taxonomic studies of the mango (Mangifera indica L.) Rhodes et al. (1970)
The Mango: botany, production and uses Litz (2003)
Morphological and genetic characterization of mango (Mangifera indica Mussane (2010)
L.) varieties in Mozambique
Morphological and bio-chemical markers for varietal characterization and Rajwana et al. (2011)
quality assessment of potential indigenous mango (Mangifera indica L.)
germplasm
Morphometric analysis of mango varieties in Sri Lanka Krishnapillai and
Wijeratnam (2016)
Morphological and anatomical characters related to dwarfness in mango Shenoy and
(Mangifera indica L.) Rajagopala (2016)
Morphological and physico-chemical diversity in some indigenous mango Raza et al. (2017)
(Mangifera indica L.) germplasm of Pakistan
Diversity of a large collection of natural populations of mango (Mangifera Zhang et al. (2020)
indica Linn.) revealed by agro-morphological and quality traits
Diversity in leaf morphology and physiological characteristics among Rymbai et al. (2014)
mango (Mangifera indica) cultivars popular in different agro-climatic
regions of India
Inflorescence The flowering of mango Hartless (1913)
Studies on blossom biology and pollination in mangoes (Mangifera indica Mukherjee and Rao
L.) (1943)
Mango (Mangifera indica L.) flowering physiology Ramırez and
Davenport (2010)
Morphological, physico-chemical characterization and evaluation of Ali (2013)
mango (Mangifera indica L.) germplasm in Multan (Pakistan)
Physiology of flowering – the case of mango Sandip et al. (2015)
Mango (Mangifera indica L.) pollination Ramırez and
Davenport (2016)
Genetic differences and cluster analysis of pollen quantity of 53 mango Xu et al. (2018)
cultivars
(continued)
78 X. H. He et al.

Character Work done References
Fruit The mango Lakshminarayana
(1980)
Variation in physico-chemical and morphogenetic characters of some Desai and Dhandar
mango varieties of Goa (2000)
Descriptors for mango (Mangifera indica L.) IPGRI (2006)
Analysis of the correlations between fruit traits and diversity of Quality Li et al. (2010)
traits within Mango (Mangifera indica L.) germplasm resource in Nujiang
hot-dry valley
Morphological characteristics and distribution of wild germplasm Fan et al. (2012)
resources of Mangifera indica in South and North Pan River Valley
Divergence for fruit characters in mango (Mangifera indica L.) Barholia and Yadav
(2014)
Fruit trait diversity of mango (Mangifera indica L.) germplasm resources Xie et al. (2018)
in Lancang River basin
Seed A study of the endosperm and embryo in Mangifera indica L Sachar and Chopra
(1957)
Genetics of mango polyembryony Sturrock (1968)
Performance studies on polyembryonic varieties of mango (Mangifera Prasad and Prasad
indica L.) (1972)
Somatic embryogenesis in angiosperms Tisserat et al. (1979)
Classical breeding and genetics Iyer and Degani (1997)
Degani et al. (1993) reported that isozymes as

5.3 Biochemical Diversity Analysis biochemical markers were used in mango germ-
plasm evaluation. The different kinds of proteins
Biochemical markers include a series of mea- have been separated through electrophoresis and
surement indicators, such as total soluble solids, various alleles are detected between them for
total sugars, antioxidants, flavonoids, vitamins, genetic variability. Selfed and outcrossed offspring
phenolics, non-reducing sugars, reducing sugars, were identified using the triosephosphate isomerase
and isozymes. These are widely used to identify (TPI) isozyme system (Daga et al. 1999). Peroxi-
variations in mango cultivars/varieties (Khan dase isozymes can be used as a biochemical genetic
et al. 2015). The isoenzymes are often used in index for the genetic relationship among mango
biochemical diversity analysis. Isozyme markers species (Chen and He 2000). The 11 enzyme sys-
are codominant in nature, and the allelic variants tems were used in the identification of the six
of enzymes are detected by electrophoresis and commercial Thai mango cultivars, whereas 6-
specific staining. It demands only small amounts phosphogluconate dehydrogenase, isocitrate
of plant material for its detection. However, only dehydrogenase, glucose-6 phosphate dehydroge-
a limited number of enzymes as biochemical nase, glutamate dehydrogenase, phosphoglucose
markers are available, and these enzymes are not mutase, malate dehydrogenase, diaphorase, shiki-
alone but it has complex structural and special mate dehydrogenase, and transaminase exhibited
problems; therefore, the resolution of genetic maximum resolution (Jintanawongse and Chang-
diversity is limited to exploration (Govindaraj tragoon 2000). The peroxidase variation existed
et al. 2015). among polyembryonic mango seedlings from the
same seed (Mo et al. 2005). A lot of enzymes have presenting the most widely used molecular
been found to play an important role in various fruit markers in genomics era. Different molecular
crops, whereas three enzymes (peroxidase, cata- systems such as random amplified polymorphic
lase, and aspartate) have most commonly been used DNA (RAPD), amplified fragment length poly-
in mango diversity evaluation (Karibasappa 1995; morphism (AFLP), inter-simple sequence repeat
Khan et al. 2015). For example, peroxidase, cata- (ISSR), simple sequence repeat (SSR), expressed
lase, and aspartate amino acids were used in iden- sequence tag-simple sequence repeat (EST-SSR),
tification and characterization evaluation of zygotic start codon targeted (SCoT), sequence-related
mango seedlings. Many quantitative characters amplified polymorphism (SRAP), and single
clearly described the diversity in mango accessions nucleotide polymorphism (SNP) marker will be
(Khan et al. 2015). further discussed.
Fruit quality and its production are mainly
affected by diseases, insects, and some physio-
logical disorders which may result to narrow 5.4.1 Random Amplified
genetic diversity (Jintanawongse and Changtra- Polymorphic DNA (RAPD)
goon 2000). The biochemical attributes of fruit Marker
quality about 17 cultivars were discussed, among
which only five mango cultivars (‘Kala Chaunsa’, One of the most straightforward PCR-based
‘Faiz Kareem’, ‘Camal Wala’, ‘Sufaid Chaunsa’, techniques for genetic variation evaluation
and ‘Late Ratole 12’) displayed the distinguished involves the use of RAPD marker. This particular
physiognomies (Rajwana et al. 2011). PCR-based technique has been widely used for
different purposes, such as to identification and
classification of cultivars, breeds, or accessions
5.4 Genetic Diversity Analysis (Fukuoka et al. 1992), and diversity studies (Yu
in Genomics Era and Paul 1992; Cao and Oard 1997). Technically,
the process of using RAPD marker depends on
Markers play a crucial role in assessing the vari- the utilization of a single arbitrary primer that
ability and diversity of the studied organism. The amplifies numerous DNA segments, resulting in
drawbacks of the morphological-based approach an efficient and effective screening of polymor-
became quickly apparent. Morphological-based phism or a wide variation of loci in the DNA.
approach in assessing genetic diversity shows However, this particular technique has several
limited numbers of discriminating traits and can drawbacks that should be considered, especially
be influenced by environmental conditions, its reproducibility and nature of inheritance in a
making it difficult to accurately evaluate the dominant mode. In order to address the repro-
varietal variability. Genomics-based marker sys- ducibility issue that may result in errors, most
tems were introduced to overcome these prob- past studies applied similar control samples for
lems. Genomics-based marker systems comprised every experiment. Furthermore, its application in
various DNA marker types, which can be used to genetic studies is rather limited as the reaction
evaluate the genetic variation. These DNA conditions, DNA quality, and PCR temperature
markers can detect the variation that comes from profiles highly influence the outcomes of using
duplication, deletion, insertion, and/or inversion, this particular technique (Kumari and Thakur
of the DNA in the chromosomes. They are 2014).
inherited both in dominant and codominant pat- Despite that, one of the strengths of using
terns. Different markers have different genetic RAPD marker lies in its appropriateness to
traits (Govindaraj et al. 2015). Some authors evaluate the genetic variation of underexplored
reviewed different markers techniques in detail species, as this particular technique does not
(Semagn et al. 2006; Govindaraj et al. 2015; require genomic information of the organism
Khan et al. 2015). In this section, we are under study. In addition, the use of
80 X. H. He et al.
electrophoresis gel and the scoring that is sub- or any electrophoresis that is based on the
jected to the presence (or the absence) of the genotyping platform.
band, simplify the overall technical process of One of the strengths of using AFLP marker
using RAPD marker. The use of an extensive lies in its capacity to disclose numerous poly-
range of universal primers also contributes to its morphic bands in a single lane. Unlike other
robust analytical power. There are many reports existing PCR-based techniques, this particular
on the application of RAPD marker in assessing technique is highly efficient given its capacity to
genetic diversity of germplasm and commercial concurrently analyze a huge number of generated
varieties in mango (Schnell et al. 1995; Jaya- bands on a gel and a substantial amount of loci
sankar et al. 1998; Xu et al. 1998; Kumar et al. for polymorphism. In other words, its detection
2001; Karihaloo et al. 2003; Xie et al. 2005; rate for the number of polymorphism per reaction
Rahman et al. 2007; Rajwana et al. 2008; is significantly higher. Besides that, studies have
Matallana et al. 2009; Jena et al. 2010; Bhargava proved the superior performance of this particu-
and Khorwal 2011; Majumder et al. 2011; lar technique, specifically on the amount of
Ramessur and Ranghoo-Sanmukhiya 2011; amplified sequences per reaction and repro-
Souza et al. 2011; Mansour et al. 2014; Kumar ducibility. The produced results appeared to be
and Sreekala 2016; Pruthvish and Chikkaswamy more reliable and reproducible across different
2016; Galal et al. 2017; Dao 2019). laboratory settings. The nature of every segre-
gated AFLP fragment is dominant type DNA
marker. Moreover, this particular technique does
5.4.2 Amplified Fragment Length not require any genomic information, which
Polymorphism (AFLP) explains its appropriateness for samples of any
Marker origin or level of complexity.
AFLP represents a valuable and robust tool for
Zabeau and Vos (1991) discovered this particular identification, characterization, genetic diversity
technique of using the AFLP marker and the analysis, and genetic relationships assessment
previously patented by Keygene NV (Wagenin- among mango species or cultivars or rootstocks
gen, The Netherlands) (Blears et al. 1998). (Eiadthong et al. 1999a; Kashkush et al. 2001;
Similar to the RAPD marker, the identification of Yamanaka et al. 2006; Gao et al. 2010; Shi et al.
genetic polymorphisms of AFLP is established 2011; Zhang et al. 2014; Luo et al. 2015b).
based on the presence or the absence of DNA AFLPs are highly reproducible and identifiable,
fragments (bands) after the amplification and which makes it an attractive technique for iden-
restriction of the genomic DNA takes place. tifying polymorphisms and for determining link-
Through the PCR process with the aid of the ages by analyzing individuals from a segregating
restriction enzyme, the AFLP marker selectively population (Mohan et al. 1997). AFLPs have
amplifies the restriction fragments from the been employed efficiently for detailed molecular
genomic DNA. Fundamentally, restriction linkage maps in Mangifera species or cultivars
enzymes with two different forms, specifically (Fang et al. 1999; Chunwongse et al. 2000;
with four-base pair recognition site and six-base Kashkush et al. 2001; Yamanaka et al. 2006;
pair recognition site, slice the total genomic Gálvez-López et al. 2009, 2010; Ying 2012; Li
DNA into fragments prior to the ligation of these 2016; Dang and Chen 2017).
fragments through the recognition site-specific
adapter oligonucleotides. Following that, a sub-
set of approximately between 50 and 100 5.4.3 Inter-simple Sequence Repeat
restriction fragments is selectively amplified in (ISSR) Marker
the PCR process, which are subsequently
resolved and separated through electrophoresis The development of inter-simple sequence repeat
on high-resolution polyacrylamide gels or Li-Cor (ISSR) marker serves to address the limitations
of other markers, such as the reproducibility areas of genetic diversity, gene tagging, genome
problem (RAPD marker), high operating cost mapping, phylogenetic studies, and evolutionary
(AFLP marker), and the absence of genomic biology in a diverse range of crop species (Reddy
sequence information (SSR marker). The use of et al. 2002). There are some reports of the
ISSR marker is one of the PCR-based techniques application of ISSR marker to evaluate the
that amplify the DNA segment at an amplifiable genetic diversity of mango worldwide (Gonzalez
distance between two identical (but opposing et al. 2002; He et al. 2005, 2007; Pandit et al.
directions) microsatellite repeat regions. The use 2007; Bajpai et al. 2008; Samant et al. 2010;
of ISSR markers involves microsatellites that Gajera et al. 2011; Luo et al. 2011; Tomar et al.
typically range between 16 bp and 25 bp (in 2011; Damodaran et al. 2012; Rocha et al. 2012;
length) as single arbitrary primers to aim at Samal et al. 2012; Dang and Chen 2017).
several genomic loci for the amplification of the
inter-SSR sequences with different sizes. As
primers, these microsatellite repeats can be di-, 5.4.4 Simple Sequence Repeat
tri-, tetra-, or even penta-nucleotide, which can (SSR) Marker
be either unanchored (Meyer et al. 1993; Gupta
et al. 1994) or anchored (which is more com- SSR marker or also known as microsatellite rep-
monly used) at 3’ or 5’ ends with one to four resents the repeat sequences of one to six found
degenerate bases that are stretched into flanking throughout the genome (Buschiazzo and Gem-
sequences (Zietkiewicz et al. 1994). mell 2006). It is broadly distributed throughout
Basically, ISSR markers are mainly segre- the genome (Phumichai et al. 2015) and mainly
gated as dominant markers with respect to the present in the noncoding area (as compared to the
simple Mendelian inheritance (Gupta et al. 1994; coding region) of the genome (e.g., introns,
Ratnaparkhe et al. 1998) but, in several cases, the intergenic spaces, and untranslated regions). The
use of ISSR marker can be segregated as presence of SSR marker in the coding or gene
codominant markers; thus, allowing the differ- region is generally lesser given its high mutation
entiation between homozygotes and heterozy- rate that affects the gene expression.
gotes (Akagi et al. 1996; Sankar and Moore Meanwhile, a motif is basically a repeat
2001). Unlike the previously discussed markers, nucleotide sequence. Its length represents the
such as RAPD marker (only about 10 mers), number of nucleotide bases in the repeat motif
ISSR marker possesses higher reproducibility (where n refers to the repeat frequency): (1) mono-
due to their longer primers (only between 16 and nucleotide, [A]n; (2) di-nucleotide, [AG]n; (3) tri-
25 mers) considering that a longer primer is nucleotide, [AAG]n; (4) tetra-nucleotide, [CCAT]
linked to high annealing temperature that n; (5) penta-nucleotide, [GAATT]n; (6) hexa-
enhances its stringency. Moreover, the irrepro- nucleotide, [AAGGTA]n (Scribner and Pearce
ducibility of only the faintest bands across 2000). Referring to the repeat motif pattern,
diverse experimental settings was successfully microsatellites are grouped as (1) perfect with
demonstrated in several past studies, which re- continuous repeat of a single motif (AGAGA-
affirmed the reproducibility of ISSR marker. GAGAGAGAGAG), (2) imperfect with a base
Several other studies used polyacrylamide gel pair disruption between repeats (AGAGAGA-
and demonstrated high reproducibility of about GAGTAGAGAG), and (3) compound with mul-
92% to 95% of the scored fragments for different tiple types of repeat motif (ATATATATCACAC-
DNA samples of similar cultivar and different AATATATATCACACA). Basically, the devel-
PCR runs (Fang and Roose 1997). Considering opment of microsatellites can be either from the
its strengths, this particular technique is widely genomic DNAs (gSSRs) or expressed sequenced
applied across diverse genetic fields for plants, data, resulting in the formation of EST-SSRs (re-
such as mango (Godwin et al. 1997; Krishna and sult of the expressed sequence tags [ESTs]) that
Singh 2007) and can be particularly beneficial for are said to be more superior given its link to the
82 X. H. He et al.
expressed genes that directly contribute to phe- 100 bp to 400 bp), and appropriate sequence
notype. Meanwhile, when it comes to plants, SSRs length for primer design to target the regions
that are developed from the nuclear DNA flanking the repeat motif (Squirrell et al. 2003). In
(nuSSRs) can be grouped as nuclear SSRs addition, the occurrence of null alleles and stutter
(nuSSRs) whereas SSRs that are developed from band also has limited the application of the
the chloroplast DNA can be grouped as chloro- microsatellite markers. But, using software such
plast SSRs (cpSSRs). as Micro-Checker is able to resolve this issue.
The progression of the next-generation There are a lot of reports on application of this
sequencing (NGS) technologies has signifi- type of marker in assessing the genetic diversity
cantly affected the development of microsatellites and population structure analysis of the mango
given their capacity to identify and develop accessions and varieties (Eiadthong et al. 1999b;
thousands of SSR markers from the generated Duval et al. 2005; Schnell et al. 2005, 2006;
reads by the sequencer (Ekblom and Galindo Hirano et al. 2010; Huang 2010,2011; Shamili
2011). Notably, the highly informative and et al. 2012; Singh et al. 2012; Surapaneni et al.
polymorphic attributes, codominance in the 2013; Tsai et al. 2013; Dinesh et al. 2015; Rav-
Mendelian inheritance, and multi-allele genetic ishankar et al. 2015a; Wang et al. 2015; Alves
markers that experimentally reproducibility and et al. 2016; Azmat et al. 2016; Bajpai et al. 2016;
transferability across closely related species have Ganogpichayagrai et al. 2016; Gitahi et al. 2016;
contributed to the extensive use of SSR marker Lal et al. 2017; Nazish et al. 2017; Ab Razak et al.
for plant genotyping in the genetic fields for the 2019; Yamanaka et al. 2019).
past two decades (Mason 2015). Apart from
being used in evolutionary studies, the use of
SSR marker has been widely adopted to assess 5.4.5 Expressed Sequence Tag-
genetic diversity and DNA fingerprinting as well Simple Sequence Repeat
as to develop linkage and quantitative trait loci (EST-SSR) Marker
(QTL) map and conduct parentage studies and
marker-assisted breeding. Conventional methods used for SSR develop-
Despite its strengths, particular for the genetic ment markers are usually considered time- and
field, the use of SSR marker can be a disadvan- cost-consuming, labor intensive, and also with
tage for certain studies particularly underexplored less efficiency (Ellis and Burke 2007). Thus, as
species, as this particular technique requires the an alternative approach, the source of SSRs
genomic information in order to develop their development is the development of the expressed
primers (Selkoe and Toonen 2006). The need for sequence tag- (EST-) based SSRs. EST-SSRs are
de novo development on the basis of species-by- transferable across the closely related species
species often takes place since it may not be which make it valuable compare to neutral SSR
possible to retain the primers from closely related markers (Chapman et al. 2009). EST-SSRs are
taxa (Whitton et al. 1997). The conventional noticeably linked to the expressed genes, and
techniques of developing SSR marker involve the hence, denote potentially functional markers for
generation of a genomic library through anticipated results. According to Bandopadhyay
microsatellite repeats enrichment, cloning, plas- et al. (2004), about 80–90% of the EST-SSRs are
mid isolation, and Sanger sequencing (Zane et al. characteristically found to be polymorphic in
2002). Although this process yields about hun- nature. Identification and development of SSR
dreds of sequences, only a small subset is deemed markers were gradually increased as a lot of
fitting for the ensuing primer design considering mango genes and EST sequences were deposited
that the design of microsatellite primers requires into the database. Additionally, advancement in
several criteria to be met. Some of the key criteria computational approach especially for primer
are that the sequence must contain a desired designing also has eased the researchers to work
repeat, appropriate in size (typically ranges from with SSR markers (De Keyser et al. 2009).
Fig. 5.1 Representative examples of PCR products amplified using several EST-SSR primer pairs and separated by
electrophoresis on 6% denaturing polyacrylamide gels. (Luo et al. 2015a)
Dillon et al. (2014) studied 32 M. indica SCoT PCR primers were designed from the short
cultivars and related species with EST-SSRs in conserved region flanking the start codon
Australia, and out of it, 24 EST-SSRs showed (ATG) that is conserved for all genes. Their PCR
polymorphisms and could distinguish between product will be resolved on the standard agarose
all of the Mangifera studied cultivars/selections. gel electrophoresis, which make it simple and
Luo et al. (2015a) developed 230 pairs EST-SSR easy to handle. These attributes have contributed
primers, of which 218 primer pairs for seven to the appropriateness of this particular marker
mango genotypes showed stable amplification across numerous studies. However, this particu-
and 93 of the primer pairs yielded polymorphic lar marker has a major limitation that lies in its
products (Fig. 5.1). Zhou et al. (2019) analyzed inheritance in a dominant manner despite being
the genetic diversity and relationship of 43 reported as being codominant in the case of
mango varieties by EST-SSRs. Among the 43 insertion–deletion mutation in the region—nev-
varieties, 26 pairs of primers amplified 140 ertheless, such cases of codominance (e.g.,
bands, of which 128 were polymorphic, with the RAPD marker and ISSR marker) are deemed
polymorphism rate of 90.79%. Therefore, EST- insignificant (Zhang et al. 2015). Unlike other
SSRs have tremendous potential to be used for dominant markers or random DNA markers,
identification and genetic diversity analysis of SCoT marker is a gene-specific marker that
mango germplasm and other Mangifera species yields critical insights that are related to biolog-
(Khan et al. 2015). ical traits. Moreover, Luo et al. (2010, 2011,
2012) and Gajera et al. (2014) also successfully
proved the polymorphic nature and efficiency of
5.4.6 Start Codon Targeted (SCoT) the use of SCoT marker in the assessment of
Marker genetic diversity for mango. The genetic relat-
edness and variability among 168 mango (M.
The use of SCoT marker involves the use of a indica L.) germplasm resources were studied
single primer as both forward and reverse primer with SCoT markers (Fig. 5.2). Forty-five SCoT
in the PCR reaction, which is similar to the use of primers generated unambiguous and reproducible
RAPD and ISSR markers (Collard and Mackill bands and a total of 337 fragments, 244 bands
2009). Unlike these two previously discussed were polymorphic. These results demonstrate
techniques, the ATG start codon of the genes on that SCoT markers are useful for cultivar iden-
both DNA strands becomes the focus of this tification and genetic diversity analyses of mango
particular technique that uses SCoT marker. The cultivars (Zhou et al. 2020).
84 X. H. He et al.
Fig. 5.2 Amplification

products generated by SCoT6,
SCoT17, and SCoT63 with
portion mango varieties (Zhou
et al. 2020)
5.4.7 Sequence-Related Amplified markedly lower technical effort and cost when it
Polymorphism (SRAP) comes to the same band-pattern variability and
Marker reproducibility (Li and Quiros 2001; Levi and
Thomas 2007). Besides that, up to 20% of the
Sequence-related amplified polymorphism tested SRAP markers demonstrated codominance
(SRAP) marker is a straightforward and low-cost pattern (Li and Quiros 2001).
PCR-based marker that exhibits high levels of Accordingly, the most typical approach to
reproducibility and versatility. The use of this scoring the band fragment for this dominant
particular marker was first introduced for gene marker involves the binary system with the
tagging in Brassica oleracea L., specifically for presence (1) or absence (0) of the band. Never-
the amplification of the coding regions of the theless, certain studies modified their approach
genome with ambiguous primers, targeting GC- by opting for fluorescent labeling at the forward
rich exons (forward primers), AT-rich promoters, primers when it comes to the capillary
introns, and spacers (reverse primers). For this, electrophoresis-based system (Alghamdi et al.
these primers comprised 17 to 18 nucleotides and 2012). Likewise, SRAP marker is similar to other
core sequences from 13 to 14 bases. The “filler” dominant markers that demonstrate the capacity
sequences with no specific constitution were to detect the variation in genetic at different
positioned at the first 10 to 11 bases at the 5′ end. levels of taxonomy (Uzun et al. 2009). The use
The CCGG (forward) sequence or –AATT (re- of this marker is typically applied for inter-
verse) sequence and three other random selective specific and intraspecific hybrid analyses (Liu
nucleotides at the 3′ end (Li and Quiros 2001) et al. 2007), linkage, and QTL analyses which
were next. Subsequently, the output of PCR was are highly valuable when it comes to crop
resolved in standard agarose gel electrophoresis. improvement (Zhang et al. 2009; Levi et al.
Numerous comparative studies reported that 2011). Zhang et al. (2016) have used SRAP
SRAP marker exhibited comparatively similar markers to evaluate the genetic diversity and
extent of variation to AFLP marker but with relationship of 20 mango germplasms. Liu et al.
Fig. 5.3 Amplification of SRAP primer pairs M11E9 in mapping populations (Li et al. 2016)
(2019) assessed the genetic diversity of 13 on the genotyping platform) per reaction (Xiong
mango germplasm resources by SRAP marker. and Jin 1999), resulting in a lower cost, establish
A population of Guifei mango, Jinhuang mango, this particular marker as the preferred choice.
and their hybrids were used to construct a linkage Accordingly, SNP marker is closely linked to a
map of mango and analyze their genetic diversity single base variation in a DNA sequence. This
by SRAP markers. The genetic map constructed particular marker displays a specific attribute
by Joinmap4.0 covered 801.6 cM with an aver- where the least frequent allele for a base position
age marker interval of 9.32 cM, containing 20 with an alternative base in the genomic DNA
linkage groups and 113 markers (Fig. 5.3) (Li sequence should account for at least 1%. Theoret-
et al. 2016). ically, SNP marker, in most cases, is bi-allelic for
the automation practices considering the presence
of any four possible nucleotide bases at every
5.4.8 Single Nucleotide position of a sequence stretch. Certain studies
Polymorphism regarded one base pair indels (insertion or deletion)
(SNP) Marker as SNP marker despite the manifestation of dif-
ferent mechanisms. In other words, SNP marker
The most abundant form of genetic variation in the reflects the existence of polymorphism between
genome is the single nucleotide polymorphism DNA samples with respect to the single base.
(SNP) marker (Mammadov et al. 2012). High- The SNP mutation may modify the character-
density SNP markers were found at specific regions istics of phenotype due to the variation in amino
of maize (with 1 SNP per 104 bp) and barley acid. Non-synonymous SNP reflects functional
genomes (1 SNP per 189 bp) (Tenaillon et al. polymorphism. Despite the bi-allelic nature of
2001; Kanazin et al. 2012). The abundance of SNP SNP marker, which makes this marker less
markers in the genome with its responsiveness is to informative than multi-allelic marker (e.g.,
be multiplexed up to a substantial amount (based microsatellite), its amenability toward high-
86 X. H. He et al.
throughout multiplexing and abundance in the information of nucleotide sequence. Besides that,
genome enables the use of more loci in research. the integration of NGS technologies and bioinfor-
Unlike other forms of markers, especially matics techniques also contributes to the
microsatellites, SNP marker displays less mutable advancement of high-throughput genetic markers
marker system, resulting in higher evolutionary and genome-scale investigation of genotypes for
stability (Coates et al. 2009). This particular crops.
marker yields superior performance in evaluating As of December 15, 2019, 533 species of land
complex genetic traits and grasping the genomic plants have undergone sequencing as deposited
evolution. With that, the simple application of in the NCBI database (http://www.ncbi.nlm.nih.
SNP marker is deemed fitting for population gov/genome/browse/). In particular, even though
studies. 381,535 SNPs were identified in 28,959 M. indica or commonly known as mango is not
transcripts from 24 mango cultivars, and these listed in the NCBI list (that has been sequenced)
SNPs have been used for genotyping of mapping but certain studies demonstrated that this species
populations and germplasm collections (Kuhn was sequenced using the NGS platform for the
et al. 2014). Sherman et al. (2015) developed 239 development of high-throughput SNP and SSR
SNPs from mango cultivars ‘Keitt’ and ‘Tommy markers (Ravishankar et al 2015b; Sherman et al.
Atkins’ and was used to genotype 74 Israeli 2015). For instance, Warschefsky and Wettberg
accessions. Kuhn et al. (2017) reported that they (2019) applied the NGS technology to address
have observed a significant association between the genetic diversity of mango. Adding to that, a
trait and SNP markers for the vegetative trait of web database for mango (MiSNPDb) was
branch habit and the fruit traits of bloom, ground developed which deposited with 1.25 M of
skin color, blush intensity, beak shape, and pulp SNP. Notably, the use of SNP marker benefits
color. Recently, 272 SNP markers were used for the genetic improvement programs and manage-
identifying over 520,000 mango genotypes (Kuhn ment of mango germplasm in terms of genome-
et al. 2019). assisted breeding, linkage and QTL mapping,
traceability or parentage studies, varietal differ-
entiation and purity assessment.
5.5 Next Generation Sequencing
(NGS) of Mango
5.6 Genetic Diversity Analysis
Essential insights on the population structure and from Molecular Data
diversity of species under study can be acquired
based on the dataset of genomic-scaled DNA It is crucial to understand the various analysis
polymorphism. Based on these essential insights, methods of the data generated by molecular bio-
the relationships between phenotypic variations logical techniques before their applications in
and genetic polymorphisms, particularly using diversity analyses. Generally, there are two main
genome-wide association study (GWAS), can be types of analysis that are followed: (i) genetic
effectively determined. A whole-genome relationship analysis and (ii) parameter calculation
sequence and a well-annotated genome are sig- about population genetics. The analysis of genetic
nificant in exploring useful genes, determining relationships among samples initiates with the
their physical location in the genome, and pre- construction of a matrix, sample sample pair-
dicting their biological functions. wise genetic distance (or similarities) based on the
The development of NGS technologies has amplification bands (Govindaraj et al. 2015).
introduced several radical innovations to interpret Genetic distance and/or similarity between
species diversity using a large dataset. The pro- different populations, genotypes, or individuals
posed NGS technologies have significantly bar- may be calculated by different statistical calcula-
gained the cost and time required in order to obtain tions depending on the dataset. The common
a substantial amount (up to gigabases) of measures of genetic similarity (GS) or genetic
distance (GD) are (i) Nei and Li’s (1979) coeffi- genomic map, which can be employed for
cient (GDNL), (ii) Jaccard’s coefficient determination of genetic relationship between
(GDJ) (Jaccard 1908), (iii) simple matching exact heritable and desired characters. Mango
coefficient (GDSM) (Sokal and Michener 1958), genetic resources for future exploitation in
and (iv) modified Rogers’ distance (GDMR). breeding and correct assessment of mango vari-
Mohammadi and Prasanna (2003) reviewed about eties or cultivars are great demands of the present
different GD measures in detail. There are two time. Major goal of breeding is to obtain quick
main methods of analyzing the similarity (or fruit-bearing pattern, high yield, excellent fruit
distance) matrix, namely, principal coordinate quality, and strong resistance cultivars against
analysis (PCA) and dendrogram (or clustering). biotic and abiotic stresses. Morphological, bio-
Various algorithms were employed for clustering, chemical, and molecular markers are very useful
but some common methods include unweighted not only in assessment and documentation, but
pair group method with arithmetic averages also extremely necessary concerning mango
(UPGMA), neighbor-joining method, and Ward’s germplasm conservation and management for
method (Karp et al. 1997). Govindaraj et al. future strategies to broaden the scope of mango
(2015) carried on a brief description of common industry in the world. Regarding future scenar-
or basic statistical methods and its principle with ios, exploitation and utilization of various
the advantage and disadvantage of each method markers for uncultivated wild mango germplasm
for analyzing genetic diversity. Therefore, the and variety identification diagrams are much
features and approaches of measures were not imperative. Availability of the whole mango
much discussed separately in the text. genome may be very helpful in breeding excel-
A lot of software programs are available for lent quality, high-yielding and good-resistance
evaluating genetic diversity in the postgenomic cultivars. Next generation sequencing reduced
era, such as Arlequin, DnaSP, DARwin, Power- the time and cost required for sequencing the
Marker, NTSYSpc, MEGA, PAUP, STRUC- whole genome. With the development of high-
TURE, fastSTRUCTURE, ADMIXTURE, throughput molecular biological technologies
fineSTRUCTURE, POPGENE, GENEPOP, and ensuring speed and quality of data generated, it is
GenAIEx, most of them are freely available possible to analyze the larger number of germ-
through Internet. Many of these perform same plasm with limited time and genetic resources.
tasks, with the main differences being in the Many software packages are available for eval-
platform, type of data input and output, and user uating phenotype and genetic diversity that
interface. Therefore, choosing which to use enhanced the efficiency of mango germplasm
depends largely on personal preferences curators, breeders, and producers to accelerate
(Govindaraj et al. 2015). the mango improvement and effective utilization
of genetic resources.
5.7 Conclusion
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Alternate Flowering in Mango
6
Hutchappa Ravishankar, Nimisha Sharma,
and V. K. Singh
Abstract sub-continent continue to be gripped with

the alternate bearing rhythm resulting in low
Alternate bearing is the tendency of fruit trees
productivity and economics of commercial
to produce a heavy crop in 1 year (on-year), orcharding. Greater and in-depth understand-
followed by a light crop or no crop production ing of mechanisms involved in floriferous
in the next (off-year). This phenomenon in
condition of mango fruit crop is essential to
perennial fruit crops appeared to be governed strategize appropriate orchard protocols to
by positive and negative regulatory factors minimize or smoothen alternate bearing
and their interplay decided the fate of meris-
rhythms. Further, genomics and transcriptome
tems under optimum environmental cues. approaches along with physiological events,
Mango production dynamics in different parts elucidate the complete understanding of bear-
of the world in the recent years are gripped
ing and non-bearing tendency of mango crop.
with considerable uncertainties arising due to
the occurrence of weather extremes, inade-
quacies of water, and nutrient management,
Abbreviations
and impacts of altered pests and disease
prevalence. In mango especially, in which AB Alternate bearing
the issue though has been investigated exten- ABI Alternate bearing index
sively yet the problem eludes tangible solu- ABI Alternate Bearing Intensity
tions, the choice varieties in the Indian ABA Abscisic acid
AFL2 Apple floricula/lfy
AP Apetala
BBI Biennial bearing index
H. Ravishankar V. K. Singh BFT Brothers of ft
ICAR-Central Institute for Subtropical Horticulture,
Lucknow 227107, UP, India
CH Carbohydrates
e-mail: drhravishankar@gmail.com CiFT Citrus flowering locus T
V. K. Singh
CO Constans
e-mail: vksingh.icar@gmail.com; DEGs Differentially expressed genes
singhvk_cish@rediffmail.com FBD Fruit bud differentiation
N. Sharma (&) FI Flower induction
Division of Fruits and Horticultural Technology, FLC Flowering locus c
ICAR-Indian Agricultural Research Institute, FUL Fruitful
New Delhi 110012, India
e-mail: nims17sharma@gmail.com
GAs Gibberellins

https://doi.org/10.1007/978-3-030-47829-2_6
96 H. Ravishankar et al.
GUs Growth units by a variety of factors, the direct cause of alter-

LFY Leafy nate bearing is the lack of floral buds in the ‘Off’
MABI Modified alternate bearing index year rather than lack of fruit set. Greater and in-
miRNA Micro RNA depth understanding of the mechanisms involved
NGS Next-generation sequencing in floriferous condition of fruit trees is essential
SAMs Shoot apical meristems to strategize appropriate orchard protocols to
SoC1 Suppressor of over expression of minimize or smoothen alternate bearing rhythms.
constants In the ensuing review, though based on a few
SPL5 Squamosa promoter binding fruit crops, we have tried to critically present the
SVP Short vegetative phase status on understanding of the problem, the pre-
TFL1 Terminal flower1 vailing gaps, the challenges ahead, and the way
forward.
6.2 The Alternate Bearing

Phenomenon
6.1 Introduction Flowering is an important event in the plant life
cycle, as blooming is the key factor in fruit
Alternate bearing (synonymously termed as a production. Under favorable growth conditions
biennial or uneven bearing) is the tendency of the timing and intensity of flowering greatly
fruit trees to produce a heavy crop in 1 year (on- determine where and how much fruits are pro-
year), followed by a light crop or no crop produced. However, in several times there are very
duction in the next (off-year). This phenomenon contrasting phenomena where prolific flowering
is widespread among fruit trees, including both takes place without appreciable fruit set. Many
deciduous and evergreen (Monselise and Gold- important details about flowering are becoming
schmidt 1982).In mango especially, in which the clearer, especially in annual/herbaceous plants at
issue though has been investigated extensively, the physiological, biochemical, and molecular
the problem eludes tangible solutions, the choice level, but this complex biological phenomenon is
varieties in the Indian sub-continent continue to less understood in perennial fruit crops. Flower-
be gripped with the alternate bearing rhythm ing is promoted by photoperiod, temperature or
resulting in low productivity and poor economics autonomous factors, or some combinations
of commercial orcharding. The International thereof (Léchaudel et al. 2005), suggesting that
Mango Research Network targets to achieve flowering is triggered environmentally and
mango productivity of 40 tons ha−1 in order to genetically. Thus, to gain further insights into
make the world mango industry sustainable. The environmental adaptation, it is important to
prevailing scenario of mango productivity world understand the regulation of seasonal flowering
over is not more than 17–18 tons ha−1 (Brazil) in fruits like mango, litchi, guava exhibiting
while in India it being 7–8 tons ha−1. Flowering different flowering characteristics in varying agro
of plants is a complicated developmental process climates both in the tropics and subtropics. Fruits
that involves a series of morphological and like mango, when grown in the subtropics (lati-
physiological stages under the control of a tude 23°–30°) where substantial seasonal tem-
number of external signals and internal factors. perature changes occur, show floral induction
Genes have been identified as genetically gov- from exposure to night temperatures of 10–15 °C
erning floriferous identity of meristems and fruit (Davenport 2007). The flowering response to
development. The expression of these genes is temperature occurs in mangoes growing in sub-
reportedly regulated by photoperiod and hor- tropical latitudes where cool temperature is the
mones. Alternate bearing though found triggered dominant induction factor. The effects of
6 Alternate Flowering in Mango 97
temperature and water relations in determining understanding of AB phenomenon in mango, no

vegetative and reproductive growth of mango study till date statistically outlined the AB in this
have been addressed by several research groups species that captured the true behavior of the
(Davenport 2000; Kulkarni 2004). Many culti- crop/variety. There existed extensive
vars flower erratically in the low-latitude tropics, biological/horticultural literature on AB,
providing continuously warm temperatures with although they are crop-specific with different
high soil and atmospheric moisture. Under such issues dealt with being relevant for the respective
conditions, the age of stems is the dominant crops. These broadly though highlighted different
inductive factor (Ravishankar et al. 1979; Batten explained and unexplained factors of AB, many
and Mc-Conchie 1995; Davenport 2007), and of them however, failed to come to grips with the
occasional cool night temperatures in the upper precise approaches for quantification of ABI
latitude tropics have a positive moderating effect including mango. Evaluation of ABI itself has
(Davenport 2003). In tropics, the age of the last been a matter of considerable interest to
leaf was recently considered as dominant factor researchers of perennial fruit trees for quite some
regulating the flowering (Davenport 2011). time. Based upon an exhaustive survey of liter-
ature available on the subject, we strongly
believe that the precise evaluation of degree of
6.2.1 Quantification of Alternate AB has either been underestimated or seriously
Bearing misestimated in majority of the studies. For
example, Hoblyn et al. (1936) proposed two
Alternate bearing (AB) phenomenon refers to the parameters ‘B’ and ‘I’ to quantify alternate
tendency of a fruit tree to produce a high yield bearing tendency, with ‘B’ expressing bienniality
(‘On’ year) followed by a low yield (‘Off’ year). as a percentage of occasions (pairs of successive
This results in the operation of fundamental years) where each trend of increase or decrease in
hypothesis that yield in 1 year affects yield in the yield is reversed in calculations. This was sub-
subsequent year, however necessitating then sequently re-evaluated by Pearce and Doberšek-
need to quantify the extent to which this serial Urbanc (1967) who concluded that ‘B’ is very
dependence takes place (Rosen stock et al. 2010). insensitive, as alternation of positive and nega-
Evaluation of Alternate Bearing Intensity tive signs could continue by chance for 8 years
(ABI) has been a matter of intense deliberations so that cent percent value became significant at
by many researchers of fruit crops in the recent the 5% level, only if obtained after 9 consecutive
past as it exerted severe negative economic years. Full bienniality as per this approach,
impacts on the commercial fruit industry. The however, may not accrue in actuality due to its
occurrence of AB is also highly variable among very nature of simplicity, parameters used for
the mango (Mangifera indica L.) varieties, across calculation of bienniality over long period of
mango producing agro-ecologies impacted by years. The other index‘I’ is a measure of intensity
diverse factors. Different researchers have of deviation in yield in successive years which is
attempted to address this problem from many estimated by adopting the procedure outlined by
angles in the past but without appreciable success Pearce and Doberšek-Urbanc (1967).
(Ravishankar 1987; Chacko 1991). However, a The ‘I’ value was applied for the first time in
chemical manipulation of this problem had been mango to quantify ABI, following the applica-
successfully demonstrated (Singh and Singh tion of different treatments to manage alternate
2003) which, however, could have serious con- bearing (Ravishankar 1987) in ‘Alphonso’
sequences on the tree and environment health if mango by applying the method of Pearce and
pursued on a continuum besides posing the Doberšek-Urbanc(1967). Huff (2001) reported
problem of consistency of results obtained across that I = 1, showed an extreme alternate bearing
varieties and geographical areas. Despite exis- pattern in which no crop being produced in ‘Off’
tence of voluminous information on years and I = 0, showed an absence of influence
between successive crops, rather than complete production. Under favorable growth conditions,
absence of variation. It was opined that ‘I’, a the timing and intensity of flowering greatly
descriptive statistics had a limited value in the determined where and how much fruits were
absence of a test for significance (Huff 2001). produced. However, several times there existed
The absence of statistical testing, the long very contrasting phenomena where prolific
prevailing bias of‘I’, and the differential behavior flowering took place without appreciable fruit
of mango varieties across agro-ecologies/years set. Many important details about flowering are
generated questions about the predominance of now becoming clearer, especially in
AB problem in mango. Singh et al. (2014) sta- annual/herbaceous plants at the physiological,
tistically tested AB occurrence using one hun- biochemical, and molecular levels, but this
dred physiologically matured 25 years old complex biological phenomenon continued to
‘Langra’ mango trees grafted on seedling root- remain less understood in perennial tree fruit
stock with 5 years of production data under crops. Flowering was shown promoted by pho-
uniform cultural conditions. The study tested the toperiod, temperature or autonomous factors, or
null hypothesis that yields were random patterns some combinations thereof (Léchaudel et al.
against the alternative hypothesis that yield of 2005; Léchaudel and Joas 2007), suggesting that
subsequent year is dependent on the yield of flowering was triggered environmentally and
previous year, along standing premise to define genetically. Thus, to gain further insights into
AB phenomenon by adopting time series meth- environmental adaptation, it is important to
ods which could be very useful for documenting understand the regulation of seasonal flowering
and predicting the magnitude of yield variations in fruits like mango, litchi, guava exhibiting
across years based on historical yield data. Their different flowering characteristics in varying agro
study could possibly assist researchers based on climates both in tropics and subtropics. Fruits
at least 10 years yield data in the development of like mango, when grown in the subtropics (lati-
predictive models of yield in perennial fruit crops tude 23°–30°) where substantial seasonal tem-
as a component of decision support to empower perature changes occurred, showed floral
growers for optimizing inputs management for induction from exposure to night temperatures of
sustained tree health despite being gripped with 10–15 °C (Ravishankar 1979; Davenport 2007).
alternate bearing rhythms. The flowering response to temperature occurred
in mangoes growing in subtropical latitudes
where cool temperature played the dominant
6.3 Mango (Mangifera indica L.) induction factor. The effects of temperature and
water relations on determining vegetative and
Different varieties of mango exhibited distinct reproductive growth of mango have been fairly
patterns of alternate bearing tendency manifest- well addressed by different researchers (Daven-
ing ‘On’ and ‘Off’ phases in fruit production. An port 2000; Kulkarni 2004). Many cultivars
ideal mango variety is described as the one that flowered erratically in the low-latitude tropics,
had characters of regularity in bearing; dwarf tree providing continuously warm temperatures with
size; precocity, high yield (40 MT ha−1 with 40 high soil and atmospheric moisture. Under such
percent ‘A’ grade (>250 g) fruits); quality (at- conditions, the age of stems was the dominant
tractive color; 21° Brix, firm pulp consistency, inductive factor (Ravishankar et al. 1979; Batten
freedom from spongy tissue/internal breakdown: and Mc-Conchie 1995; Davenport 2007;
improved shelf-life; for export less sweet); Ramirez and Davenport 2012), and occasional
resistance to pests and diseases. Till date, the cool night temperatures in the upper latitude
world mango industry is yet to harness such an tropics had a positive moderating effect
ideal variety. (Davenport 2003). In the tropics, age of the last
Flowering is an important event in the plant leaf was recently considered as the dominant
life cycle, as it is the key factor of fruit factor-regulating flowering (Davenport 2011).
Floral stimulus, most commonly photoperiod or and high elevation locations provided additional
temperature, leads to floral initiation. The juve- stimulus to flower in stems of a given age. Effect
nile phase was the first which lasted for several of different parameters and their functions are
years during which time no flowering or fruiting presented in Table 6.1.
occurred. Thereafter, the interactions between Armed with the basic information provided
vegetative growth, flowers, and fruit of the pre- here, growers could be empowered to manage
vious year on floral initiation in the current year, flowering responses to occur at any desired week
affected production through phenomenon such as of the year. Local environmental conditions may,
alternate bearing. Verreynne and Lovatt (2009) however, alter the expected responses, but it is
reported that for the ‘Pixie’ mandarin in Cali- hoped that scrutiny of all of the factors in deci-
fornia, the alternate bearing cycles appeared to be sion support mode to develop management
a crop load-dependent inhibitory effect of fruits strategies should bring consistent success.
on bud-break. No single hypothesis could, however, explain
Two major differences reportedly existed the problem of alternate bearing or irregular
between tropical and temperate deciduous fruit flowering. A number of theories have been pro-
trees with respect to floral initiation. The tropical posed by the researchers from time to time to
species such as mango initiated flowers in provide answer to this problem, but very few of
response to an environmental stimulus, while them have met with some success and the puzzle
temperate deciduous species, such as apple, ini- continues.
tiated flowers autonomously. On the other hand,
temperate deciduous fruit trees underwent, a
period of dormancy between floral initiation and 6.3.1 Environmental Control of Floral
anthesis. While in the tropical species, including Initiation
mango, floral development was continuous from
floral induction to anthesis. Induction of flower- With respect to floral initiation, mango has been
ing in the subtropics was found primarily gov- more extensively researched than any other
erned by chilling temperatures from passing cold tropical or subtropical tree species. The juvenile
fronts during winter-spring months. The age of period for mango varied with cultivars but could
the previous flush modified the cool-temperature- be approximately 3 years. Floral initiation
induced floral response, with older stems occurred during late autumn and early winter;
exhibiting a higher probability of a floriferous flower panicles emerged from the terminal and
response and younger stems displaying a higher subterminal buds and grew continuously until
probability of a vegetative response. In the anthesis occurred in the spring. Phenomenon of
tropics, however, the age of the last flush is the ‘cauliflory’ also occurred. Mango flowering
dominant factor-regulating flowering (Chen and occurred during the coolest months of the year,
Huang 2001). Several researchers have averred and required 4–6 weeks of shoot dormancy and
that stems must be in rest for sufficient time, cool night temperatures to trigger floral induction
generally about 4–5 months to be induced to of the terminal shoot apical meristems (SAMs).
flower in the absence of chilling temperatures. The absolute temperature needed for floral
This extended rest period occurred naturally as induction varied among cultivars and climates,
trees increased in architectural configuration, but but night temperatures between 8 and 15 °C (46–
it could also be achieved by mild plant water 59°F) with day temperatures around 20 °C (68°
stress or ensuring low nitrogen fertility. Some F) were typically needed. Better flowering was
studies also indicated that moderately cool tem- seen in trees growing in the subtropics where the
peratures that often reached deep into tropical dry seasonal temperature differences were stronger
Table 6.1 Impact of hormones, carbohydrate metabolism, and genetic factors on alternate bearing in mango
Factor Summary References
Hormone Autonomous GA pathways play an important Nakagawa et al. (2012), Kachru et al. (1972),
role in both biennial bearing and flowering Tongumpai et al. (1991), Nuñez-Elisea and
control in mango. Davenport (1991), (1998), Blaikie et al.
Hormone study (2004), Davenport (2007, 2009), Bangerth
et al. (2004), Bangerth (2009)
Flowering Flower bud phenomenon Blaikie and Kulkarni (2002), Ramirez et al.
Studied florigenic promoter, required to induce (2010), Ramírez and Davenport (2010, 2012),
flowering in mango Tiwari et al. (2018)
Carbohydrate Source-sink relationship Chacko and Randhawa 1971; Kalayanaruk
Metabolism Biochemical changes in the leaf of bearing and et al. (1982), Ravishankar (1987), (Whiley
non-bearing trees of some mango (Mangifera et al. 1989; Stitt and Quick 1989; Chacko
indica L.) varieties (1991), Urban et al. (2004), Urban Alphonsout
Studies on changes in carbohydrate (2007), Singh and Rajan (2009), Singh et al.
metabolism in regular bearing and ‘Off’ season (2011), Jyothi et al. (2010), Shivu Prasad et al.
bearing cultivars of mango during flowering. (2014), Urban et al. (2004))
Fruit load study
Differential Differential expression of flowering control Nakagawa et al. (2012), Sharma et al. (2015,
Gene genes like FT, LFY, AP1, TFL, and miR156- 2017, 2019, 2020), Mahato et al. (2016)
Expression regulated SPL5 was seen due to the effect of
Studies fruit load in leaves and buds of mango.
Differential pathways studies in regular and
irregular mango varieties.
Deep RNA sequencing of regular and irregular
varieties of mango.
Association Association mapping studies were done in 60 Lal (2016), Lal et al. (2017), Sharma et al.
Mapping mango genotypes using 100 genic SSR (2020)
Studies markers.
Phylogenetic analysis showed that mostly
apple and olive genes have shown close
association with genus Mangifera.
and more reliable than in the hot tropics. In there are non-bearing units which can be attrib-
Hawaii, the main flowering was found between uted to the differential potentiality of the shoots to
December and April (Bally 2011). form flower buds (Singh et al. 2011). Some
Floral induction in mango as mentioned above Indian cultivars are reportedly alternate bearing,
occurred in response to cool temperatures per- having distinct ‘On’ and ‘Off’ years and many
ceived by mature leaves (L), which were neces- exotic cultivars grown in different countries,
sary for floral initiation. Flower panicles (FP) flowered irregularly but without predictable ‘On’
originated from terminal or subterminal buds of and ‘Off’ years (Blaikie and Kulkarni 2002).
the most recent vegetative flush. Many mango Under subtropical conditions also mango flow-
cultivars flowered irregularly. This has been lar- ered in response to cool temperatures (Whiley
gely attributed to variation in flowering and fruit et al.1988, 1989; Nunez-Elisea and Davenport
retention in subtropical areas. Variations in the 1995). The suitable day/night temperature in
amount of flowering may be within trees from majority of the cultivars was found 15/10 °C and
year to year, between trees in the same year, and at 20/15 °C. However, floral-inductive tempera-
between branches on the same tree besides vari- tures varied between cultivars (Sukhvibul et al.
ation in flowering behavior within the varieties 2000). Temperature also has a negative effect on
(Ravishankar 1979). Thus, even in bearing trees, inflorescence size (Dambreville et al. 2013) and
on the number of flowers per inflorescence et al. 2013). But there is no complete mango crop
(Sukhvibul et al.1999). It is possible that the lar- as of now available. Climate and weather play
ger diurnal temperature difference appeared a critical roles in the economic success or failure of
significant factor for flowering in mango. tropical fruit tree species including commercial
Both light and temperature are important fac- mango production. Air temperatures and rainfall
tors for photosynthesis besides CO2 concentration patterns could influence vegetative and pheno-
(Searle and Coupland 2004). Increase in the logical phases in mango and are two of the most
levels of these factors would have a positive effect important factors determining suitability or
on photosynthesis. However, some studies have otherwise of an area’s climate for successful
indicated that higher temperatures and CO2 con- mango production. Weather-related changes have
centrations have counterbalancing effects because already brought widespread changes in the flow-
they increase both photosynthetic assimilation ering and fruiting patterns of mango in different
and respiratory losses. Extreme temperatures mango producing regions of the country during
(>45 °C) or high levels of light intensity provoke the current decade. This is adversely affecting
damages to the photosynthesis machinery. The fruit production in some areas. But rising tem-
warmer climates during flowering and the warmer perature in areas previously too cold for mango
and wetter climates during the season of vegeta- production is now making them more suitable for
tive rest will probably lead to a lower floral mango production. For instance, an increase in
induction. On the opposite, the hot and wet cli- temperature during the coldest month has made
mates during fruit growth and vegetative growth mango cultivation possible in the valley areas of
will promote good fruit growth and important Himachal Pradesh and Uttarakhand previously
vegetative growth after harvest. But fruit quality thought not possible. In several parts of the globe,
could be reduced and pests and diseases problems increasing temperatures are likely to offer
and other disorders could increase. Provided opportunities for mango production in new areas.
nutrient and water are not limiting, the increasing
temperature will lead to more rapid growth
rhythms (shorter time-lag between successive 6.3.2 Importance of Stress
vegetative flushes) and development of growth in Flowering
units and leaves and to the delay or the avoidance
of growth cessation at the beginning of winter. In the tropics of India, floral induction of mango
Reports on the duration of cold temperature tree is mainly driven by stress conditions during
needed for floral initiation vary from 4 days to the period preceding fruit bud differentiation
2 weeks in mango cultivar ‘Haden’ and up to (FBD) (Ravishankar 1979) and any intervening
35 days in ‘Tommy Atkins’ and ‘Keitt’ (Yeshitela precipitation would predispose growth units
et al. 2004). In mango and litchi, cool temperatures (GUs) to predominantly, manifesting vegetative
may be sensed in the leaves because mature leaves phenology. The type of irrigation adopted for
appear to be the source of an essential floral mangoes, hence, assumes an important consid-
stimulus (Ying and Davenport 2004). eration if flowering management is desired.
The prediction of the effects of climate change Majority of the growers in the tropics, with irri-
on mango production and cultivation requires, gation infrastructure provided water to the trees
therefore, a complete mango crop model. Several through the typical 6-month annual dry season,
partial models, simulating specific processes of used furrow irrigation along the tree rows. Row-
the mango tree, are available: a biochemical furrow irrigation has the disadvantage of pro-
model of photosynthesis (Urban et al. 2007), a viding water periodically around the base of
model of stomatal conductance (Damour trees. The major problem, however, was many
et al. 2010), a model of fruit growth and quality roots outside the limits of the irrigation ditches
build-up (Léchaudel et al. 2005; Lechaudel et al. never got hydrated during the dry season; hence,
2007), and thermal time models (Dambreville water moved away from roots located in or near
the irrigation ditches to not only the canopy but interactions between genotype and environment.
also out to the dry roots in response to water Photosynthesizing organs, known as sources,
potential gradients in the root system (Boyer mainly mature leaves, produced photosynthates,
1985; Passioura 1988; Canny 1995). This back- mainly carbohydrates, translocated by the sieve
wards xylem flow towards root tips reportedly tubes of the phloem to non-photosynthetic organs
prevented upward xylem movement of shoot (fruits, roots, and tubers) and immature leaves,
initiating hormones (cytokinins) that are synthe- known as sinks. High, yearly consistent yields,
sized in the root tips (Mok 1994) and the cyto- and fruit quality required an adequate leaf-fruit
kinins, instead, accumulated in the tips of the ratio (number of leaves, certain leaf area per fruit,
roots. Active water uptake by these roots when or fresh weight unit). Fischer et al. (2012) based
the first rains set in moved the accumulated on their studies remarked that fruit production and
cytokinins to stem buds in the canopy, thus quality depended upon adequate source-sink
providing the stimulus to initiate an undesired relationships. They observed carbohydrates
flush of vegetative growth in insufficiently (CH) translocated from leaves or reserve organs
physiologically mature stems (Davenport 2008). were the most important for the growth and
In some areas, the first rains of the rainy season development of sink organs (mainly fruits) and it
stimulated flowering in those stems that had is also paradoxical that up to 60% of CH pro-
attained sufficient time in rest and attained duced daily could be lost through respiration.
physiological maturity due to lack of flushes Carbohydrates constituted over 65% of the dry
during the dry season. This underscored the matter of tree crops. Increasing the leaf-fruit ratio
importance of initiation of vegetative phenology generally increased fruit growth and CH content.
well in advance so that it has a reasonable time to They further observed photosynthesis increased
physiology mature to provide fruiting wood. with fruit load and the leaves next to fruits were
Evidently, this aspect formed the crux of the the strong sources for CH. It was surmised, leaf-
problem of alternate bearing in perennial fruit fruit ratio is species, cultivar, and geographic
trees. Drought and flooding reportedly have both location dependent. Ravishankar (1987) studied
negative effects on the vegetative development of the pattern of 14C-Sucrose translocation and
mango trees as they potentially reduce tree assimilation patterns in distinctly alternate
growth. (‘Alphonso’) and regular (‘Totapuri’) bearing
mango varieties during pre-FBD and post-FBD
stages. Based on 14C-Sucrose translocation,
6.3.3 Physiological Aspects assimilation, and metabolic labeling pattern, he
provided evidence on the possible nature of
6.3.3.1 Source-Sink Relationships interrelationships between the shoot apex and
A nutritional concept was given by Goldschmidt other parts of the mango tree, viz., stem portion
et al. (1985). This theory explained how the and leaves and the presumptive role of root sys-
developing fruit provides a strong sink for photo- tem in the regulation of translocation and assim-
assimilates and further explains the mechanism of ilation in flowering of mango. His studies also
depletion of photo-assimilates, especially carbo- pointed out to the strong possibilities of regular
hydrates from the bud that prevents flower bearing feature of ‘Totapuri’ attributable to higher
induction. Producing and exporting organs in the metabolic turnover, energy transducing mecha-
plant (typically mature leaves) are known as nism probably under up/down regulation of genes
sources, while non-photosynthetic organs (fruits, at specific stages of fruit bud differentiation in
roots, and tubers) and immature leaves are known response to environmental cues via hormonal
as sinks (Taiz and Zeiger 2006). Marschner route since, Paclobutrazol mediated flower
(2012) pointed out that the source (supply of induction in mango have been widely and suc-
photosynthates)—sink (utilization of photosyn- cessfully practiced globally. Further, the
thates) limitations were strongly affected by the increasing concentration of atmospheric CO2,
which is a main driving force of climate change, events resulting in reproductive shoot formation.
has to be considered for appraising consequences A balance or ratio of endogenously regulated
of climate change on mango production too, phytohormones, thought to be auxins from leaves
because CO2 is involved in such key process as and cytokinins from roots, appeared to govern
photosynthesis; besides impacting temperature the initiation cycle independently from inductive
dynamics. Empirical studies have indicated that influences (Fig. 6.1). Induction of reproductive
probably more dry matter would be allocated to or vegetative shoots is thought to be governed by
the roots under increasing CO2 concentrations to the ratio of a temperature-regulated florigenic
some limits. promoter and an age regulated vegetative pro-
moter at the time of shoot initiation. Management
of off-season flowering in mango trees is being
6.3.4 Hormonal Regulation accomplished in the tropics by successfully
synchronizing shoot initiation through tip prun-
Flowering time is mainly influenced by impor- ing and use of nitrate sprays coupled with man-
tant chemical constitutes like plant hormones agement of the stem age to induce flowering such
(Domagalska et al. 2010). How hormones influ- that it could be accomplished during any desired
ence the plants, mainly governed by three core week of the year (Davenport 2006, 2007).
factors like (i) time of release, (ii) target tissue A direct inhibitory role of GA in mango floral
susceptibility, and (iii) concentration of the hor- initiation was reported (Davenport 2008; 2010).
mone (Achard et al. 2006). Studying the mech- The concentration of GA in terminal bud
anism of hormones influencing the flowering decreased before panicle emergence in fruit trees
time and their interactions with the other plant including mango that subsequently flowered, and
metabolites is useful to infer the bearing phe- increased over the same period that remained
nomenon. Mango flowering involved hormonal vegetative (Tongumpai et al. 1991; Upreti et al.
regulation of shoot initiation and induction 2013). It suggested the direct inhibitory role of
Fig. 6.1 Conceptual flowering model of mango. The the vegetative or reproductive outcome of that growth
model summarizes the proposed roles for various phyto- (induction). Single lines in the scheme are promotive and
hormones in the initiation of shoot growth and in defining double lines are inhibitory (Davenport 2006)
GA in mango floral initiation. Exogenous appli- Arabidopsisbuds (Corbesier et al. 2007). Similar
cations of GA may indirectly regulate mango mechanisms are likely to exist in mango.
flowering by delaying bud release. This may be Davenport et al. (2006) isolated a CONSTANS
because applied GA delayed bud release and did like gene (MiCOL) from mango leaf DNA. The
not inhibit flowering so long as bud release mango ortholog has 79%, 76%, and 62%
occurred under florally inductive conditions homology with two apple CO genes, MdCOL2
(Nunez-Elisea and Davenport 1998). GA and MdCOL1, and the Arabidopsis CO gene
biosynthesis inhibitors such as Paclobutrazol (AtCO), respectively. Studies with mango indi-
(Rademacher 1995) both hastened and increased cated that a FP is synthesized in leaves during
the flowering intensity and reduced vegetative exposure to cool, floral-inductive temperatures,
vigor of mango (Blaikie et al. 2004). So and moved to buds to induce flowering (Daven-
Paclobutrazol directly promoted flowering or port et al. 2006). The putative, temperature-
acted indirectly by increasing the likelihood of regulated FP is reportedly short-lived in situ.
bud release during floral-inductive conditions. Davenport et al. (2006, 2007) demonstrated the
Therefore, GA could inhibit floral initiation quantitative movement of mango FP with photo-
endogenously or acted indirectly by influencing assimilates in phloem from donor leaves to buds
the timing of bud release. in the receiver stems. The conditions controlling
floral transition were determined by certain
complex growth correlations (Tan and Swain
6.3.5 Molecular Approaches 2006; Nocker and Gardiner 2014) and are diffi-
cult to know about the certainty of branch that
In plants phase transition from vegetative to produced flowering buds that posed main hurdles
reproductive is a complex mechanism (Huijser in understanding the mechanism of flowering in
and Schmidt 2011). This leads to explore the fruit trees. However, recent studies have indi-
regulatory mechanisms to understand the phase cated that epigenetic modification, alternative
transitions. Recently, the development of next- splicing, antisense RNA, and chromatin silencing
generation sequencing (NGS) tool, genomic, and regulatory mechanisms played an important role
transcriptome has contributed to a thorough in this process, by regulating related flowering
understanding of the metabolic and molecular gene expression (Kumar et al. 2013; Khan et al.
processes involved in floral biology. Molecular 2014). Dynamic changes between chromatin
biology of flowering in the facultative, long-day, states facilitating or inhibiting DNA transcrip-
model plant, Arabidopsis thaliana provided tion, regulated the expression of floral induction
insight into the nature of the floral stimulus (FP). pathways, in response to environmental and
A network of four interacting genetic signaling developmental signals (Meijon et al. 2010).
pathways may result in flowering in response to
photoperiodic, vernalization, gibberellin, and 6.3.5.1 Present Concepts About
autonomous environmental cues (Zhang et al. the Genes Involved
2005). The photoperiodic pathway involved in Signal Perception,
activation of the CONSTANS (CO) gene that Transduction on Flower
encoded a zinc-finger protein, which in turn Bud Differentiation
induced expression of the FLOWERING LOCUS Major pathways to flowering in fruit trees
T (FT) gene in the phloem tissue of leaves. FT is included environmental induction through pho-
the terminal, integrating gene of the four path- toperiod, vernalization, gibberellins, autonomous
ways regulating flowering in Arabidopsis. Its floral initiation, and aging by sequentially oper-
transcribed mRNA was initially thought to be the ating miRNAs7 (typically miR156 and miR172)
FP that is transported in phloem to buds (Huang responding to endogenous cues. The balance of
et al. 2005); however, evidence indicated that the signals from these pathways is reportedly inte-
translated protein product of FT is translocated to grated by a common set of genes (FLOWERING
LOCUS C, FLOWERING LOCUS T, LEAFY, despite the presence of cool temperatures

and SUPPRESSOR OFOVEREXPRESSION OF (Davenport 2000). Shalom et al. (2012) study
CONSTANS 1) that determined the flowering highlighted among genes induced in ‘Off’-crop
time. Gene regulation studies during vegetative trees was one homologous to SQUAMOSA
to flowering and fruiting transition at transcrip- PROMOTER BINDING-LIKE (SPL), which
tion and post-translational level are required to controlled juvenile-to-adult and annual phase
understand the ‘On’ and ‘Off’ mechanism oper- transitions, regulated by miR156. The expression
ating in perennial fruit trees (Khan et al. 2014; pattern of SPL-like, miR156, and other flowering
Sharma et al. 2015). Differential gene expression control genes suggested that fruit load affected
studies were carried out in various fruit crops for bud fate, and therefore development and meta-
example in leaves of mango few genes, viz., FT, bolism, a relatively long time before the flower-
AP1, and LFY were up-regulated during the ing induction period. Their results shed light on
flower induction period. As a principle, the some of the metabolic and regulatory processes
expression of flower control genes in mango is that are altered in ‘On’ and ‘Off’ buds. This data
induced in leaves, buds, and stems in coordinate could be utilized. Recently, Bouché and col-
with the onset of the flower induction period leagues provided FLOR-ID, the flowering inter-
(November–December) in regular bearing vari- active database to the public domain, which is
eties, and in alternate bearers during the ‘Off’ freely available at www.flor-id.org (Bouché et al.
crop year, while GA treatment decreased their 2016). Interestingly, FLOR-ID is a simple and
expression (Nishikawa et al. 2007; Muñoz- effective tool (UniProt, www.uniprot.org) and
Fambuena et al. 2011; Shalom et al. 2012; PubMed (www.ncbi.nlm.nik.gov/pubmed) data-
Goldberg-Moeller et al. 2013). Biennial bearing base finder combined with information taken
is an apparently genetic trait that is governed from other sources (Wellmer 2017). Further-
both by multigene as well as environmental cues more, orthologs and co-orthologous detection
and cultural factors (Guitton et al. 2011). Despite were done to study the evolutionary relationship
the fact, flowering genes may not directly regu- between alternate bearing genes of different fruit
late biennial bearing, their control by phytohor- plant species like avocado, litchi, apple, mango,
mones might be one of the mechanisms leading olive, pistacia, prunus, etc. (Sharma et al. 2019).
to biennial bearing tendencies in perennial fruit A total of 1,282 nucleotide sequences were
crops. It has, however, been observed that MdFT compared with all-against-all BLASTP utilizing
and MdTFL1 flowering genes in Malus are not the data from NCBI (ESM1) and phylogenetic
responsible for biennial bearing (Mimida et al. tree (Fig. 6.2) was constructed using Mega
2009; Kotoda et al. 2010). However, in biennial (version 7.0, https://www.megasoftware.net)
bearing mango trees FLOWERING LOCUS T- Kumar et al. (2016). Recently Sharma et al.
like and gibberellins metabolism genes were (2020) studied the alternate bearing phenomenon
identified by Nakagawa et al. (2012). The FP in contrasting regular (Neelam) and irregular
appeared to be up-regulated during the exposure (Dashehari) mango genotypes using differential
of leaves to cool temperatures and down- gene approach. Deciphering the differentially
regulated to a constant basal level when tem- expressed genes (DEGs) and potential candidate
peratures were warm (Davenport 2000, 2003, genes associated with alternate bearing, hor-
2008). For example, floral induction of initiating mone, and carbohydrate metabolism pathways
shoots during exposure of trees to cool, sub- will help for illustrating the molecular mecha-
tropical temperature conditions is considered to nisms underlying the bearing tendencies in
be the result of elevated levels of up-regulated mango. In mango, the availability of the draft
FP. High VP levels in young stems, however, genome sequence is expected to greatly assist the
may counterbalance the impact of FP, such that candidate gene approach to solve the mystery of
exposure to cool temperatures at the time of alternate bearing at gene level (Singh et al.
shoot initiation caused vegetative shoot induction 2016). The improved understanding of mango
Fig. 6.2 Phylogenetic tree represents the evolutionary relationship among gene sequences of different alternate bearing
fruit crops (Sharma et al. 2019)
genetics and adoption of molecular genetics in

breeding programs is enabling breeders to greatly 6.4 Conclusions
improve their breeding efficiency through
improved selection of parents and progeny. This Presently, it may not be possible to draw a gen-
along with research in mango genomics and gene eral scenario for India in the absence of infor-
discovery will identify genes and markers asso- mation on the extent, magnitude, and complexion
ciated with traits of interest and improve the of regional and seasonal variability and different
breeding outcomes. mango cultivar responses as there is no precise
scientific information available on response of with annual/biennial plants and the involvement of
the mango tree to each weather variable and plant hormones. Sci Hort 122:153–163. https://doi.
org/10.1016/j.scienta.2009.06.014
interactions between variables with reference to Batten DJ, McConchie CA (1995) Floral induction in
the effect of the tree phenological stage, cultivar growing buds of litchi (Litchi chinensis) and mango
effects, and optimal threshold values of these (Mangifera indica). Aust J Plant Physiol 22:783–791
variables. Future researches need to articulate on Blaikie SJ, Kulkarni VJ, Müller WJ (2004) Effects of
morphactin and Paclobutrazol flowering treatments on
mining of genes of climate resilience among the shoot and root phenology in mango cv. Kensington
large variability of genetic resources available in Pride. Sci Hort 101:51–68. https://doi.org/10.1016/j.
the sub-continent and integrate them into com- scienta.2003.09.009
mercial cultivars in order to fit mango in the Blaikie SJ, Kulkarni V (2002) Manipulating flowering in
mango, cv, Kensington Pride. Acta Hort 575:791–796
emerging paradigms of weather dynamics. Need Bouché F, Lobet G, Tocquin P, Perilleux C (2016) FLOR-
for elucidating weather dynamics and behavior ID: An interactive database of flowering-time gene
of mango cultivars, developing dwarf ideotypes networks in Arabidopsis thaliana. Nucleic Acids Res
conforming to ‘ideal mango’ variety (regularity 44:D1167–D1171. https://doi.org/10.1093/nar/
gkv1054
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scored. Researchers have indicated that genetic standing of the factors affecting flowering in mango
control of the target genes as of now is elusive in (Mangifera indica L.). Andhra Agri J 18:226–36
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and Director, ICAR-IARI. Searle I, Giakountis A, Farrona S, Gissot L, Turn-
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Taiz L, Zeiger E (2006) Plant Physiology. 4th edn. 32:132–137
Sinauer Associates, Sunderland, MA, p 690 Zhang X, Garreton V, Chua NH (2005) The AIP2 E3
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and development in annual and perennial plants. signaling by promoting ABI3 degradation. Genes Dev
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1399-3054.2006.00724.x
Classical Genetics and Breeding
7
M. Sankaran, M. R. Dinesh,
and K. V. Ravishankar
Abstract chromosomes. On accord of its cross polli-

nated and heterozygous nature, M. indica L.
Mango (Mangifera indica L.) is believed to be
and other related species possess very huge
originated as an allopolyploid most probably variability that is useful for mango improve-
amphidiploid with chromosome number, ment programme. More than 1000 mango
2n = 40 with the size of 0.2–2.0 lm. As
centres of India. Depending on the number of
revealed by cytological studies, these chro- embryos that a mango fruit produces, mango
mosomes undergo regular pairing and dis- varieties are classified as monoembryonic and
junction in 20 bivalents during meiosis. The
polyembryonic. Systematic hybridization
mango (Mangifera indica L.) has been orig- work has resulted more than 50 hybrids across
inated from north-eastern India covering the the globe and several of them are being
Indo Myanmar border region and Bangladesh,
cultivated commercially. Genetical studies
where still wild mango trees with very small conducted have shown Amrapali to be a good
fruits are found. Mangifera genus has more combiner as female parent whereas Vanraj,
than 60 species with Myanmar-Siam- Janardhan Pasand, Sensation, and Tommy
Indochina or Malay Archipelago being its Atkins have been found to be good combiners
primary center of diversity comprising of for shelf life, peel color, and sugar: acid blend.
highest diversity where as the Sunda Islands Studies on inheritance of traits have been
(Java, Sumatra, Bornco)–the Philippines and conducted and pre-selection indices for early
Celebes–Banda-Timor are considered as the screening of hybrids have been established.
secondary center of diversity. There are cer- Attempts have been made to introgress genes
tain species such as M. odorata, M. zeylanica, for biotic and abiotic stress
M. caloneura, M. sylvatica, M. foetida, and M. resistance/tolerance from the wild species.
caesia that are cross compatible with each Molecular markers such as RAPD, AFLP,
other owing to the identical number of SSR, and SNP are being employed for
diversity analysis and hybridity confirmation
in mango breeding.
M. Sankaran (&) M. R. Dinesh
K. V. Ravishankar
ICAR-Indian Institute of Horticultural Research,
Hesaraghatta Lake Post, Bengaluru 560089,
Karnataka, India
e-mail: kmsankaran@gmail.com; m.
sankaran@icar.gov.in

https://doi.org/10.1007/978-3-030-47829-2_7
7.1 Introduction this chapter, an attempt has been made to com-

pile all the works pertaining to genetics and
Mango being a perennial has inherent charac- breeding of mango.
teristics such as outbreeding, heterozygosity,
sterility, self-incompatibility and polyembryony,
etc. which forces the breeders to raise large 7.2 Cytology
populations for effective selections. Fruit breed-
ing in general aims for creation of genetic vari- Mango (M. indica L.) was found to be a diploid
ability and selection of desired genetic variation (2x) with somatic chromosome number (2n) of
is one of the critical objectives. The basic 40 (Mukherjee 1950; Roy and Visweswaraiya
knowledge on classical cytogenetic is very 1951) and a polyembryonic variety, Vellaiko-
important for a breeder as it gives the information lamban was as tetraploid with 2n = 4x = 80
on structure and properties of chromosomes (Roy and Visweswaraiya 1951). This report was
during mitosis and meiosis as well as their contradicted by Akbar Hussain (1983) (Pandey
influence on phenotype besides the factors 1984). Later, it was confirmed to be a diploid
causing the chromosomal changes. In the recent with 2n = 2x = 40 by Majumder and Sharma
past, with advent of molecular cytogenetic tech- (1990) The reason for this anomaly was the
niques, it is possible to delineate genetic marker choice of plant material which had supposedly
order, define contig order and gap size, undergone chromosome doubling but was
heterochromatin-euchromatin regions and unavailable for further studies (Singh 1960).
genetic events such as addition, deletion, rever- Mango chromosomes show regular pairing and
sion, and chromosome rearrangement. Cytoge- disjunction into 20 bivalents suggesting a normal
netic studies are also important to reduce the risk meiotic division. The chromosomes are of small
of genetic erosion and to broaden the genetic size, i.e., 0.2–2.0 lm and can be classified into
base in cultivated types/varieties, economically eight types based on the size and presence or
important genes could be introgressed from wild absence of primary and secondary constrictions
relatives in fruit crops (e.g., Mango). Tropical and satellites. Eleven common chromosomes
fruit species like mango are highly suitable for have been reported in M. indica L. and M. syl-
arid and semi-arid regions and hence, increase in vatica Roxb. and they differ from one another
genetic diversity of these crops will in turn lead primarily in the assortment of these eleven
to their increased adaptability in the changing chromosomes(Mukherjee 1950). The wild rela-
climatic scenario. Furthermore, as an important tives of mango are supposed to have originated
export commodity, the commercial cultivation of through allopolyploidy and most probably
mango is limited to only a few cultivars in order through amphidiploidy (Mukherjee 1950).
to meet the export criteria and consumer demand. Mango genotypes are divided into two distinct
The continuous neglect of available germplasm groups on the basis of their origin such as
and increased practice of monoculture may lead monoembryonic (Indian types) and polyembry-
to genetic erosion, loss of the wild crop relatives onic (Southeast Asian types). The seeds of
which are reservoirs of several important traits monoembryonic mangoes contain a zygotic
and increased threat of diseases or pest (Camp- embryo, and the fruit skin is highly colored
bell 2007). The diversely rich gene pool of (mixes of red, purple, and yellow), while the
mango comprising of wild, semi-cultivated spe- seeds of polyembryonic mangoes have several
cies are under the threat of extinction and hence, embryos originated from nucellar tissue and the
several in situ and ex situ measures are being skin is soft or pale in color (green to light green
taken to conserve the available germplasm. In to yellow) (Iyer and Degani 1997; Viruel et al.
7 Classical Genetics and Breeding 113
2005). The present day mango varieties are with whole genome coverage will be the basis for
mainly a result of spontaneous mutation, selec- many genetic analyses such as quantitative trait
tion, and hybridization. Mukherjee (1950) loci (QTL) analysis, map-based gene cloning,
reported mango to be allopolyploid based on the comparative genomics studies, and genome-wide
characteristics like more chromosome number, association studies (Liu et al. 1996; Milbourne
high number of nucleolar chromosomes, sec- et al. 1998; Fukino et al. 2008; Huang et al.
ondary association of bivalents, regular pairing, 2010; Li et al. 2013). With the advances in whole
absence of multivalent formation, and good genome sequencing technology and EST
pollen fertility. Haploid genome size of mango is sequencing projects in several crop species such
0.91 pg, which is three times larger than Ara- as barley (Pasam et al. 2012), maize (Li et al.
bidopsis thaliana (L.) Heynh. and comparable to 2013), and rice (Huang et al. 2010), genome
that of rice (Arumuganathan and Earle 1991). wide association studies of mango become
Owing to the presence of secondary associations feasible.
at meiotic metaphase stage, Mukherjee (1950)
suggested that the basic chromosome number of
Mangifera is 8. In addition, the high number of 7.3 Genetic Studies
somatic chromosomes and the correspondingly
high number of nucleolar chromosomes led him One of the main problems in mango breeding has
to conclude that mango is an allopolyploid. been the lack of information on inheritance pat-
Molecular markers can be used to identify true tern of traits, high heterozygosity, and formation
hybrids in polyembryonic species such as of single seed per crossing which in turn is
Indochinese type mango and some citrus species. highly prone to fruit drop have further com-
Furthermore, MAS allows early selection of pounded the problem. However, some data gen-
major genes controlling traits and thus reduces erated though not conclusive can be used as
the time and space needed for growing out indicator in the breeding programme. Genetical
seedlings. The molecular markers such as studies revealed that the traits such as dwarf,
microsatellite markers are available in mango regular bearing, and precocity are recessive
(Viruel et al. 2005; Duval et al. 2005; Schnell genes wherein, regular bearing was tightly linked
et al. 2005; Honsho et al. 2005; Ukoskit 2007; with precocity and biennial bearing was found to
Ravishankar et al. 2011; and Suprapaneni et al. dominant over regular bearing habit Sharma and
2013). Microsatellite, or simple sequence repeat Majumder (1988a). Flesh color was reported to
(SSR), markers are polymerase chain reaction be governed by additive genes (Sharma 1987)
(PCR) based markers which detect differences in whereas, Iyer (1991) found light yellow colour
the copy numbers of short stretch repetitive DNA was dominant over orange-yellow in the proge-
sequences. There were several reports on appli- nies of Alphonso x Neelum cross. In a another
cations of mango microsatellite markers, includ- study carried out by Dinesh (2003) using half-sib
ing genetic diversity (Duval et al. 2005; population revealed that traits such as fruit
Suprapaneni et al. 2013), cultivar identification weight, TSS and pulp percentage were found to
(Eiadthong et al. 1999), and pedigree analysis be governed by non-additive factors with low
(Olano et al. 2005). With the vast germplasm in heritability. Selection of parents based on phe-
the Indian sub-continent and Southeast Asia notypic characters is not recommended as the
(Bompard and Schnell 1997) would help for progeny performance is highly unpredictable in
better understanding and utilization of genetics such cases (Lavi et al. 1998). With regard to peel
controlling agronomic and quality traits and colour, it was found that hybridization between
subsequent introgression. In order to utilize red with green colored varieties resulted in pro-
marker technology to its full potential, more genies with gradation of colour indicating that
markers are needed to construct a high-density peel colour is governed by a several loci (Sharma
mango genetic linkage map. The saturated map 1987; Iyer and Subramanyam 1987). The
presence of beak on the fruit was dominant when Sensation, Lafra, Kalapadi, Manipur, and the
‘Totapuri’ (with prominent beak) was used as hybrid variety, Amrapali can have good
one of the parents in hybridization, all the potential for dwarfing. Evaluation of germ-
resulting progenies were having beaked fruit plasm for good skin color has shown that
(Iyer and Subramanyam 1979). Similarly, bunch several varieties have very good skin color.
bearing habit was found to be dominant over The cultivars, Janardhan Pasand, Suvarna
single fruiting (Sharma et al. 1972). Lavi et al. Rekha, Fernandina, Rosa, and Sindhura can be
(1989) observed that in an open-pollinated pop- good gene donors. The exotic varieties,
ulation, there is no female parent effect on Tommy Atkins, Kensington, Irwin, and Sen-
juvenile period and fertility; however, it was sation have also been found to have good
observed on harvest season and fruit color and potential as a donor source for skin color. Till
there was a slight effect on fruit size and taste. date the works carried out to find a resistance
Resistance to bacterial canker was reported to be source for some of the pests and diseases have
of cytoplasmic inheritance since all the progenies yielded no satisfactory result. The varieties,
were bacterial canker susceptible when Neelum which were initially observed to be resistant,
was used as female parent irrespective of the have shown susceptibility in later stages and
male parent (Sharma and Majumder 1988a). Iyer using them in breeding programme based on
(1991) observed that recessive genes govern the earlier findings resulted in susceptible proge-
internal breakdown (Spongy tissue). Sharma and nies. The main bottlenecks in mango breeding
Majumder (1988a) found that susceptibility to arise from the inherent nature of this species
mango malformation is governed by dominant such as long juvenile phase, high heterozy-
genes, as hybrid progenies of Bhadauran (resis- gosity, and single seed per fruit. Inheritance
tant variety) lacked resistance. pattern of traits in mango is as follows:
Use of improved crossing technique, i.e., use 1. Upright tree habit is dominant over
of few flowers from large number of panicles spreading and spreading is dominant over
for hybridization and covering the fertilized dwarf.
flowers with polythene bags instead of crossing 2. Dwarfness is governed by recessive genes.
large number of flowers in single panicle and 3. Bearing habit and fruit quality are strongly
use of muslin clothes for covering has linked traits.
increased the fruit set percentage in mango. 4. Biennial bearing is dominant over regular
Additionally the information on gene donors bearing.
and crossing between the varieties with desired 5. Regular bearing is controlled by recessive
traits has further improved the efficiency of genes which is linked with precocity.
hybridization and resulted in saving of 6. Bunch bearing habit is dominant over single
resources on indiscriminate hybridization fruit bearing.
between varieties. Work carried out at various 7. Presence of beak on fruits is a dominant trait.
centres has revealed that the varieties Totapuri, 8. Heterosis and transgressive segregation for
Neelum, Banganapalli, and Lazzat Baksh are fruit size was observed in the F1 hybrids.
good source regular bearing. The variety of 9. Red peel color was found to be dominant
Neelum can also be used as a source for and gradations in skin color of F1 have
extending crop duration. However, Totapuri suggested the role of duplicate genes, same
whenever has been used, the progenies were is the case with flesh color.
found to have beak in fruits which is undesir- 10. Floral malformation appears to be con-
able. The varieties Creeping, Kerala Dwarf, trolled by recessive genes.
Rumani, and Mohammada Vikarabad were 11. Bacterial canker is governed by cytoplasmic
observed to be good source for dwarfness; genes.
work on evaluation at various places has shown 12. Spongy tissue is controlled by recessive
that varieties like Totapuri, Red Small genes.
It was reported that many fruit quality traits 7.3.2 Inheritance of Qualitative
such as fruit weight, fruit shape, ground skin Characters
color, fruit width, and pulp depth have high
heritability, and thus, can be improved by Out of 30 qualitative characters studied in 400
breeding programme. Fruit flavour was relatively germplasm, the fruit shape distribution was
high in progenies derived from the combinations observed to be oblong (67.5%),.elliptic (1.50%),
involving Kensington Pride. Subsequent studies roundish (30.5%), ovoid (0.25%), and obovoid
also confirmed that blush colour and fruit flavour (0.25%), fruit attractiveness, fibre free, pulp
have a strong genetic component and high fre- recovery (>70%), pulp aroma (mild 55.50 (%),
quency of hybrids with red or burgundy blush intermediate (28.75%), and strong (15.75%));
can be obtained from crosses where one parent TSS and eating quality (poor (16.75%), good
has an intense red blush colour. High variation (63.50%), very good (15.50%) and excellent
between phenotypic coefficient of variation (4.25%) are very important for commercial
(PCV) with high genetic advance was observed point of view (Sankaran et al. personal
for yield per plant and fruit weight in 31 chance communication).
seedlings of mango (Singh et al. 2004). Sharma (1987) observed that flesh colour is
governed by additive genes but light yellow pulp
colour was found to be dominant over orange-
7.3.1 Inheritance of Quantitative yellow in the progenies of Alphonso x Neelum
Traits (Iyer 1991). The non-additive factors and low
heritability governs the fruit weight, TSS, and
While selecting the parents for hybridization pulp percentage traits (Dinesh 2003). The pro-
programme, the quantitative characters such as genies of Amrapali (yellow peel colour) and
fruit weight, fruit length, fruit thickness, fruit Sensation (red peel colour) were observed to
diameter, and pulp recovery should be considered have various peel colour thus suggesting that red
as all of them have high heritability. Iyer and peel colour is not dominant over yellow peel
Subramanyam (1987) observed the transgressive colour. Cross between red peeled varieties
segregation for fruit size whereas Sharma and Totapari Red Small and Sensation and yellow-
Majumdar (1988a) observed it to be controlled by peeled varieties Dashehari and Amrapali yielded
additive genes. Prabhuram (1998) reported that progenies with varying shades of pink blush and
the heritability, expected genetic advance, and few hybrids with green peel colour suggesting
total genetic variance for fruit weight was influ- that red peel colour is heterozygous dominant
enced by environmental conditions whereas the and is governed by duplicate genes. Iyer and
high degree of broad sense heritability for fruit Subramanium (1987) reported fruit peel colour to
length, fruit weight, peel weight, and stone weight be governed by a number of loci.. Prabhuram
in different mango varieties was observed by (1998) observed fruit pulp colour is highly her-
Rajan et al. (2009). Fruit length was suggested to itable and controlled by additive genes. On the
be a polygenic trait as it shows transgressive basis of study conducted on Amrapali and Mal-
segregation and is highly influenced by environ- lika, fibre content in pulp was found to have high
mental conditions (Pandey 2012). Additionally, heritability and high genetic advance suggesting
total beta carotenoid pigments and TSS content additive nature of genetic variance. The pulp
was also found to have transgressive segregation aroma was found to have high heritability cou-
(Sharma and Majumder (1988)). In the progenies pled with genetic advance which suggest the
of Alphonso x Neelum, light yellow pulp colour contribution of both additive and non-additive
appeared to be dominant over orange-yellow genetic variance while fruit taste was governed
(Iyer 1991). by non-additive genes.
7.4 Diversity Studies recorded in cultivated mango as well as wild

types and cultivars Southeast Asia. Pandey and
Mango (Mangifera indica L.) is originated from Dinesh (2010) revised and updated the names
the Indo-Burma region and so far 69 species have mango varieties and the updated list now con-
been reported under the genus Mangifera from tains the names of 1682 cultivars. They also
the regions of Malayan Peninsula, Borneo, and identified the donors for traits such as dwarfness,
Sumatra having the highest diversity (Bompard regular bearing, fruit weight, fruit shoulder col-
1993). Mango has known to be under cultivation our, high pulp recovery, high TSS, long shelf-
for almost 4000 years and more than 1000 vari- life, precocity and lateness in fruit maturity and
eties are reported to be in cultivation (Mukherjee good processing quality. Dinesh et al. (2012)
1953). Most of the varieties in present day cul- characterized and catalogued 223 genotypes of
tivation are selection from open-pollinated mango using Bioversity International Descriptors
seedlings or hybrids of unknown parentage and barcodes were developed for the same
(Singh. 1963). Centers of mango variability in through molecular characterization. These
India are (i) Subtropical humid region (south include some polyembryonic varieties and 34
Assam, Manipur, Tripura and Mizoram), pickling varieties known as Appemidi from
(ii) Chhota-Nagpur Plateau (Madhya Pradesh, Western Ghats. Dinesh et al. (2017) character-
Odisha and Bihar), (iii) Santhal Paragana, ized and catalogued another 177 genotypes of
(iv) Southern Madhya Pradesh (tribal area) mango including the appemidi types and three
adjoining Odisha and Andhra Pradesh, (v) Dhar Mangifera species.
Plateau of Madhya Pradesh adjoining South Pandey and Dinesh (2010) grouped mango
Rajasthan and Gujarat, (vi) Tropical humid varieties based on the fruit weight as below:
region of southern peninsular India and
(vii) Andaman and Nicabar group of islands S. Group Varieties
(Yadav and Rajan 1993). no
1 Very small (up Bhowani Chowras (50–
to 99 g) 70 g)
7.4.1 Characterization 2 Small (100– Amrapali (130 g) and Rataul
149 g) (107 g)
and Cataloguing
of Mango 3 Medium large Dashehari, Alphonso
(150–299 g) Bombay, Pairi, Langra, Pusa
Arunima, Himsagar,
Earliest scientific description of mango was done Totapari, Neeleshwari,
by Watt (1891). Maries (1902) collected more Neelum, Suvarnarekha,
than 500 varieties of mango across the globe Ambika, Zardalu, Bombay
Green, Arka Puneet, Arka
including Indian mangoes and described them Anmol (India), Tommy
with botanical terminology. Wood house (1909) Atkins, Eldon and Sensation
described 40 mango varieties based on the key (Florida), Aroumanus and
characters. Burns and Prayag (1927) described Golek (Indonesia), Kyo
Savoy and Okrong
89 mango varieties collected from the Bombay (Thailand), Vallenato of
Presidency. Popenoe (1932) described 300 vari- Colombia and Momi-K
eties collected from across the world. Mukherjee (Momi Kinney) (Hawaii).
(1948) has described 72 varieties of Bengal, 4 Large (300– Arka Aruna, Mallika,
Bihar, and Uttar Pradesh. Simultaneously, Naik 500 g) Alfazli, A.U. Rumani,
Manjeera, Mulgoa, Rajapuri,
and Gangolly (1950) have described 335 vari-
Samarbehist Chowsa and
eties of South India. Apart from the fruit char- Sukul (India), Amelie (West
acters, they have also laid great stress on the Africa), Bourbon (Brazil);
vegetative characters. Huge variability has been (continued)
S. Group Varieties malformation. The mango hybrid ‘Amrapali’ is

no highly susceptible to floral malformation.
Golden Brooks, Florigon, Most of the mango varieties of South India
Davis Haden, Zrifin, Glenn like Mulgoa Neelum, Bangalora, Banganpalli,
and Van Dyke (Florida, Suvarnarekha, etc., are found to be free from
USA), Kensington
malformation in south India; however, they
(Australia); Nam Doc Mai,
Nuwun Chan, Namtal and exhibited malformation in North India. All the
Pak-Kra Bok (Thailand) and commercial mango varieties are susceptible to
Tahar and Naomi (Israel) fungal and bacterial diseases and hence, proper
5 Very large SufedMulgoa (1813 g), management practices are important to minimize
(more than HimamPasand (536 g), the loss. The varieties such as ‘Parish’, ‘Fair-
500 g) Anardana (717 g),
Balakondapari (647 g), child’, and ‘Tommy Atkins’ are moderately
Tenneru (944 g), Cowasji resistant to fungal disease, anthracnose, caused
Patel (713 g), Sora (1166 g), by Colletotrichum gloeosporioides Penz (Yee
Gaddemar (713 g), 1958) whereas the Janardhan Pasand, Neelum,
Hathijhool, Pansera and
Fazli of India, Manzanillo and Zardalu show tolerance to powdery mildew
Nunez of Mexico, Osteen, (Oidium mangiferae Berthet) and ‘Bombay
Keitt, Anderson and Haden Green’ is found to be tolerant to bacterial canker
of Florida (U.S.A) and R2E2 caused by Xanthomonas campestris pv. Mangi-
of Australia.
ferae indicae (Gupta 1976; Om Prakash and
Srivastava 1987).
Out of 61 mango varieties of U.S.A., 19 are
reported to bear large to very large fruits (Brooks
and Olmo 1972). Mango cultivars show great 7.6 Problems in Breeding
variations in fruit quality and climatic require-
ments. Varate Giduga is one of the unique There are several problems in mango breeding
genotypes from Sirsi region of Karnataka and it which have hindered the progress. Some of the
has got potential for commercial cultivation important ones are discussed hereunder with
(Dinesh et al. 2019). possible solutions.
7.5 Resistant Sources for Biotic

Stress Tolerance 7.6.1 Fruit Drop
There are several mango cultivars that possess Inspite of the large number of flowers being
the tolerance/resistance against biotic and abiotic crossed, because of heavy fruit drop, the number
stresses like ‘Golden Brooks’ has cold tolerance, of progenies generated is very low. Several
both ‘Bhadauran’ and ‘Elaichi’ are resistant to studies have been conducted to minimize fruit
mango malformation (Pandey 1984). RamNath drop using growth regulators; however, their use
et al. (1987) reported that ‘Bhadayan- in the breeding programme is very low owing to
daula’,‘Samar Bahist Rampur’, and ‘Mian Sahib’ the less flowers remaining in panicle. Use of
were found to be free from malformation in field embryo rescue technique has been recommended
conditions whereas the cultivars such as Dashe- by Iyer and Subramanyam (1972) for culturing
hari, Langra, Samarbehist Chowsa, Bombay more hybrid progenies. The performance of
Green, and Rataul of North and Central India, exotic cultivars of mango under South Indian
Gulab Khas, KishenBhog and Zardalu from conditions has also shown that some of the cul-
Bihar and Alphonso, Pairi and Kesar of Maha- tivars like Kensington had higher percentage of
rashtra and Gujarat are susceptible to bisexual flowers. Probably these varieties if used
in the breeding programme may help in devel- et al. (1998), and Brettell et al. (2004) reported that
oping varieties having higher fruit retention. polyembryony is controlled by dominant genes.
However, they also observed that polyembryony
varied with the site. Cordeiro et al. (2006) deter-
7.6.2 Long Juvenile Phase
mined in the mango cv. Rosinha using RAPD
markers the polyembryonic origin of platelets.
Mango seedlings generally take 3 to 10 years for
Globally, the maximum traded mangoes are
first fruiting. The identification and multiplica-
polyembryonic varieties but in India all the
tion of selected progenies on a desirable root-
commercial cultivars are monoembryonic in
stocks can shorten juvenility. Iyer (1991)
nature. There is a less effort or no efforts have
observed the significant differences among
been made to breed the polyembryonic scion
seedlings and grafted plants of the same geno-
varieties except the screening of some them for
type for fruit size, quality, and even colour.
their rootstock traits. The mango varieties such as
Singh (1969) reported that mango seedlings can
Bappakai, Bellary, Chandra Karan, Goa, Goa
be induced to flower and fruit if defoliated and
Kasargod, Kurukkan, Mazagaon, Mylepilian,
girdled scions are grafted into comparable shoots
Muvandan, Nekkare, Nileswar Dwarf, Olour,
of a bearing tree few days before flowering.
Peach, and Salem are polyembryonic in India
Ethephon has been shown to induce flowering
whereas Cambodiana, Carabao, Corazon,
(Chacko et al. 1974). Paclobutrazol was also
Edward, Palo, 13–1, Pahutan, Pico, Senora,
observed to induce flowering in the variety
Starch, Strawberry, and Florigon in other coun-
Dashehari (Sant Ram 1996).
tries (Singh 1960; Shukla et al. 2004). Lopez-
Valenzuela et al. (1997) differentiated mango
7.6.3 Polyembryony cultivars by their embryo type and identified their
geographical origin using RAPD marker. The
Polyembryony comes in the way of using good studies on genetic relatedness based on RAPD
polyembryonic varieties as female parents as isola- markers using genomic DNA and chloroplast
tion of zygotic seedlings from nucellar ones becomes DNA, RFLP analysis, and lineage among
difficult. The use of polymorphic enzyme systems polyembryonic and monoembryonic varieties
(isozymes) to identify zygotic seedlings (Degani indicated that these two types of Indian mango
et al. 1990, 1992, 1993, Schnell and Knight 1992; cultivars have a different genetic base (Ravis-
Truscott 1992) is based on the fact that nucellar hanker et al. 2004; Abirami et al. 2008).
seedlings should possess the same isozyme alleles as Polyembryonic varieties were observed to have
that of the female parent. The difference at a locus been introduced in India from other parts of
coding for an enzyme suggests that the plant has Southeast Asia (Ravishankar et al. 2004). The
originated zygotic embryo. The zygotic seedlings important rootstocks such as ‘Kurukkan’of India
arising from self-pollination can be distinguished and 13-1 of Israel are polyembryonic that are
from nucellar seedlings by being homozygous at one tolerant to salt while Olour as rootstock has been
or more loci as the female parent is heterozygous. found to have dwarfing effect on ‘Himsagar’ and
Similarly, zygotic seedlings from cross-pollination ‘Langra’ in West Bengal. ‘Bappakai’ rootstook
are distinguishable from those resulting from self- was found to be superior to ‘Olour’ rootstock for
pollination if they express an allele not carried by the tree vigour, spread, and productivity for Neelum
female parent. The degree of the occurrence of variety at Coimbatore conditions. Trials on
zygotic seedlings varies among the polyembryonic polyembryonic varieties as rootstocks for tree
cultivars (Degani et al. 1993; Schnell and Knight vigour in high-density plantation and biotic and
1992). Sturrock (1968) suggested that the polyem- abiotic stresses must be continued for a longer
bryonic condition in mango is a recessive factor and time before coming to the conclusion for their
is governed by a pair of genes. Contrarily, Aron recommendation on commercial scale.
7.7 Breeding diseases and pests (Iyer 1991). With regard to

rootstock breeding, the main desirable features
7.7.1 Objectives are polyembryony, dwarfing, tolerance to
adverse soil conditions (high pH, calcareous soil,
The objectives in mango breeding are set sepa- etc.), and good scion-compatibility. However,
rately for scion and rootstock breeding wherein combining all the desired traits in a single variety
the objectives may vary from place to place is difficult owing to high heterozygosity and long
within the country and between the countries. juvenile period (Singh 1977). Hence breeding
The performance varieties are specific to a par- objectives have to be defined for specific pur-
ticular region (e.g., Alphonso suffers from the poses (Sharma 1988).
internal break down ‘spongy tissue’ in western
parts of India). Hence, the breeding programme
undertaken in these parts has as one of the 7.7.2 Methods of Mango Breeding
objectives in screening against this malady. With
the expansion of export market, demands for 7.7.2.1 Selection
coloured mango varieties are increasing making Most of the commercial cultivars of mango are
it one of the most important objectives of scion the results of selections made from chance
breeding especially in Bangladesh where major- seedlings. Many of the present-day cultivars in
ity of varieties are green in colour. Besides col- Florida were selected from open-pollinated
our, development of dwarf, and regular bearing seedling progenies. The variety ‘Haden’ was
mango hybrids is one of the major breeding found to be a seeding of ‘Mulgoba’ a Indian
objectives in India in a view of increasing the variety. The cultivars Edward, Lippens, Tommy
productivity per unit area. Till date no polyem- Atkins, and Zill were found to have originated
bryonic rootstock has shown consistent dwarfing from ‘Haden’. In Israel, the varieties ‘Maya’ &
effect on the scion and true to type rootstocks ‘Nimrod’ are a selection from open-pollinated
cannot be raised using monoembryonic seeds, seedlings of Haden (Oppenheimer 1967). Like-
hence, transfer of character is important. Root- wise ‘Dahar’ was found to be a seedling of
stock breeding programme in Israel are mainly ‘Irwin’ (Slor and Gazil 1982) and ‘Naomi’ is a
concerned with developing rootstocks for prob- seedling of ‘Palmer’ (Tomer et al.1993). Two
lematic soils in addition to varieties with better selections MDCH-1 and STH-1 are dwarf, and
yield and quality parameters (Lavi et al. 1993). In flower within 1 year in Manipur, India (Singh
Australia, the major breeding objective is to 1996).
improve the cv. ‘Kensington’, that is susceptible
to anthracnose and bacterial black spot and has 7.7.2.2 Clonal Selection
poor shelf life by using Floridian and Indian It is one of the important tools in the improve-
mango cultivars as parents through hybridization. ment of perennial crops. Asexual propagation
The Brazilian mango breeding aims at develop- helps in the preservation of accumulated muta-
ing varieties with improved fruit yield and tions over the years. Naik (1948) has reported
quality, regular bearing, and small tree size significant variation due to bud mutation in trees
(Pinto and Byrne 1993). Hence, objectives in of the same clone in an orchard with respect to
mango breeding vary from country to country as fruit shape, size, colour, and quality. Oppen-
well as with growing states within a country. In heimer (1956), after a survey of many orchards
general, the scion-breeding objectives are to reported wide variability in the performance of
develop dwarf, regular bearing, precocity bear- the same variety in the same orchard.
ing, medium to large size fruits with better fruit Singh and Chadha (1981) selected four
quality, shipping quality couple with resistant superior clones C24, C18, C35, and C45 from
the variety ‘Dashehari’ at Lucknow. Two high shoots of off-season flowering cv. Royal Special
yielding clones have been identified from ‘Lan- and allowing open pollination between the
gra’ by Singh et al. (1985). One off-season clonal desired parents. As no other cultivar flowers
selection has also been reported by Deshmukh during this season, this is a safe technique.
and Budrukkar (1985). ‘Paiyur-1’ a clonal
selection from Neelum has also been made at Selection of Hybrid Progenies
Tamil Nadu, India. Whiley et al. (1993) have The hybrid progenies are subjected to primary
reported the strains of Kensington resistant to selection for the traits such as precocity, fruit
bacterial black spot. Rajput et al. (1996) have size, fruit shape, skin colour, high pulp percent-
isolated a high yielding and regular bearing clone age, free from physiological disorders, and fruit
Dashehari 51 from Uttar Pradesh, India. quality. The selected hybrids are retained for
further screening and also grafted and at least ten
7.7.2.3 Hybridization grafts per hybrid are planted in row trial and
The traditional method of pollinating the flowers evaluated for yield, regularity in bearing, and for
on a panicle for several days has now been screening against diseases and pests. The selec-
replaced by one-time pollination of about ten ted progenies are compared with local check and
flowers per panicle at the most as it is rare that national check for yield and other attributes for
not more than one fruit/panicle is carried to 3 years before deciding on their release.
maturity. By doing so fruit set can be up to
3.85% from 0.23 to 1.57% obtained by other Pre-selection Indices
methods (Mukherjee et al. 1968; Singh et al. Mango breeding is time consuming as it has long
1980). juvenile phase and need more land for evaluation
Another improvement in crossing has been of progenies. Inspite of difficulties, breeding time
the use of 24 21” perforated polythene covers can be hastened by using pre-selection indices
of 100 gauges instead of muslin bags (Mukherjee that can help in overcoming the said problem to a
et al. 1961). Studies carried out on inheritance of greater extent.
traits such as colour of young leaves, panicles Young leaf aroma was found to be directly
and beaked characteristic of fruit by Sharma et al. correlated with fruit aroma (Majumder et al.
(1985) helped in assessing the hybrid nature of 1972; Whiley et al. 1993). The emergence of new
F1 seedlings Singh et al. (1980) suggested that growth flushes simultaneously with fruiting or
once the flower is carefully pollinated since the immediately after harvest is indicative of regular
stigmatic surface is very small, the pollen bearing Sharma et al. (1972). Higher phloem:
deposited first has an advantage, there is very xylem ratio was found to be associated with
rare possibility of contamination from foreign dwarfness. If the ratio more than 1.0, they tend to
pollen, the fruit set can be as high as 3.85 per- be least vigorous; if it is 0.6–1.0 they have
cent, without covering the flowers. medium vigour and less than 0.6 are most vig-
After the discovery of sporophytic self- orous (Kurian and Iyer 1992). A higher levels of
incompatibility, a specialized insect-proof cages phenol in the apical bud was found to be asso-
were used for mango breeding (Sharma and ciated with dwarfing (Iyer 1991) and Majumder
Singh 1970) in which both self-incompatible et al. (1981) also reported that lower stomata
(female) and male parents planted and freshly density is an indication of dwarfness which could
reared house flies, or any other suitable pollina- not be confirmed by other workers (Iyer 1991).
tors are introduced to effect cross pollination Appemidi mangoes possess a typical pleasant
(Sharma et al.1972). odor due to the presence of Terpenoids in fruit
A new off-season crossing technique was sap mainly monoterpenoids like a and b-
suggested by Kulkarni (1986). It involves the Phellandrenes, limonene, b-terpinene, a-Pinene,
induction of flowering in the desired parents by Camphene, trans-Ocimene, and 3-Carene. More
veneer grafting of defoliated shoots on to normal odor intensive types have higher content of
Phellandrenes and other odors depend on the than 50 hybrids across the globe. Several of these
relative proportion of the above compounds. The hybrids are slowly growing in popularity with the
tender mangoes also recorded very high total mango growers. At ICAR- Indian Agricultural
phenols and flavonoids which were up to 450 and Research Institute, New Delhi, two hybrids,
30 mg/100 g, respectively. This will give them Mallika, a cross between Neelum and Dashehari
the high anti-oxidant capacity. Some of the with a fruit size of 300–350 g, high T.S.S. high
genotypes also found to have high vitamin C. pulp recovery and fibreless pulp and Amrapali, a
This also can be used as pre-selection indices or cross between Dashehari x Neelum, which is
biochemical markers for hybridity confirmation. dwarf with a precocious bearing habit, good
quality fruit rich in vitamin A were developed.
Breeding Achievements Mango improvement work at ICAR-Indian
In India, most of the cultivars are results of Institute of Horticultural Research, Bangalore
selections from naturally occurring, open- resulted in six hybrids ArkaAruna (Banganpalli x
pollinated seedlings (Singh 1963) With the Alphonso), Arka Puneet (Alphonso x Bangan-
introduction of inarching technique, the process pall), Arka Anmol (Alphonso x Janardhan
of selecting mango varieties was initiated during Pasand), ArkaNeelkiran (Alphonso x Neelum),
1650–1820 of the Mughal period (Mukherjee Arka Udaya (Amrapali x Arka Anmol) and Arka
1953). Breeding work was first initiated by Burns Suprabhath (Amrapali x Arka Anmol). ArkaAr-
and Prayag (1921) during the year 1911 with the una has high pulp recovery with a fruit size of
aim of obtaining varieties having regular bearing 500 g and is ideal for homestead planting as it is
habit, fruit quality, high yield with resistance or dwarf. Arka Puneet is similar to Alphonso but is
tolerance to pests and diseases. Three hybrids free from spongy tissue. Arka Anmol is a late
from the cross Cowasji Patel x Pairi were isolated season variety with good sugar-acid blend and
from 153 crosses (Sen et al. 1946). Wagle (1929) good keeping quality (Iyer and Subramanyam
made attempts to improve Alphonso by 1993). Arka Neelkiran is also a late season hybrid
hybridization. Systematic hybridization work with attractive colour and good keeping quality.
was started during 1940 at Anantharajupet with Recent hybrids (Arka Udaya and Arka Suprab-
special reference to South Indian varieties hath) are having excellent fruit quality, bunch
(Bhujanga Rao and Rangacharlu 1958) and at bearing, and late maturing. Currently, work is
Sabour with special reference to north and east- being done on introgression of peel colour from
ern region cultivars (Sen et al 1946 and). The Vanraj on Amrapali and Alphonso background.
main objective was to breed regular bearing Two hybrids ‘Ratna’, a hybrid between Nee-
varieties having good quality. The mango lum and Alphonso and Sindhu (Ratna x
breeding work at Kodur (Andhra Pradesh) Alphonso) have been developed at Fruit
resulted in release of four hybrids, namely, Research Station, Vengurla. Ratna has an excel-
Neeleshan (Neelum x Baneshan), Neelgoa lent fruit quality comparable to Alphonso and is
(Neelum x Yerramulgoa), Neeluddin (Neelum x free from spongy tissue (Salvi and Gunjate
Himayuddin), and Swarnajehangir (Chinna- 1988). ‘Sindhu’ is a parthenocarpic mango vari-
Survarnarekha x Jehangir) (Bhujanga Rao et al. ety having good fruit quality and very thin stone
1963). The breeding work started at Krishnagar, (Gunjate and Burondkar 1993).
Saharanpur, and Punjab did not result in the These hybrid varieties ‘Au-Rumani (Rumani
release of any hybrid. However, the mango x Mulgoa)’, Manjeera (Rumani x Neelum), and
improvement programme carried out at Sabour KMH-1 (Cherukurasam x Khader) have been
resulted in two hybrids, viz., Mahmood Bahar developed by the Andhra Pradesh Agricultural
and Prabha Shankar, both of the combination University. ‘Au-Rumani’ is a prolific bearer.
Bombay and Kalapady (Mallik 1951). Manjeera and KMH-1 is dwarf having good
In 1950s, systematic hybridization work star- quality. In Gujarat, three mango hybrids have
ted in several centres in India that resulted more been released, namely, Neelphonso (Neelum x
Alphonso), Neeleshan Gujarat (Neelum x Bane- In Israel, the seedlings were evaluated on
shan), and Neeleshwari (Neelum x Dashehari). calcareous soils of which 9 were selected based
These hybrids have high TSS, total sugars, and on their performance with regard to rootstock
Vitamin C in addition to being dwarf (Sachan traits (Lavi et al. 1993). A new cultivar ‘Naomi’
et al. 1988). which had originated from the cv. ‘Palmer’ either
At Fruit Research Station, Sabour, four by self pollination or by cross pollination with
mango hybrids developed and released as Sundar ‘Maya’, Haden, ‘Nimrod’ or ‘Irwin’ was released
Langra (Sardar Pasand x Langra) having Langra (Tomer et al. 1993). Another new variety
quality and regular bearing habit; AlFazli ‘Tango’, a open-pollinated seedlings selection of
(Alphonso x Fazli) early ripening with Fazli the variety ‘Naomi’ has been released. It has
quality; Sabri (Gulabkhas x Bombai) having attractive skin colour with good quality. In South
Bombai fruit shape and colour of Gulabkhas with Africa, four new cultivars ‘Heidi’, Neldica
regular bearing habit and Jawahar (Gulabkhas x ‘Neldawn’, and ‘Ceriese’ were identified by mass
Mahmood Bahar) having high pulp recovery, selection (Marais 1992). The list of hybrids
fibreless pulp and early bearing habit have been released in India and Australia is given in
developed (Hoda and Ramkumar 1993). Table 6.
S. No Hybrid Parents Place of release

1 ArkaAruna Banganpalli X Aplhonso ICAR-IIHR, Bangalore
2 Arka Puneet Alphonso X Bangapalli ICAR-IIHR, Bangalore
3 Arka Anmol Alphonso X Janardhan pasand ICAR-IIHR, Bangalore
4 ArkaNeelkiran Alphonso X Neelum ICAR-IIHR, Bangalore
5 Arka Udaya Amrapali X Arka Anmol ICAR-IIHR, Bangalore
6 ArkaSuprabhath Amrapali X Arka Anmol ICAR-IIHR, Bangalore
7 Swarna Jehangir Chinnasuvarnarekha x Jehangir FRS, Kodur
8 Neeluddin Neelum X Himayuddin A.P.A.U.
9 Au Rumani RumanixYerramulgoa A.P.A.U.
10 Manjeera RumaniXneelum A.P.A.U.
11 KMH-1 Cherukurasam X Khader A.P.A.U.
12 Neelgoa Neelum X Yerramulgoa A.P.A.U.
13 Neeleshan Neelum X Baneshan A.P.A.U.
14 Neelphonso Neelum X Aplhonso GAU, PARIA
15 Neeleshwari Neelum X Dashehari GAU, PARIA
16 Neeleshan Neelum X Baneshan GAU, PARIA
17 Mahmood Bahar Bombay X Kalepad FRS, Sabour
18 Prabhashankar Bombay X Kalepad FRS, Sabour
19 Al Fazli Alphoso X Fazli FRS, Sabour
20 Sundar langra Sardar Pasand X Langra FRS, Sabour
21 Sabri Gulab Khas X Bombai FRS, Sabour
22 Jawahar Gulab Khas X M. Bahar FRS, Sabour
23 Ratna Neelum X Alphonso FRS, Vengurla
(continued)
S. No Hybrid Parents Place of release

24 Sindu Ratna X Alphonso FRS, Vengurla
25 PKM-1 ChinnaswarnarekhaXNeelum Periyakulam,T.N.A.U.
26 PKM-2 Neelum X Mulgoa Periyakulam,T.N.A.U.
27 Mallika Neelum X Dashehari IARI,N.Delhi
28 Amrapali Dashehari X Neelum IARI,N.Delhi
29 Pusa Arunima Amrapali x Sensation IARI,N.Delhi
30 Pusa Surya Amrapali x Sensation IARI,N.Delhi
31 Pusa Pratibha Amrapali x Sensation IARI,N.Delhi
32 PusaShreshth Amrapali x Sensation IARI,N.Delhi
33 PusaPeetamber Amrapali x Lal Sundari IARI,N.Delhi
34 PusaLalima Dushehari x Sensation IARI,N.Delhi
35 Ambika AmrapaliX Janardhan pasand CISH
36 Arunika Amrapali x Vanraj CISH
37 Sai sugandh Totapuri x Kesar MPKV, Rahuri
38 CISH-M-2 Dasheharixchausa CISH
39 CISH–M-1 Amraphalixjanardhanpasand CISH
40 Konkan Samrat Alphonso x Tomy Atkins BSSKKV
41 Suvarna Alphonso x Neelum DAPOLI
42 NMBP-1243 Irwin x Kensington Pride Australia
43 Neeleshan Gujarat Neelam x Baneshan AES, Paria
44 Sonpari Alphonso x Baneshan AES, Paria
45 NMBP-1201 Irwin x Kensington Pride Australia
46 NMBP-4069 Van Dyke and Kensington Pride Australia
47 Hybrid-949 Amrapalli x Vanraj ICAR-CISH
48 Hybrid-1084 AmrapalixVanardhanpasand ICAR-CISH
49 GMH-1 Alphonso X Baneshan GAU
50 Hybrid 45 (Bennet Alphonso x Himayuddin), ICAR-CISH
51 Hybrid 87 (Kalapady x AlampurBenishan) ICAR-CISH
52 Hybrid 151 (Kalapady x Neelum) ICAR-CISH
Sankaran and Dinesh (2018) against anthracnose. M. orophila, a species from

Malaysia, and M. dongnaiensis from Vietnam,
7.7.2.4 Wide Hybridization which are restricted to mountain forests l000–
Wild relatives of mango are the reservoirs of l700 metres above sea level may make growing
useful traits that can be introgressed on any mango in the high altitude areas of Mediter-
commercial variety background provided wild ranean region.
species should have edible fruits with other The species M. magnifica (free from fibres),
desirable characters and species that could act as M. Rufocostata and M. swintonioides (off-season
gene donors for specific improvements like bearing habit), M. paiang and M.foetida (good
resistance to pests and diseases (Iyer 1991). quality fruits), M. caesia var.Wani from ‘Bali &
Bompard (1993) has discussed the potential use Borneo has a distinctive taste, M. casturi occur-
of M. laurina as a potential source of resistance ring in South Kalimantan is a prolific bearer that
can be used as gene donors in mango breeding disease resistant genes and gene markers (SSRs
programme (Bompard 1993; Kostermans and and single nucleotide polymorphisms (SNPs) will
Bompard 1993). The other species M. altissimo be done by cloning of genes from resistant and
has been reported to be resistant to hoppers, tip susceptible accessions to look for sequence dif-
borers, and seed borers (Angeles 1991). Strains ferences (Dillon et al. 2013). Molecular markers
of M. sylvatica which are polyembryonic in have also been used to identify or fingerprint
nature with good fruit quality have been reported individual mango varieties by unique patterns of
from northeastern Indian States (Yadav 1996). marker alleles. DNA fingerprinting data have been
Hybrids with good quality pollen can be pro- used to support plant breeders’ rights and patents
duced by crossing pentamerous mango flowers (IP AUSTRALIA 2008) and in maker assisted
with the Indian mango having only one fertile selection (MAS). In U.S.A, although several
stamen (Fairchild 1948). Thirty-two inter-specific varieties have shown moderate resistance to
hybrids involving M. odorata & M. zeylanica anthracnose so far no commercial cultivar is
developed (Bhujanga Rao et al. 1963) suggesting resistant to be produced in humid areas without
that different Mangifera spp. are cross compatible fungicide application. Zebda, a Egyptian cultivar,
(Mukherjee 1963). However, in order to use these is aesthetically unacceptable since it is green at
species in mango improvement programme, their maturity but do possess resistant to this disease.
thorough evaluation is paramount hence, extensive The cv. Kent and Haden are important in inter-
research is warranted in order to conserve, screen, national trade but are highly susceptible to
and utilize them in future breeding programme. anthracnose when grown humid areas however
they are produced in arid production areas (Ploetz
7.7.2.5 Breeding for Biotic Stress 2007). Singh et al. (2014) have already released
Tolerance the draft genome of Mangifera indica with a small
M. laurina ‘Lombok’ has been reported to be genome size of about 450 Mbp. Molecular
resistant to anthracnose which was confirmed genomics technologies are being used to assist our
through artificial inoculation screening. This par- understanding of mango genetics and the diversity
ticular accession is being used as the male parent of the world mango gene pool. In recent years
in a cross with the advanced breeding line M. many studies using molecular marker to discover
indica ‘NMBP4046’ (Bally et al. 2009) to intro- the diversity and phylogenetic relationships
gress the anthracnose resistance. A total of ten between mango varieties and related Mangifer-
candidate disease resistant genes have been iden- aspecies have been undertaken. The gene dis-
tified from an expressed sequence tag (EST) and covery for specific trait is yet to be taken in mango
EST-SSR markers have been developed for six across the globe. In order to develop fruit fly
genes and screened for polymorphism across a tolerant varieties, M.camptosperma, EC95862 and
selection of 32 accessions identified from the VarateGiduga are being used as male parents at
diversity analysis, as representing the major IIHR, Bengaluru.
groupings in the Australian National Mango
Genebank (ANMG). Further, six EST-SSR puta- 7.7.2.6 Mutation Breeding
tive disease resistance markers have shown to be Mutation is an important tool in creating vari-
polymorphic in 32 Mangifera accessions were ability. Although mutations and chimeras occur
assessed. The number of alleles identified varied frequently, they are generally marked by intra-
from two to nine with an average of 5.3 alleles per somatic selections. In mango, mutants establish-
locus and these EST-SSR markers will be tested ing as cultivars are rare. Two somatic mutants
in future to determine their ability to detect post- have been reported in mango. The variety ‘David
harvest anthracnose disease resistance by screen- Haden’ was reported to be sport of ‘Haden’. It is
ing them across the segregating disease resistant larger than ‘Haden’ & matures early (Young and
hybrid population generated between M. indica Ledin 1954). Another mutant ‘Rosica’ from
and M. laurina. Identification of further putative seedless variety Peru was reported to be a mutant
of ‘Rosado de Ica’. It is high yielding and regular et al. 1989), hence several genetic markers
bearing (Medina 1977). A mericlonal chimera of including isozymes, RAPD, AFLP, ISSR, SSRs,
Alphonso was observed by Roy (1950), it dif- and VNTRs have been developed which can be
fered with respect to fruit shape and mutants of used for more robust characterization of mango
‘Puthi’ was developed Roy and Viswesvariya cultivars.
(1951). In mango, isozymes were used to detect pos-
Induction of mutation was first tried using sible genetic variation among the clones (Gan
gamma irradiation by Siddique et al. (1966). The et al. 1981). Degani et al. (1992) used isozymes
dormant buds of cv. Langra were irradiated and for characterization and parentage analysis in
grafted on rootstocks. Those bud sticks which mango cultivars. They could distinguish ‘Pico’
had undergone 3 kR of radiation bore fruits and ‘Carabao’ by isozyme analysis. The isozyme
which were heavier, larger and had more banding pattern was used to correlate the origin
creamish yellow pulp than control (Siddiqui of some of the cultivars such as ‘Haden’ from
1985). Sharma and Majumder (1988b) observed ‘Mulgoba’ and ‘Zill’ from ‘Haden’ (Campbell
that dosages above 5 kR are lethal for mango and 1992) and ‘Tahar’ from ‘Irwin’ (Slor and Gazit
the LD 50 doses lie between 2 and 4 kR. The 1982). The origin of some of the mango cultivars
chemical mutagens EMS and NMU were found was refuted by isozyme analysis (Degani et al.
to be optimum at 1.5% and 0.05%, respectively. 1990, 1992). Thus ‘Edward’ is commonly
The degree of mutations induced by physical and accepted to be hybrid of ‘Haden’ and ‘Carabao’
chemical mutagens was observed to be almost (Campbell 1992), the isozyme banding pattern
same, indicating the high sensitivity of only showed that ‘Carbao’ cannot be the male parent.
some loci. In spite of these few attempts, no Isozyme analysis also revealed that ‘Mulgoba’
worthwhile variety has been developed by may not be a parent of ‘Keitt’ and ‘Givataim’
mutation on mango. cannot be an offspring of the polyembryonic
cultivar ‘13-1’. Several molecular markers such
as RAPD (Schnell et al. 1995; Valdomiro and
7.8 Biotechnological Studies Paulo Sarmanho (2004)), mini- and micro-
satellite probes by Adato et al. (1995), and
The role of biotechnological methods in under- AFLP markers by Kasikush et al. (2001) have
standing the genetics and for making improve- been used for identification of mango cultivars
ment is of recent origin. These come in handy in and generation of a preliminary genetic map. The
solving the mystery of the nomenclature. major problem in tissue culture propagation of
Monoembryonic and polyembryonic mango mango is phenol exudation and explant discol-
genotypes of India are reported to have different oration. Studies at Pune have revealed that
genetic bases (Ravishankar et al. 2004). Lopez- plantlets were generated from monoembryonic
Valenzuela et al. (1997) used RAPD markers to varieties. Sahijram et al. (2005) were able to
differentiate mango cultivars by embryo type and rescue hybrid embryos 6-8 weeks after pollina-
geographical origin. The main components of tion. This holds promise for increasing the
mango genetic engineering are efficient somatic number of progeny population, which is a lim-
embryogenesis and induction of mutations in iting factor in mango hybridization. Ravishankar
embryogenic cultures, selectable markers, and et al. (2015) found that the SSR marker charac-
transformation with gene that mediates a horti- terization of Indian mango cultivars revealed two
cultural trait (Litz 2004). Mango cultivars have distinct groups of populations with geographical
been characterized using morphological traits affiliation. Six SSR loci with low PI have been
which are highly influenced by environmental identified as universal markers for mango
conditions and hence are not reliable (Tanksley characterization.
7.8.1 Research Gap in Breeding References

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In Vitro Culture and Genetic
Transformation in Mango 8
César Petri, Richard E. Litz,
Sanjay K. Singh, and José I. Hormaza
Abstract the potential to revolutionize mango improve-

ment, germplasm storage and production.
Mango is one of the world’s most important
Genetic transformation of embryogenic cul-
fruit crops and is widely grown in the tropics tures opens the possibility of improving
and subtropics. Despite its importance in local existing cultivars by incorporating into their
economies and as an increasingly important
genomes genes that target specific traits.
export crop, very little progress has been made Embryogenic mango cultures have the poten-
in terms of classical breeding and genetics that tial to rationalize germplasm storage and the
would facilitate mango cultivar improvement.
international exchange of disease-indexed
Consequently, almost all the important mango clonal materials. Finally, the development of
cultivars in its area of origin in India and efficient in vitro vegetative reproduction sys-
Southeast Asia are clonal selections that are
tems, whether this is based upon production of
several hundred years old. Biotechnology has embryogenic or shoot tip and nodal cultures,
could enable the availability of clonal root-
stocks of exotic monoembryonic selections.
C. Petri (&) J. I. Hormaza

Departamento de Fruticultura Subtropical y 8.1 Introduction
Mediterránea, Instituto de Hortofruticultura
Subtropical y Mediterránea La Mayora (IHSM La
Mayora—UMA-CSIC), Avenida Dr. Wienberg, s/n, Mango (Mangifera indica L.) is a member of the
29750 Algarrobo-Costa, Málaga, Spain family Anacardiaceae in the order Sapindales.
e-mail: cesar.petri@csic.es Mangifera indica is the most widely cultivated
J. I. Hormaza species within the genus although there are 69
e-mail: ihormaza@eelm.csic.es known Mangifera species. Mangifera indica has
R. E. Litz its natural distribution in South and Southeast
Department of Horticultural Sciences, Tropical Asia. The mango ranks fifth in total world pro-
Research and Education Center, University of
duction among fruit crops, after banana, citrus,
Florida, 18905 SW 280 Street, Homestead, FL
33031-3314, USA grapes and apples. Mango domestication most
e-mail: relitz@ufl.edu probably began ca. 4,000 years ago in different
S. K. Singh regions of Asia. There are two distinct ecogeo-
Division of Fruits and Horticultural Technology, graphic races that can be distinguished on the
Indian Agricultural Research Institute, New Delhi basis of their mode of reproduction and their
110 012, India
centers of diversity: a subtropical group with
e-mail: sanjaydr2@gmail.com

https://doi.org/10.1007/978-3-030-47829-2_8
132 C. Petri et al.
monoembryonic seeds (Indian type) and a trop- variety, ‘Batangas’ strain, where Batangas is one
ical group with polyembryonic seeds (Southeast of the provinces of the Philippines (Pateña and
Asian type) (Mukherjee and Litz 2009). Barba 2011).
Detailed botanical descriptions of mango and Conventional breeding in mango has had
some of the other Mangifera species are available limited impact on cultivar and rootstock devel-
(i.e., Mukherjee and Litz 2009).The chromosome opment due to the long juvenile phase of ca.
number is 2n = 2x = 40. Mango is a woody 7 years, low fruit set, high fruit drop, single seed
perennial evergreen tree that can reach more than per fruit, high degree of cross-pollination,
40 m height and can survive for hundreds of polyembryony and allopolyploidy. Furthermore,
years. Mango trees that have been domesticated little is known about the inheritance of horticul-
by selection from open-pollinated seedling pop- turally important traits because of its highly
ulations show variation in tree architecture (i.e., heterozygous nature, the difficulty in making
shape and size), besides fruit quality traits that controlled pollinations, and the high cost and
are unique with every chance seedling. Leaves time involved in screening large number of
are simple and alternate, with a morphology that hybrid progenies (Litz and Hormaza 2020). Most
varies among genotypes. The juvenile period of monoembryonic cultivars are vegetatively prop-
seedling trees is ca. 7 years. The root system agated seedlings resulting from natural cross-
consists of a long, vigorous taproot and abundant pollinations.
surface feeder roots. Both hermaphrodite and Currently, most significant problems in
staminate flowers are borne on terminal pyrami- mango production and post-harvest are alternate
dal panicles and are glabrous or pubescent; the bearing habit, susceptibility to anthracnose
inflorescence is rigid and erect, up to 30 cm long, (caused by Colletotrichum gloeosporioides) and
and is widely branched, usually tertiary, although issues related with postharvest handling, e.g.,
the final branch is always cymose. The inflores- storage and long distance transportation, due to
cence is densely flowered with hundreds of small its climacteric nature. Commonly, cultivar
flowers (5–10 mm diameter). The mango fruit is breeding goals in mango include tolerance of
a large, fleshy drupe, containing an edible regular bearing, dwarfing, medium size fruit
mesocarp of varying thickness. It is a climacteric (250–300 g), anthracnose tolerance, and a stable
fruit, and an increased ethylene production takes pleasant flavor combined with good storage
place during its maturation. performance (Mukherjee and Litz 2009; Litz and
Mango is currently cultivated throughout the Hormaza 2020). Desired traits for rootstocks
tropics and subtropics from the equator to ca. 37º include scion compatibility, polyembryony,
latitude in southern Europe (Spain). World pro- dwarfing, and tolerance of calcareous soils,
duction of mangoes can only be estimated since salinity and soil-borne pathogens (Chandra et al.
FAOSTAT includes mango, mangosteen and 2011; Litz and Hormaza 2020).
guava as a single production item. India is the main Although in most woody plants are regener-
producing country by far with approximately a third ation from cell and tissue cultures and genetic
of the world production, followed by China, Thai- transformation of elite selections are difficult
land, Indonesia and Mexico (FAOSTAT 2019). tasks (Song et al. 2019), regeneration of several
Monoembryonic mango cultivars are propa- mango cultivars by somatic embryogenesis from
gated by grafting onto seedling rootstocks. In maternal tissue explants (nucellus) has been
many countries, uniform nucellar seedlings from described. On the other hand, micropropagation
polyembryonic mangoes are utilized as root- by shoot tip and nodal culture has been elusive
stocks. Both types of cultivars, the monoembry- due to high endogenous levels of microbial
onic and polyembryonic, when propagated contamination, excessive polyphenol exudation
continuously may have several distinct forms and explant necrosis.
called ‘strains’, which are usually named after the Many of scion cultivar breeding objectives
place where they originated, e.g., ‘Carabao’ can be achieved using conventional breeding
8 In Vitro Culture and Genetic Transformation in Mango 133
procedures involving either controlled or open- and polyphenols are oxidized after wounding
pollinations between superior genotypes fol- and/or explant disinfestation. This leads to mas-
lowed by selection among the offspring. Most of sive necrosis and explants cannot survive long
the important mango cultivars are not amenable enough to respond to culture conditions. This has
to hi-tech cultivation practices and do not meet made it difficult to achieve any conclusions from
the requirements of modern horticultural pro- those experiments that would result in optimized
duction systems, e.g., dwarfing, precocity and procedures and plant growth conditions. The
regularity in bearing with high yield, resistance in vitro phenol exudation has been positively
to diseases, pests and physiological disorders and correlated with explant necrosis (Krishna et al.
good storage quality. 2008). Later, Krishna et al. (2010) suggested pre-
Employing biotechnology procedures to cor- treatment, i.e., etiolation of new shoot sprouts +
rect genetic flaws of existing cultivars has great spray of imidazole (200 ppm) + agitation in
potential. Inclusion of in vitro culture techniques, 0.2% PVP before explant excision improved
in vitro mutagenesis and genetic transformation culture establishment, reduction of phenolics and
in mango breeding programs would expedite the microbial infection in shoot cultures. Explants
development of improved existing cultivars, as is inoculated on the medium comprising B5 macro-
currently the case with some other woody salts excluding (NH4)2SO4 and (NH4)2NO3 plus
perennial fruit crops (Song et al. 2019). MS micro-salts and organics supplemented with
0.5 mg l−1 NAA + 2.0 mg l−1 BA during March
was most effective giving higher culture
8.2 In Vitro Shoot Establishment establishment.
and Micropropagation Several studies have attempted to overcome
these problems and some important factors
Mango is highly heterozygous and seed propa- influencing mango in vitro shoot establishment
gation does not ensure true-to-type progeny. have been determined (Yang and Lüdders 1993;
Among the different vegetative propagation Thomas and Ravindra 1997; Sharma and Singh
methods, the most commonly utilized are graft- 2002; Chandra et al. 2004; Samaan et al. 2007;
ing and budding. These methods are time con- Krishna et al. 2008).
suming and labor intensive. The standardization Shoot tip and nodal explants have been uti-
of micropropagation techniques in mango would lized (Table 8.1). Genotype significantly influ-
facilitate the production of large quantities of enced establishment; however, disinfestation
elite plant material for nurseries and growers. treatment, basal plant growth medium, growth
Polyembryonic mango genotypes, particularly regulators, etc. are also important. Different basal
those that are used as rootstocks, are usually culture media have significant different effects on
propagated by seed; a limited number of sexual, in vitro culture establishment. Thus, while some
non-clonal seedlings also develop in polyem- reports (Thomas and Ravindra 1997; Sharma and
bryonic seeds and this can cause problems in Singh 2002; Chandra et al. 2004) described less
uniformity of seedlings used for clonal rootstock phenolic exudation and improved explant sur-
and thus mature trees may differ from the clone. vival with MS medium (Murashige and Skoog
Micropropagation could resolve the problem of 1962), other reports (Yang and Lüdders 1993;
clonal rootstock multiplication. Samaan et al. 2007; Krishna et al. 2008)
Efforts to micropropagate mango have met observed better results with woody plant medium
with little success (Table 8.1). Major problems (WPM) (Lloyd and McCown 1981), B5 medium
that have been encountered with in vitro shoot (Gamborg et al. 1968) and G medium (Yang
establishment are latent microbial contamination, et al. 1984).
excessive polyphenol exudation, plant growth It is clear that the response to the combination
medium browning and explant necrosis of plant growth regulators and their concentra-
(Fig. 8.1). Secondary metabolism is stimulated tions is highly genotype dependent (Yang and
134 C. Petri et al.
Table 8.1 In vitro shoot establishment and micropropagation of Mangifera indica L

Genotype Explant Mediuma + growth regulatorsa Results Reference
‘Turpentine’, Shoot tips G medium + BA + Zeatin + 2iP Shoot establishment Yang and
‘Gomera’, ‘13-1’, and stem + IAA + IBA + Casein hydrolysate and elongation Lüdders
‘Sabre’ nodes (1993)
‘Alphonso’, Shoot tips Half MS medium Shoot establishment Thomas and
‘Totapuri’, Ravindra
(1997)
‘Amrapali’, Shoot tips MS Bud establishment Chandra
‘Dashehari’, medium + IAA + kinetin + adenine + and elongation et al. (2004)
‘Langra’, ‘Chausa’ casein hydrolysate
‘Zebda’, Stem nodes (1) WPM + Kinetin (1) Shoot Samaan et al.
‘HindySinnara’, (2) B5 medium + IBA, BA, Zeatin, establishment (2007)
‘Sukkary’, 2iP + IAA + casein hydrolysate (2) Shoot
‘13-1’ multiplication and
rooting
‘Amrapali’ Shoot tips Modified B5 macros + MS micros & Shoot establishment Krishna et al.
vit. + casein hydrolysate (2008)
‘Irwin’ Nodal Full- or half-strength WPM or ½WPM Culture Tetsumura
establishment and et al. (2016)
shoot proliferation
2iP: N6-(2-Isopentenyl) adenine; BA: Benzyladenine; G: G medium (Yang et al. 1984); IAA: Indol-acetic acid; IBA: Indol-butyric
acid; MS: Murashige & Skoog (Murashige and Skoog 1962); WPM: Woody Plant Medium (Lloyd and McCown 1980)
a
According to the authors, the most appropriate combination among the tested
Fig. 8.1 a Exudation from

an in vitro mango (cv. ‘Keitt’) a b
shoot tip after 4 days of
culture. b Medium browning
observed after few days of
in vitro culture of a ‘Gomera
1’ shoot
Lüdders 1993; Chandra et al. 2004; Samaan et al. ‘Sukkary’; however, its effect was poor for ‘13-
2007). For example, 1.0 mg/L of 2iP combined 1’ and ‘HindySinnara’ (viz. ‘Hindi be Sennara’)
with 0.5 mg/L indol-butyric acid (IBA) stimu- with only 10 and 20% positive explant response,
lated shooting (80%) from nodal explants of respectively (Samaan et al. 2007). The optimum
plant growth medium formulation must therefore It seems that the season of explant collection
be standardized for each genotype. can be a key factor to reduce phenolic compound
Different disinfestation treatments have been exudation, microbial contamination and improve
applied to disinfect explants without causing explant survival. The most appropriate periods
extreme phenolic compound exudation and tissue for collection in the Northern Hemisphere are
necrosis. Different antiseptic solutions alone and from May to June (Yang and Lüdders 1993;
in combination (NaOCl, Ca(OCl)2, HgCl2, H2O2, Thomas and Ravindra 1997) or from March to
ethanol, etc.), antibiotics, antifungal agents and April and September to October (Chandra et al.
detergents have been assayed. Often, adsorbents 2004).
(PVP, active charcoal) and/or antioxidant mole- The age of the shoots also affects the results.
cules (citric or ascorbic acid) have been used to One to four month-old shoots, with green foliage
counter the effect of oxidative stress during dis- and dark green stems, were found ideal for cul-
infestation (Yang and Lüdders 1993; Thomas ture establishment with the best response and
and Ravindra 1997; Sharma and Singh 2002; with less polyphenol oxidation and microbial
Chandra et al. 2004; Samaan et al. 2007; Krishna contamination (Thomas and Ravindra 1997;
et al. 2008). These treatments were often used Chandra et al. 2004). Younger shoots (1–
sequentially and frequent subculture to fresh 2 weeks), with reddish brown tender leaves and
plant growth medium was reported. Success was stems, showed maximum explant browning and
genotype dependent in terms of explant survival phenolic exudation, whereas older shoots, with
and contamination rates (Yang and Lüdders dark green mature foliage and thick brown stems,
1993; Thomas and Ravindra 1997; Chandra et al. showed maximum contamination (Thomas and
2004; Samaanet al. 2007; Hare Krishna et al. Ravindra 1997; Chandra et al. 2004). Explants
2008). Furthermore, pretreatments of the taken from young seedlings showed least phe-
explants by etiolation and PVP application nolic exudation and contamination but poor
(Krishna et al. 2008) or by spraying the tree with growth responses (Chandra et al. 2004). Other
a disinfectant solution followed by a plant factors that reduced microbial contamination and
growth regulator solution (Chandra et al. 2004) increased explant survival were collection of
reduced explant necrosis and improved the explants from greenhouse-grown plants or from
recovery of aseptic cultures. Earlier, Chavan mycorrhizal plants (Krishna et al. 2008).
et al. (2000) suggested dipping of apical and Size of the shoot tip explants is important
nodal segments in 0.5% PVP + 10% sucrose for (Yang and Lüdders 1993; Thomas and Ravindra
30 s to reduce in vitro explant browning. Mango 1997; Chandra et al. 2004; Hare Krishna et al.
tissues darken very quickly in vitro as a result of 2008), as it is related to endogenous microbial
action of the enzyme polyphenol oxidase load and the presence of secondary metabolites
(PPO) (Litz and Vijayakumar 1988). Sharma and that cause browning and necrosis. This seems to
Singh (2002) reported that etiolated apical be related to the number of cut petioles that are in
mango shoots upon in vitro culture showed a contact with the plant growth medium (Thomas
marked decline in PPO activity and tissue phenol and Ravindra 1997). The most appropriate shoot
content suggesting a negative correlation tip length ranges from 5 to 7 cm. Smaller
between PPO activity and phenol content and explants showed less microbial contamination
explant survival. Krishna (2006) also observed a and browning but poor culture establishment
marked decline in total phenols, peroxidase and (Yang and Lüdders 1993; Thomas and Ravindra
PPO activities in etiolated mango shoots in 1997; Chandra et al. 2004).
comparison to the non-etiolated control. The Yang and Lüdders (1993) reported the best
in vitro phenol exudation was much lower in results on mango in vitro shoot establishment,
etiolated shoots leading to higher explant sur- although their study involved young seedling
vival and reduced necrosis. shoot tips and nodal explants, not elite material.
136 C. Petri et al.
Explants were collected in May and June from 2- explant response (Thomas and Ravindra 1997;
year-old mango seedlings growing in a green- Chandra et al. 2004; Samaan et al. 2007; Krishna
house. Plant materials were surface disinfested et al. 2008); however, the procedures only suc-
by successive immersion in 2% NaOCl plus ceeded to delay microbial contamination and,
0.1% Tween® 20 for 15 min, and after 5–10 h, eventually, high contamination levels caused
re-surface disinfested for 10 min, and rinsed death (Chandra et al. 2004; Samaan et al. 2007).
three times with sterile distilled water. Subse- With respect to in vitro shoot multiplication,
quently, explants were cultured on plant growth very little information is available. Samaan et al.
medium consisting of G salts and vitamins (Yang (2007) designed a proliferation medium for
et al. 1984), 30 g/L sucrose, 300 mg/L casein shoots of the rootstock ‘Hindy Sinnara’ (viz.
hydrolysate, 300 mg/L glutamine, 100 mg/L ‘Hindi be-Sennara’). Defoliated in vitro estab-
myoinositol, 1.5 g/L gelrite and 1.5 g/L Difco lished shoots of 1–3 cm length were cultured on
Bacto-agar. Medium was supplemented with B5 (Gamborg et al. 1968) basal medium sup-
1.0 mg/L benzyladenine (BA), 1.0 mg/L zeatin, plemented with IBA (0.5 mg/L), BA, zeatin and
2.0 mg/L N6-(2-isopentenyl)adenine (2iP) IAA (each at 1.0 mg/L) and 2iP (2.0 mg/L),
1.0 mg/L indole acetic acid (IAA), and 0.5 mg/L casein hydrolysate and glutamine (300 mg/L),
IBA. Later, Krishna et al. (2010) suggested that 3% sucrose and 2.5 g/L phytagel. They described
regardless of genotype and duration of pre- the production of 3.7 lateral shoots per initial
treatments, etiolation of new shoot sprouts + shoot (Samaan et al. 2007).
spray of imidazole (200 ppm) + agitation in For successful in vitro shoot establishment, it
0.2% PVP during March before culture improved is necessary to deal with the (i) growth response,
culture establishment and reduced microbial (ii) necrosis response, and (iii) microbial con-
infection of shoot cultures. The highest explant tamination. Strong disinfestation treatments
survival and least medium browning were reduce contamination but increase necrosis; the
recorded when 4.0 cm long explants were used. use of young shoots not only reduces contami-
Likewise, explants excised from older shoots, nation but also reduces the explant response and
i.e., from 3- to 4-month-old current season stimulates exudation and necrosis. According to
shoots, registered higher survival. Explants Krishna et al. (2008), factors responsible for
inoculated on the medium comprising B5 macro- successful establishment involve ontogenetic age
salts excluding (NH4)2SO4 and (NH4)2NO3 plus and pre-treatments to mother plants and explants
MS micro-salts and organics supplemented with and future research must be focused on the
0.5 mg/L NAA + 2.0 mg/L BA during March integration of micropropagation technology with
was most effective giving higher culture estab- microbial biotechnology. Explant disinfestation
lishment in ‘Amrapali’ (85.59%) with 4 cm must not only remove microbes from surfaces,
shoot tips, while it was minimum in ‘Pusa Aru- but bacteria inhabiting inner tissues and organs.
nima’ (58.10%) with 1 cm explants. Explants In vitro conditions are designed for plant growth
were subcultured onto fresh medium for several and development, but these conditions are also
days (as needed) to salvage the tissues from often ideal for bacterial and/or fungus multipli-
oxidation products that accumulated in the plant cation (Orlikowska et al. 2017).
growth medium. They were then subcultured at
3–4 week intervals. With this procedure, authors
described nearly 100% explant survival for both 8.3 In Vitro Regeneration
sorts of explants for all genotypes tested (Yang via Organogenesis and Somatic
and Lüdders 1993). Shoot tip explants responded Embryogenesis
at a frequency of ca. 64, 43 and 42% for ‘Tur-
pentine’, ‘Gomera’, and ‘Sabre’, respectively. Plant regeneration, both in nature and in vitro, is
Other studies also reported, in the best of the de novo organogenesis, in which plant cuttings
cases, 50% of explant survival and 25% of or explants first turn out in ectopic apical
meristems and subsequently develop shoots supplemented with 5 mg/L IBA for 24 h. Sub-
and/or roots. Plants can also regenerate through sequently, micro-shoots were transferred to
somatic embryogenesis in vitro, whereby isolated auxin-free semisolid rooting medium. A dark
protoplasts or cells first develop zygotic embryo- incubation period of 2 weeks, before culture
like structures that afterwards generate whole under a 16:8-h light:dark photoperiod
plants. De novo regeneration can occur directly (60 µmol m−2s−l), stimulated rooting compared
from parental tissues or indirectly through the with shoots under the photoperiod regime (Ara
formation of calluses. For more details about et al. 1998). Other studies also reported suc-
cellular origins and molecular mechanisms cessful rooting with plant growth medium sup-
involved in plant regeneration, see Ikeuchi et al. plemented with IBA but with lower efficiencies;
(2016). 20% and 0.4% for ‘Amrapali’ and ‘Hindy Sin-
nara’ (viz. ‘Hindi be Sennara’) shoots, respec-
tively (Raghuvanshi and Srivastava 1995;
8.3.1 Shoot and Root Organogenesis Samaan et al. 2007). In these cases, cultures were
directly incubated at 25 °C with a 16 h pho-
Singh et al. (1997) reported induction of callus toperiod provided by cool white fluorescent
on different explants such as epicotyl segment, lights (50–70 µmol m−2s−1).
leaf petiole and shoot tip excised from in vitro
germinated embryos. Maximum callus was
recorded on epicotyl segments, while direct root 8.3.2 Somatic Embryogenesis
organogenesis was noted in epicotyl and shoot
tip cultures with low level (0.5 mg/L) of 2,4-D Contrary to organogenesis, somatic embryogen-
alone. Raghuvanshi and Srivastava (1995) esis has been successfully achieved with different
described indirect shoot regeneration from fully cultivars (Table 8.2). The main source of
expanded, young ‘Amrapali’ leaves (Table 8.2). explants used for initiation of the culture
The pretreatment of explants in an agitated liquid involves nucellar tissue (maternal) excised from
plant growth medium was essential to overcome immature fruits. Nucellus derived plants are
the problem of phenol exudation and improved generally free from viruses and other endophytic
explant survival. Before cultivation of leaf pieces disease causing organisms, due to the absence of
on agar-gelled MS medium, explants were cul- vascular connection between the surrounding
tured in 100 ml liquid MS medium supplemented maternal tissue and the nucellus. Therefore,
with 0.05% PVP in 250 ml flasks on an orbital efficient recovery of somatic embryos particu-
shaker at 75 rpm for 24 h with the liquid medium larly in monoembryonic mango cultivars would
refreshed at 2-h intervals. For the shoot induction eliminate systemic pathogens (Litz 1984).
medium, multiple shoots were produced with Embryogenic cultures have also been reported
several combinations of plant growth regulators. from immature cotyledons of zygotic embryos
The optimum medium contained 1.1 µM IAA (Xiao et al. 2004). Mango somatic embryogen-
and 17.8 µM BA, with >4 shoots per explant esis from nucellar explants was first reported by
(Raghuvanshi and Srivastava 1995). Litz and collaborators (Litz et al. 1982, 1984;
Root formation has been obtained from Litz and Schaffer 1987). Two publications by
in vitro shoots. Ara et al. (1998) developed an DeWald and collaborators in 1989 have formed
efficient two-step protocol for microshoots the basis for most subsequent work (DeWald
obtained from nucellar somatic embryos et al. 1989a, b). The procedure broadly com-
(‘Amrapali’). Maximum rooting success prises four stages (Fig. 8.2): (1) induction,
(89.71%) was achieved when explants were first (2) maintenance (proliferation), (3) maturation,
cultured in liquid rooting induction medium and (4) germination of somatic embryos.
138 C. Petri et al.
Table 8.2 Regeneration of Mangifera indica L. by organogenesis and somatic embryogenesis

Genotype Explant Medium + growth Results Reference
regulators
‘Turpentine N2- Ovules Modified MS + CW Somatic Litz et al. (1982)
17-2’, ‘Heart’, embryogenesis
‘Sabre’, ‘Ono’,
‘Chino’
‘Chino’, ‘Ono’ Nucellus & (1) Modified MS + CW or (1) PEM, Litz et al. 1984
globular 2, 4-D proliferation
adventitious (2) Modified MS (2) Somatic
proembryos (3) Modified MS + BA embryogenesis
(3) SE germination
‘Parris’, ‘Peach’, Nucellus Modified MS + 2, 4-D Somatic Litz and Schaffer
‘Irwin’, ‘Keitt’, embryogenesis (1987)
‘Tommy Atkins’
‘Parris’, ‘James Nucellus (1) Modified B5 (1) PEM DeWald et al.
Saigon’, ‘Tommy macros + MS micros & (2) Proliferation (1989a, b); Litz
Atkins’, vit. + 2, 4-D (3) Somatic and Yurgalevitch
‘Tutehau’ (2) Modified B5 embryogenesis (1997)
macros + MS micros & (4) SE maturation
vit. + 2, 4-D + kinetin (5) Germination
(3) B5 macros + MS
micros & vit + CW
(4) B5 macros + MS
micros & vit + CW
(5) Half
B5 + CW + casein
‘Alphonso’, Nucellus (1) MS + 2, 4-D & GA3 (1) PEM, direct Jana et al. (1994)
‘Mundan’, (2) Half somatic
‘Baneshan’ MS + ABA + CW embryogenesis
(3) MS + BA (2) SE maturation
(3) SE germination
‘Hindi’ Nucellus (1) B5 macros + MS (1) PEM Monsalud et al.
micros & vit. + 2, 4-D (2) Somatic (1995)
(2) B5 macros + MS embryogenesis
micros & vit. + BA (3) SE maturation
(3) B5 macros + MS
micros &
vit. + AC + CW + ABA
‘Amrapali’ Young fully (1) MS + BA + IAA or (1) Bud Raghuvanshiand
expanded NAA regeneration & Srivastava (1995)
leaves (2) MS + IBA elongation
(2) Root formation
‘Carabao’ Zygotic B5 macros + MS micros & Zygotic embryo Pliego-Alfaro
embryos vit. + CW maturation and et al. (1996a)
germination
‘Hindi’ Nucellus (1) B5 macros + MS (1) PEM Pliego-Alfaro
micros & vit. + 2, 4-D (2) Somatic et al. (1996b)
(2) B5 macros + MS embryogenesis
micros & vit. (3) S. E. maturation
(3) B5 macros + MS
micros & vit. + ABA
+mannitol
(continued)

regulators
‘Carabao’ Nucellus (1) B5 macros + MS (1) PEM, Lad et al. (1997)
micros & vit. + 2, 4-D proliferation
(2) B5 macros + MS (2) Somatic
micros & vit. embryogenesis
(3) B5 macros + MS (3) S. E. maturation
micros &
vit. + Kinetin + BA
‘Hindi’, Nucellus Modified B5 macros + MS PEM Litz et al. (1998)
‘Nam Doc Mai’, micros & vit. + 2, 4-
‘Lippens’, D + nurse culture
‘Tommy Atkins’
‘Amrapali’, Nucellus (1) Modified MS + 2, 4-D (1) PEM, Ara et al. (2000b)
‘Chausa’ (2) B5 macros + MS proliferation
micros (2) Somatic
(3) Half MS + GA3 embryogenesis &
S.E: maturation
(3) Germination
‘Arka Anmol’ Nucellus (1) RO + AC + 2, 4- (1) PEM, Somatic Thomas (1999)
D + GA3 embryogenesis
(2) Modified (2) S. E.
B5/RO + AC + 2, 4- development
D + GA3 + CW + Casein (3) S.E. maturation
(3) Modified (4) Germination
B5/RO + ABA
(4) Modified B5 + TDZ
‘Amrapali’ Protoplasts (1) B5 macros + MS (1) Microcalli Ara et al. (2000a)
from nucellus micros & vit + 2, 4-D formation
micros & vit + Kinetin embryogenesis,
(3) B5 macros + MS proliferation
micros & vit + GA3 (3) Germination
(4) B5 macros + MS (4) Shoot and root
micros & vit elongation
‘Carabao’ Nucellus (1) BP medium + 2, 4- (1) PEM, Somatic Pateña et al.
D + CW embryogenesis, (2002)
(2) BP maturation,
medium + CW + AC germination
(2) Plantlet
conversion
‘Ataulfo’ Nucellus 1)Modified B5 (1) PEM, Rivera-
macros + MS micros & proliferation Dominguez et al.
vit + 2, 4-D (2) Somatic (2004)
(2) Modified B5 embryogenesis
macros + MS micros & (3) SE maturation,
vit + BA germination
(3) Modified B5
macros + MS micros &
vit + CW
‘Zi-Hua’ Immature (1) MS + 2,4- (1) PEM Xiao et al. (2004)
cotyledons D + GA3 + CW + AC (2) Embryogenesis,
(2) B5 macros + MS maturation
micros & vit + IBA + AC (3) Germination
(3) B5 macros + MS
micros & vit + Kinetin
(continued)
140 C. Petri et al.

regulators
‘Amrapali’ Nucellus (1) Modified MS (1) PEM Ara et al. (2004)
(2) Modified MS + 2,4-D (2) PEM
or NAA maintenance
micros & vit embryogenesis
(4) Modified B5 (4) Maturation,
macros + MS micros & germination
vit + GA3
‘Chaunsa’, Nucellus MS + 2,4-D PEM Usman et al.
‘Anwar Rataul’ (2005)
‘Kurakkan’ Nucellus (1) MS + 2,4-D + malt (1) PEM Mishra et al.
extract + spermidine (2) PEM (2010)
(2) MS +2,4-D maintenance
(3) (3) Somatic
MS + ABA + IAA + PEG embryogenesis
(4) MS + NAA (4) Maturation,
+kinetin + glutamine germination
‘Carabao’ Nucellus (1) B5 macros + MS (1) PEM, Pateña and Barba
micros & vit + 2,4- proliferation, (2011)
D + CW germination
(2) B5 macros + MS (2) Plantlet
micros & conversion
vit + AC + kinetin
‘Zebda’, Nucellus (1) B5 + 2,4-D (1) PEM, Nower (2013)
‘Sedeek’, ‘Hindi’ (2) B5 Proliferation
(3) B5 macros + MS (2) Maturation
micros (3) Germination
‘Baramasi’ Nucellus (1) B5 macros + MS (1) PEM Al-Busaidi et al.
micros & vit + 2,4- (2) Proliferation, (2016)
D + BA + Glu + ME Maturation
(2) B5 macros + MS (3) Germination
micros & BA
(3) B5 macros + MS
micros &
vit + Kinetin + GA3
‘Alphonso’, Nucellus (1) B5 macros + MS (1) PEM Shukla et al.
‘Carabao’, micros & vit + 2,4- (2) Proliferation (2016)
‘Turpentine’ D + BA (3) Maturation
(2) B5 macros + MS (4) Germination
micros & vit
(3) B5 macros + MS
micros &
vit + IAA + ABA
(4) B5 macros + MS
micros & vit
‘Olour’, Nucellus (1) RO + MS micros & (1) PEM, Sajana et al.
‘Carabao’ vit + AC + 2,4-D + GA3 Proliferation (2019)
2,4-D: 2,4- dichlorophenoxy acetic acid; ABA: Abcisic acid; AC: activated charcoal; B5: (Gamborg et al. 1968); BA:
Benzyladenine; BP = Barba & Pateña formulation (Pateña et al. 2002); CW: Coconut water; GA3: Giberellic acid; IAA:
Indol-acetic acid; IBA: Indol-butyric acid; MS: (Murashige and Skoog 1962); NAA: Naphtalen-acetic acid; PEM: Pro-
Embryogenic Masses; RO: Rugini Olive medium (Rugini 1984); SE: Somatic embryos; TDZ: Thidiazuron; WPM:
Woody Plant Medium (Lloyd and McCown 1980)
Fig. 8.2 a Embryogenic

‘Tommy Atkins’ mango a b
suspension. b Globular stage
‘Hindi be Sennara’ somatic
embryos. c Heart stage
somatic embryos of ‘Keitt’.
d Mature ‘Nam Doc Mai’
somatic embryos beggining to
germinate. e Plant recovery
from ‘Keitt’ somatic embryo
c d
e
142 C. Petri et al.
8.3.2.1 Explant Collection 2,4-D together with other growth regulators, such
and Induction of Cultures as gibberellic acid, NAA or kinetin (Jana et al.
Immature fruits from 30 to 40 days after polli- 1994; Thomas 1999; Ara et al. 2004; Shukla
nation are used as the source of nucellar explants. et al. 2016). When immature cotyledons were
Embryogenic competence has been related to the used as explants, indole butyric acid (IBA) suc-
developmental stage of the nucellus at the time of cessfully induced the generation of embryogenic
explanting and is influenced by the physiological cultures (Xiao et al. 2004). The induction of
condition of the tree (Litz and Hormaza 2020). embryogenic competence has been shown to be
The fruits are surface-sterilized for 10 min with highly genotype dependent but unrelated to
ethanol 70% (v/v), 30 min with 20–30% (v/v) polyembryony or monoembryony (Litz et al.
domestic bleach containing Tween 20, and then 1998; Ara et al. 2000b; Wei et al. 2013, Shukla
rinsed twice in sterile distilled water. The ovules et al. 2016). An interesting study with ‘Tommy
are removed from fruits that have been bisected Atkins’ (monoembryonic) and ‘Tutehau’
along the longitudinal axis. The embryo mass is (polyembryonic) revealed more ethylene pro-
discarded from each bisected ovule. Ovule halves duction in the monoembryonic cultures than in
are positioned so that the nucellar tissue is in those of the polyembryonic genotype (Litz and
contact with the induction medium (DeWald Yurgalevitch 1997). Induction of embryogenic
et al. 1989a). Alternatively, the nucellus can be competence is more sensitive to the activity of
removed from the bisected ovules and placed on spermidine synthase than to the activity of SAM
the induction medium (Litz and Hormaza 2020). decarboxylase, which confirmed earlier studies
DeWald et al. (1989a) optimized a number of involving the effects of spermidine on induction
parameters for induction of somatic embryogen- of somatic embryogenesis in mango (Litz and
esis from nucellar explants. They determined that Schaffer 1987).
growth of the cultures in suspension was more Currently, a ‘standard’ procedure with nucel-
efficient than on solid medium. However, sub- lar explants utilizes a basal medium consisting of
culturing onto semisolid medium with gellan B5 (Gamborg et al. 1968) major salts without
gum was crucial to obtain morphological normal (NH4)2SO4, MS minor salts and vitamins (Mur-
somatic embryos. They also determined that the ashige and Skoog 1962), 60.0 g/L sucrose,
optimum induction growth medium consisted of 400.0 mg/L glutamine, 4.5 µM 2,4-D and
modified B5 basal medium (Gamborg et al. 2.0 g/L gellan gum (Litz and Hormaza 2020).
1968) (with 25 mM KNO3 as the only source of The cultures are incubated in darkness at
inorganic nitrogen) and 5–6% sucrose to aug- 25 ± 1 °C. Medium must be refreshed fre-
ment the recovery of normally differentiated quently (sometimes as frequently as 1 or 2-day
heart-shaped embryos. intervals) to reduce phenolic exudation and
The plant growth regulator 2,4- explant necrosis.
dichlorophenoxyacetic acid (2,4-D) is essential
for induction of embryogenic competence from 8.3.2.2 Maintenance
the nucellus. Lad et al. (1997) determined that a Three to nine weeks after nucellus explanting,
minimum of 7-day pulse with 4.5 µM 2,4-D was embryogenic cultures usually appear and are
necessary for induction from ‘Carabao’ nucellar creamy-white and friable, and consist of pro-
explants and embryogenic competence was embryonic masses (PEMs) (DeWald et al.
optimum after a minimum of 28-day exposure to 1989a). PEM proliferation is normally performed
2,4-D. Most reports indicate that 2,4-D is by inoculating ca. 200 to 300 mg of PEMs and
essential for induction (DeWald et al. 1989a, b; culturing it in liquid maintenance medium of the
Pliego-Alfaro et al. 1996b; Lad et al. 1997; Ara same formulation as the induction medium (Litz
et al. 2000b; Singh et al. 2002; Sulekha and et al. 1984; DeWald et al. 1989a; Pliego-Alfaro
Rajmohan 2004), although other studies used et al. 1996b; Lad et al. 1997; Ara et al. 2004;
Rivera-Domínguez et al. 2004). The PEMs are heart shaped and early cotyledonary stage
subcultured into liquid medium in Erlenmeyer somatic embryos (Shukla et al. 2016).
flasks and maintained on a rotary shaker at about Approximately 3 weeks are required for heart
100 rpm at 22–25 °C in darkness (Fig. 8.2A). stage somatic embryos to develop from PEMs.
Subcultures to fresh medium are usually done at Subsequently, somatic embryos are transferred to
5–7 day intervals. The establishment of rapidly semisolid maturation medium for 2–5 more
proliferating suspension cultures is highly culti- months (Fig. 8.2C). Maturation is an important
var dependent (Litz and Hormaza 2020). step to establish bipolarity, minimize fasciation
The PEMs develop globular somatic embryos and synchronize the development of somatic
(Fig. 8.2B) in the presence of a primary induc- embryos.
tion agent, generally 2,4-D. In suspension culture Mango somatic embryos that develop on
and semisolid medium, the PEMs increase in size semisolid medium usually grow more vigorously
and their protoderm dedifferentiates becoming and they appear morphologically normal.
embryogenic. After that, in the presence of 2,4- Somatic embryos that develop in suspension
D, secondary globular somatic embryos develop culture can exhibit developmental abnormalities,
from embryogenic cells in the protoderm (Litz i.e., polycotyledony, loss of bipolarity, fasciation
and Hormaza 2020). Although culture into liquid and hyperhydricity. Typically, somatic embryos
medium reduces tissue browning, some authors become hyperhydric during the early cotyle-
maintain the cultures on semisolid medium. donary stage of development. Following sub-
Shifting the base medium from B5 medium culture onto semisolid maturation medium these
(Gamborg et al. 1968) to Barba and Pateña hyperhydric somatic embryos rapidly increase in
(BP) medium (Pateña et al. 2002) has been size; however, they are unable to develop to
reported to control browning. maturity and they never germinate (Monsalud
et al. 1995).
8.3.2.3 Somatic Embryo Production Zygotic embryos of mango require 3–
and Maturation 4 months to reach maturity. Because of the long
Somatic embryo development is stimulated by maturation period for somatic embryos, manip-
transferring globular PEMs from the maintenance ulation of the culture medium is necessary to
medium onto semisolid or into liquid medium inhibit precocious germination and abnormal
without growth regulators. DeWald et al. (1989a) embryo development (Fig. 8.2D). The addition
found subculture onto semisolid medium essen- of abscisic acid (ABA) to the maturation med-
tial for high-frequency recovery of morphologi- ium, high osmolarity or low temperatures
cally normal somatic embryos. They also reported reduced precocious germination and permitted
that sucrose concentration (5–6% w/v) and filter the production of good quality somatic embryos
sterilized coconut water (CW) at 20% (v/v) (Monsalud et al. 1995; Pliego-Alfaro et al.
enhanced embryo development (DeWald et al. 1996a, b). The increase of sucrose concentration
1989a, b). Some reports indicate that the addition up to 6% for ‘Parris’ improved the maturation of
of cytokinins in the proliferation medium is normal somatic embryos. Similar results were
beneficial. Addition of kinetin (4.6 µM) observed with ABA combined with coconut
improved the subsequent production of ‘Amra- water with lower sucrose concentration (3%), but
pali’ somatic embryos that could mature normally the effect of ABA was masked when 6% sucrose
(Ara et al. 2000a). BA (2.2 µM) allowed the was used (DeWald et al. 1989b).
generation of large numbers of somatic embryos Standard maturation medium consists of
from nucellar explants of ‘Alphonso’, ‘Carabao’ modified B5 major salts, MS minor salts and
and ‘Turpentine’ and accelerated the development vitamins, 2.74 mM glutamine, 0.025% (w/v)
from PEMs and globular somatic embryos into casein hydrolysate, 20% (v/v) coconut water,
144 C. Petri et al.
40 g/L sucrose and 2 g/L gellan gum (DeWald strength B5 medium without organic addenda (35
et al. 1989b). The sucrose concentration is and 27%, respectively) (DeWald et al. 1989b).
gradually reduced to 10 g/L during sequential Plantlet conversion rate from germinated
subcultures to fresh plant growth medium. Cul- embryos has averaged 30–40% (Ara et al. 2000a,
tures are maintained in darkness at 25 ± 1 °C b, 2004; Rivera-Domínguez et al. 2004; Xiao
(Litz and Hormaza 2020). et al. 2004; Pateña and Barba 2011). In vitro
plants can be directly potted in soil or ex vitro
8.3.2.4 Germination and Conversion grafted. Successful acclimatization of directly
into Plantlets potted plants has been reported for several cul-
Mango somatic embryos are able to germinate tivars such as ‘Alphonso’ (67% survival rate),
after a 3- to 5-month maturation period, at which ‘Carabao’ (27% survival rate), ‘Turpentine’
time they are transferred to light conditions (16-h (50% survival rate) and ‘Parris’ (survival rate not
photoperiod and 60–70 µmol m−2 s−1 light indicated) (DeWald et al. 1989b; Shukla et al.
intensity) and sucrose concentration is reduced to 2016). As the root system develops slowly,
10 g/L. During germination the hypocotyl elon- periodic applications of macro- and micro-
gates, followed by growth of the single tap root elements as a foliar spray have been necessary
from the radicular end. The shoot apex emerges for successful acclimatization of ‘Parris’ plantlets
approximately 2 weeks after germination. (DeWald et al. 1989b). For ‘Carabao’, ex vitro
Survival rate and conversion to plantlet is grafting performed significantly better than direct
variable among genotypes and is affected by transfer of plantlets to soil, with percent survival
different factors. Germination rate was signifi- ranging among trials from 14.3% to 50.0%
cantly increased in liquid medium reaching up to compared to 0%–16.7% for the potted plants.
71.56 and 51.56% for ‘Chausa’ and ‘Amrapali’ Plants grafted ex vitro grew and produced new
somatic embryos, respectively, compared with leaves and shoots within 14–27 days (Pateña and
12.67 and 6.82% in semisolid medium (Ara et al. Barba 2011).
2000b). Furthermore, conversion into plantlets
was only achieved when embryos were cultured
in liquid medium (Ara et al. 2000b). However, 8.4 Encapsulation
germination and conversion of ‘Parris’ and and Cryopreservation
‘Carabao’ somatic embryos have been reported
in semisolid medium (DeWald et al. 1989b; Cryopreservation is a method for long-term
Pateña and Barba 2011) (Fig. 8.2E). storage of plant cells or tissues in liquid nitro-
The germination medium has been modified by gen (−196 °C), keeping them viable, with no
the addition of gibberellic acid (GA3) or cytoki- metabolic deterioration and cell division, free of
nins such as kinetin, BA or thidiazuron germs, and revivable upon thawing. A typical
(TDZ) (Lad et al. 1997; Thomas 1999; Ara et al. cryopreservation cycle consists of stages of
2000a, b, 2004; Xiao et al. 2004). Nevertheless, selection of tissue, preparation of material,
germination and plantlet development have been freezing, storage in liquid nitrogen, thawing,
achieved without any plant growth regulators but washing, reculturing, and, finally, regeneration of
with the addition of complex organic addenda plantlets (Reed 2008). Another important method
such as coconut water (CW), malt extract or casein for preservation is the encapsulation-dehydration
hydrolysate (DeWald et al. 1989b; Pliego-Alfaro method. Explants such as shoot tips or somatic
et al. 1996a; Rivera-Domínguez et al. 2004; embryos are encapsulated in alginate beads to
Shukla et al. 2016). Modified B5 medium sup- form artificial seeds. After revival, these can be
plemented with CW and casein hydrolysate sig- used for direct germination. The use of somatic
nificantly increased ‘Parris’ embryo germination embryos for synthetic seed production has been
rate (63%) compared with full-strength or half- considered. Cotyledonary-stage somatic embryos
originating from nucellar explants of ‘Amrapali’ recovery for evaluation. Hence, in ovulo, embryo
were encapsulated individually in 2% alginate culture was proposed to improve breeding effi-
gel (Ara et al. 1999). The encapsulated somatic ciency, which can be achieved by pollinating
embryos germinated successfully more flowers per panicle (8–12) followed by
(73.61 ± 7.08% germination rate) on 0.6% agar- in vitro embryo culture. Immature fruitlets
gelled medium containing B5 major salts, MS (45 days) of different cross combinations
minor salts and organics, 3% sucrose and 2.9 (‘Amrapali’ ‘Sensation’, ‘Amra-
mM GA3. From these germinated somatic pali’ ‘Tommy Atkins’) were cultured on
embryos, about 45% developed into plantlets and solidified MS medium supplemented with
were successfully established in soil (Ara et al. 1.0 mg/L BA, 0.5 mg/L IAA, 400 mg/L glu-
1999). This report demonstrated the possibility of tamine, 200 mg/L casein hydrolysate, 100 mg/L
plant regeneration from synthetic seeds. Wu et al. activated charcoal, and 45 g/L sucrose. The
(2007) found embryogenic mango cultures hybridization efficiency was enhanced with the
(‘Zihua’) to be more responsive to regeneration higher recovery of hybrid embryos per panicle
after cryopreservation. (Fig. 8.3). The cultured embryos could be
effectively matured, germinated and hardened in
glass jars filled with sterile peat: perlite (4:1)
8.5 Embryo Culture moistened with ¼ MS salts solution (pH 5.8).
This technique was also effective in rescuing
High fruit drop and embryo abortion in hand- dropped developing fertilized fruitlets due to
pollinated panicles in mango are the major lim- adverse weather conditions. The technique
iting factors, which lead to meager seedling (F1) increased the breeding efficiency in mango where
Fig. 8.3 a In vitro embryo

culture initiation. b Initiation
of germination of matured
a b
embryo. c Formation of a
rooted hybrid seedling.
d ‘Amrapali’ x ‘Sensation’
hybrid seedling in primary
in vitro hardening
c d
146 C. Petri et al.
the final in vivo fruit recovery is not more than 1 transformed PEMs in liquid selection medium
percent, i.e., one or two fruits per panicle until ceased at 12.5 mg/L kanamycin, whereas the
maturity. This procedure may also aid in recov- growth of PEMs and mature somatic embryos on
ering hybrids in cross combinations where semisolid medium was inhibited by 200 mg/L
embryo degenerates due to pre- or post-zygotic kanamycin (Mathews and Litz 1990).
barriers in conventional breeding.
Later, Sahijram et al. (2005) standardized the
method for raising hybrids in the cross 8.6.1 Transformation Procedures
‘Alphonso’ ‘Kerala Dwarf’ in 3 months. They
further proposed ex vitro shoot-tip grafting for Agrobacterium tumefaciens-mediated transfor-
rescuing in vitro raised hybrid plants on in vivo mation procedures are briefly described accord-
raised rootstocks under shade net. Graft union ing to Mathews et al. (1992). Embryogenic
was successful in 67% of the hybrids in 4– cultures are established according to the proce-
6 weeks. Perez-Hernandez and Grajal-Martın dure described by DeWald et al. (1989a, b).
(2011) suggested the role of coconut water in For bacterial culture preparation, a single
embryo culture in ‘Lippens’ and ‘Keitt’. Com- colony from semisolid LB medium of a disarmed
plete plantlets could be obtained at a frequency A. tumefaciens strain harboring the desired bin-
above 83% for both cultivars. Recently, Singh ary plasmid is inoculated into 5 ml of liquid LB
(2016) proposed bio-hardening of in vitro raised with the appropriate antibiotics for plasmid and
mango plantlets. Hybrid plantlets (OP: ‘Amra- bacterium strain selection. After ca. 16 h at 28 °
pali’, ‘PusaArunima’, ‘Hybrid 8-11’, HP: C, the culture is transferred to 50 ml liquid LB
‘Amrapali’ ‘Sensation’ and ‘Amrapali’ supplemented with 30 µM acetosyringone, and
‘Tommy Atkins’) were successfully biohardened incubated at 200 rpm for 16 h at 28 °C.
using arbuscular mycorrhizal fungi and Asper- Actively growing PEMs are infected with A.
gilus niger during primary hardening. tumefaciens. For co-cultivation, 3.0 g of PEMs
of < 1000 µm diameter maintained in liquid
medium are lightly wounded with a sterile artist’s
8.6 Genetic Transformation paint brush and cultured in 50 ml of liquid
maintenance medium to which 0.05 ml of a log-
Genetic transformation of mango, with selectable phase of the acetosyringone-activated A. tume-
and reporter marker genes, has been demon- faciens culture is added. Flasks are maintained on
strated using Agrobacterium tumefaciens (Math- a rotary shaker at 120 rpm. PEMs are transferred
ews et al. 1992, 1993; Cruz-Hernandez and Litz to fresh maintenance medium every 24 h for
1997; Samanta et al. 2007) as well as by biolis- 3 days.
tics (Cruz-Hernandez et al. 2000) (Table 8.3). After 3 days of co-cultivation, infected PEMs
Most of these publications showed uniformly are plated on semisolid maintenance medium
transformed PEM and/or somatic embryos but containing 200 mg/L kanamycin (for transgenic
failed on the recovery of a complete plantlet cell selection) and 500 mg/L cefotaxime (for A.
following transformation. Mathews et al. (1993) tumefaciens elimination). Later, PEMs are sub-
reported the recovery of transgenic ‘Keitt’ plants. cultured onto the same medium every 3 weeks
Genetic transformation has targeted PEMs, for 10 months and are thereafter maintained on
using the nptII marker gene (resistance to selection medium (200 mg/L kanamycin) with-
aminoglycoside antibiotics; kanamycin) to select out cefotaxime. Following co-cultivation, PEMs
for transformed tissues. The sensitivity of non- turn black within 5–7 days after planting on
transformed tissues to kanamycin is dependent selection medium containing kanamycin.
on the stage of the embryogenic culture at the Agrobacterium-inoculated cultures show vigor-
time of treatment and the form of exposure ous growth on selection medium over a period of
(Mathews and Litz 1990). Growth of non- 150 days whereas non-transformed control
Table 8.3 Genetic transformation in mango

Cultivar Explant Technique Gene(s) Reference
‘Hindi’ PEM from nucellus Agrobacterium nptII, gus Mathews et al.
tumefaciens (1992)
(strain A280)
‘Keitt’ Segments of somatic embryos A. tumefaciens nptII Mathews et al.
derived from zygotic embryos (strain C58C1) (1993)
‘Hindi’ PEM from nucellus A. tumefaciens nptII, gus, Cruz-
(strain antisense ACC Hernandez and
LBA4404) synthase Litz (1997)
nptII, gus,
antisenseACC
oxidase
nptII, gus,
antisense
alternative oxidase
‘Carabao’ PEM from nucellus Biolistic nptII, gus Cruz-
‘Kesington (transient transf.) Hernandez
Pride’ nptII, gfp et al. (2000)
(stable transf.)
‘Vellaikolumban’ PEM from nucellus A. tumefaciens nptII, gus Samanta et al.
(strain (2007)
LBA4404)
‘Kent’, Somatic embryos Agrobacterium nptII, gus Chavarri et al.
‘Haden’, rhizogenes (2010)
‘Madame
Francis’
PEM Pro-embryogenic masses
PEMs do not show signs of cell proliferation. selection medium are transferred at 3–5 day
Such areas of fresh PEM proliferation in the intervals to fresh medium.
transformed cultures are very distinct and easily
separable from the dark tissue. These fresh PEMs
are subcultured onto fresh selection medium and 8.6.2 Applications of Genetic
continue to proliferate. Cultures generally consist Transformation
of both transformed and non-transformed PEMs
(Mathews et al. 1992). Therefore, a stepwise Mango genetic transformation could assist
selection strategy has been used to eliminate breeding programs to address some of the major
chimeras: (1) initial screening at 200 mg/L breeding objectives, such as resistance to
kanamycin to enable growth of transformed anthracnose and delay or control of ripening.
cells; (2) further screening at 400 mg/L kana- Anthracnose, caused by the fungus Col-
mycin to reduce chimeras; and (3) recovery of letotrichum gloeosporioides Penz., is the main
pure transformed clones of PEMs in liquid disease affecting mango fruit production and post-
selection medium with 100 mg/L kanamycin. harvest. Most commercial mango cultivars are
Pro-embryos from the liquid selection med- highly susceptible and conventional breeding to
ium are transferred to a liquid embryogenesis introduce greater resistance into new cultivars has
medium (maintenance medium without 2,4-D, been unsuccessful (Jayasankar and Litz 1998).
supplemented with 0.22 µM BA) containing Alternative approaches could involve the use of
100 mg/L kanamycin for 30–50 days for somatic in vitro selection and genetic transformation to
embryo development. All cultures in liquid enhance resistance to anthracnose in existing
148 C. Petri et al.
cultivars. Jayasankar and Litz (1998) induced 8.7 Conclusions and Future Work
somaclonal variation and selected resistant
embryogenic cultures from ‘Carabao’ and ‘Hindi’ Although mango is one of the five most important
through recurrent selection with increasing con- fruit crops worldwide in terms of production,
centrations of C. gloeosporioides culture filtrate classical genetic and biotechnological advances
and purified phytotoxin. Resistance to the patho- in this species lag well behind those in other
gen was related to the excretion of pathogenesis- woody perennial crops. New and increasingly
related proteins such as chitinases and glucanases cheaper sequencing technologies will result in a
(Jayasankar and Litz 1998). Some DNA markers qualitative change in breeding programs in
(RAPDs) were associated with the resistance trait, mango, especially since genome data are
with eight primers in ‘Carabao’ and five primers in increasingly been released in this crop. Biotech-
‘Hindi’ (Jayasankar et al. 1998). To the best our nology approaches can address several important
knowledge, quantitative trait loci (QTLs) or genes issues that limit mango production in different
associated with anthracnose resistance have not regions of the world. One example includes the
been described in mango. As soon as some can- optimization of in vitro propagation procedures
didate genes are identified, strategies involving that could reduce the dependence on polyem-
overexpression and/or silencing of those bryonic seedlings as rootstocks, facilitating the
genes/QTLs could be applied through genetic development of clonal rootstocks with selected
transformation techniques. interesting traits such as tolerance to salinity,
Cruz-Hernandez and Litz (1997) transformed drought or soil fungus diseases. Similarly, cry-
PEMs from ‘Hindi’ nucellar tissues with mango opreservation of embryogenic cultures for use as
antisense sequences of genes involved in fruit a backup for mango germplasm collections would
ripening, i.e., ACC synthase and ACC oxidase also facilitate the international exchange of
(ethylene synthesis), and alternative oxidase rapidly deteriorating genetic resources. New and
(respiratory metabolism). The antisense DNA promising genomic edition technologies such as
strategy causes silencing of the target sequence. CRISPR-Cas9 to address different major breeding
Antisense mRNA anneals to the endogenous objectives, e.g., fruit ripening, control of physio-
target mRNA. Consequently, dsRNA is formed logical disorders, tree size or resistance to pests
and post-transcription algene silencing specific to and diseases, might also be explored in mango.
the target sequence is triggered.
Stable integration of the transgenes into
mango PEMs and torpedo stage somatic embryos
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phenolic exudation, explant survival and axenic
Molecular Mapping and Breeding
in Mango 9
Pumipat Tongyoo, Janejira Duangjit,
Nimisha Sharma, and Julapark Chunwongse
Abstract etc. Further, there is lack of understanding in

heritability of the most important horticulture
The Mango (Mangifera indica L.) is a mem-
traits in mango. Therefore, by linking the
ber of family Anacardiaceae. It is one of the important traits with molecular characteristics
most important tropical fruit crops in the will help to improve the efficiency of mango
world. Most of the cultivars grown commer-
breeding programs. The genetic markers and
cially are selections rather than introducing by location in the genome that associated with
breeding programs. Although, traditional important traits are commonly identified by
breeding techniques cannot fulfill the demand
utilizing genetic map. Consequence in an
of improved cultivars to promote superior improvement of strong association between
quality traits due to many constraints like long traits and molecular marker in marker-assisted
juvenile phase, high heterozygosity, alternate
selection. With the help of genetic map,
bearing, polyembryony, heavy fruitlet drop, mango breeders can easily identify the poten-
tial parents and progeny at early stage.
Therefore, in this chapter, we have summa-
rized the linkage and genetic map generated
P. Tongyoo (&)
Center for Agricultural Biotechnology, Kasetsart
by mango researchers using various molecular
University, Kamphaeng Saen Campus, Nakhon markers, represented all 20 linkage groups
Pathom 73140, Thailand that could be utilized as valuable tool and
e-mail: pumipat.tong@ku.th database by mango breeders for trait-specific
J. Duangjit breeding.
Department of Horticulture, Faculty of Agriculture,
Kasetsart University, Bangkhen Campus, Bangkok
10900, Thailand 9.1 Introduction
e-mail: janejira.d@ku.th
N. Sharma The improvement in mango breeding program is
Division of Fruits and Horticultural Technology,
still challenging. There is huge varietal wealth
Indian Agricultural Research Institute, New Delhi
110012, India accessible; however, targeted breeding of mango
e-mail: nims17sharma@gmail.com is cumbersome. There are several constraints
J. Chunwongse generally faced by breeders like long generation
Department of Horticulture, Faculty of Agriculture at interval, inbreeding depression, poor fruit set,
KamphaengSaen, Kasetsart University, Kamphaeng unpredictable outcome due to high level of
Saen Campus, Nakhon Pathom 73140, Thailand
heterozygosity, polyembryony in some popular
e-mail: julapark.c@ku.th

https://doi.org/10.1007/978-3-030-47829-2_9
154 P. Tongyoo et al.
commercial cultivars, early post-zygotic auto- In the meanwhile, chromosomal rearrangements

incompatibility and extensive land area required (CRs) are considered as another genetic diversity
(Miller and Gross 2011). It remains an expensive factor during an evolutionary (Ayala and Coluzzi
and time-consuming process up to date. The 2005), which are also important to consider in
undesirable mango characters are incorporated breeding programs. It is obvious that molecular
by many environmental and physiological tools can facilitate development of new strategies
effects, which are commonly controlled by mul- for more efficient breeding in mango. Access to
tiple genes. To conquer these problems, molec- molecular markers linked to desirable alleles
ular biology has vast potential and further it underlying phenotypic traits greatly enhances the
reduced the uncertainty in trait-specific breeding breeding efficiency because of the possibility of
of mango. Recently, modern biotechnology, genetic screening at a very young age. In addi-
especially genomics, reviewed as a potential tool tion, the new plant breeding technologies
in the efficiency improvement in plant breeding (NPBTs) that facilitated cisgenesis and genome
program by selecting traits of interest at the editing approaches can enhance either pathogen
seedling stage using marker-assisted selection resistance or qualitative traits improvement by
(MAS). Systematic hybridization program with promoting or detracting at certain genes imme-
the help of advanced molecular approaches is in diately which a minimal modification in the tar-
progress in many countries. In molecular breed- get genome (Dalla Costa et al. 2017). Therefore,
ing program, the segregating markers in a new this will become a powerful approach in crop
generation are required which normally time improvement research under ‘green’ biotech-
consuming for developing these segregating nologies for long life crops. Thus, this chapter
population in fruit crops. Most economic traits in aims to describe how to implement molecular
crop plants show quantitative variation and are genetics in association to mango breeding.
thought to be controlled by multiple genes, most
of which have minor effects and only a few genes
have major effects (Falconer 1989). Establishing 9.2 Molecular Mapping
efficient selection based on genetic marker and Breeding in Mango
information from quantitative trait locus
(QTL) mapping would be able to increase gain The traditional way of performing plant breeding
per breeding cycle because of increased confi- is selection based on phenotypes. This method,
dence and certainty in the genetic selection. Due however, is a time-consuming especially in fruit
to the progress of DNA sequencing technology trees. The step that takes the longest time is
in the past few decades, SNPs provide the juvenile stage to become a fruit-bearing tree. In
greatest marker density, best potential for mango, it takes around 3–10 years for this juve-
automation, lowest cost per data point and as nile process (Iyer and Degani 1997; Bally et al.
unambiguous markers. The technology is also 2009). Even though, the struggles can be tackling
appropriate in data sharing because of there is no by grafting the desirable varieties onto the mature
platform-dependent information. Consequence in mango tree or by applying chemicals, the outcome
the reliable and producible analysis results can be deviated due to evolution (Bally et al.
without any uncertainty. It allows us to investi- 2009). Together with the fact that mango also has
gate a complete genome sequence of organisms. a long generation time, high natural fruit shed-
Because most trees’ genome is large, highly ding, high heterozygosity, cultivar incompatibil-
repetitive, and complex structure, genome ity and polyembryony, breeding mango
sequencing became an essential tool for the traditionally has been slow and challenging, and
genetic improvement of trees through a con- often times takes more than 20 years.
struction of physical map (Jiang et al. 2014; Selection at an early stage is needed to reduce
Poursarebani et al. 2014; Pan et al. 2016). It will the total time of the mango breeding, addition-
facilitate DNA marker traits linked identification. ally, this will also reduce amount of work, space,
9 Molecular Mapping and Breeding in Mango 155
and other resources. Early selection can be done 9.2.1 Mango Molecular Mapping
based only in some desired traits such as disease
resistance. However, other traits can be done Several genetic linkage maps were constructed
using marker-assisted selection or MAS, which is based on different molecular technologies
a technique using molecular markers that linked (Table 9.1). For example, a partial genetic link-
to a gene or quantitative trait loci (QTLs) of age map from a cross between ‘Alphonso’ and
interest. Nevertheless, molecular map construc- ‘Palmer’ was constructed based on 31 F1 pro-
tion needs to be made prior to the QTL mapping. genies (Chunwongse et al. 2015). In this study,
The development of dense molecular maps has 29 linkage groups covering a genetic distance in
sped up recently due to the advent of molecular total of 529.9 centiMorgan (cM). The genetic
markers. map is shown in Fig. 9.1. This map consisted of
Bi-parental crosses are required to construct a 67 restriction fragment length polymorphism
genetic linkage map, each parent must have (RFLP) markers and 9 microsatellite markers.
distinguishing features on either the morpholog- The same group also used RFLP and amplified
ical or molecular mapping level (e.g. difference fragment length polymorphism (AFLP) markers
in fruit color, difference in disease susceptibility). to study the genome of ‘Alphonso’ and ‘Palmer’
It is preferred to use nearly homozygous lines (Phumichai 2001). A two-way pseudo-testcross
(such as inbred lines) for genetic mapping as mapping strategy was used in this study. Genetic
used in self-pollinated species when possible. maps consisting of 74 linkage groups covering
However, it is more complicated to develop in 1,559.8 cM, and 71 linkage groups covering
bred lines from cross-pollinated species like 1,910.3 cM were constructed for ‘Alphonso’ and
mango. Moreover, there are not possible to get ‘Palmer’, respectively. Another genetic linkage
inbred lines because of inbreeding depression. map based on a cross between ‘Keitt’ and
Consequence to the used of half-sib or full-sib ‘Tommy-Atkins’ was also constructed by Kash-
progenies that developed from specific crosses kush et al. (2001). The linkage map displays 13
can be applied for genetic mapping of polymor- linkage groups that cover 161.5 cM by utilizing
phic molecular markers. 34 AFLP markers. There are some studies that
In most cases, F1 was utilized as shown in successfully constructed several linkage groups
Table 9.1. Generally, a full sib hybrid population similar with the expected number of chromo-
derived from differing phenotype parents are somes of mango haploid genomes (20). A con-
commonly used in breeding program rather than sensus map of mangoes from seven mapping
half-sib population from open-pollinated parents. populations was developed using 726 single
Furthermore, a sufficient number of individuals nucleotide polymorphism (SNP) markers. The
are also required for developing an accurate map was constructed by JoinMap and OneMap
genetic map (Staub et al. 1996). Most genetic software. The details of each linkage group are
maps constructed in mango used mapping pop- summarized in Table 9.2.
ulation in a range of 31–173 individuals A mango haploid genome size is estimated at
(Table 9.1). The three largest populations in 439 Mb, which consisted of 20 chromosome
Australia were constructed from their primary each haploid genome. The average chromosome
commercial mango cultivar ‘Kensington Pride’ size is estimated at 22 Mb. The total genetic
by crossing to ‘Irwin’, ‘Tommy-Atkins’, and distance in haploid genome is 2,890 cM, which
‘Creeper’. While the two F2 populations derived leads to the estimation for a cM at 150 Kb.
from self-pollination of ‘Tommy-Atkins’ and A specific locus-amplified fragment (SLAF)
‘Haden’ were also constructed in Florida (Arias library construction was used to generate 20
et al. 2012). linkage groups with total length 3,148.28 cM
Table 9.1 Details of genetic linkage map studies in mango (Mangifera indica L.) based on different crosses and
molecular markers
Mapping Population Population Number Type of Total Average References
population type size of markers length marker
markers spacing
(cM)
‘Alphonso’ and F1 31 197 RFLP(1) 1437.7 10.4 Phumichai
‘Palmer’ 650 AFLP (2) (2001)
‘Keitt’ and F1 29 34 AFLP(2) na(4) 4.75 Kashkush

‘Tommy- et al. (2001)
Atkins’
‘Keitt’ and F1 60 81 AFLP(2) 354.1 4.37 Fang et al.
‘Tommy- (2003)
Atkins’
‘Alphonso’ and F1 31 9 Microsatellite 529.9 6.97 Chunwongse
‘Palmer’ 67 RFLP (1) et al. (2015)
‘Jin-Hwang’ and F1 173 6,594 SLAF(3) 3148.28 0.48 Luo et al.

‘Irwin’ (2016)
‘Tommy- Self 60 726 SNPs(5) 2890.6 4.13 Kuhn et al.
Atkins’ pollinated (2017)
and‘Tommy-
Atkins’
‘Haden’ and F1 225
‘Tommy-
Atkins’
‘Haden’and Self 40
‘Haden’ Pollinated
‘NMBP1243’ F1 100
and ‘Kensington
Pride’
‘Creeper’ and F1 70
‘Kensington
Pride’
‘Irwin’ and F1 180
‘Kensington
Pride’
Tommy- F1 100
Atkins’and
‘Kensington
Pride’
(1) restriction fragment length polymorphism
(2) amplified fragment length polymorphism
(3) specific-locus amplified fragment
(4) not applicable
(5) single nucleotide polymorphism
Fig. 9.1 The 29 genetic map of mango from SSR markers (Chunwongse et al. 2015)
Fig. 9.1 (continued)
Table 9.2 Genetic map summary of mango developed by Kuhn et al. (2017) and Luo et al. (2016)
Linkage group Consensus map Kuhn et al. (2017) Integrated map (Luo et al. 2016)
Length (cM) Average distance (cM) Length (cM) Average distance (cM)
1 111.2 4.1 168.96 0.47
2 135.6 4.5 180.35 0.64
3 79.4 3.2 198.74 0.57
4 223.2 6.4 188.39 0.35
5 126.3 4.2 144.75 0.58
6 80.4 3.4 146.29 0.47
7 151.1 5.4 125.31 0.54
8 247.8 6 167.78 0.8
9 143.1 4.2 182.83 0.54
10 186.5 4.5 119.61 0.43
11 77.2 3.1 178.46 0.38
12 148.8 4.4 136.15 0.55
13 154.9 3.7 160.1 0.41
14 114.9 4.4 116.84 0.45
15 166.2 3.8 140.72 0.54
16 228 3.3 206.09 0.35
(continued)

Linkage group Consensus map Kuhn et al. (2017) Integrated map (Luo et al. 2016)
Length (cM) Average distance (cM) Length (cM) Average distance (cM)
17 156.7 2.8 132.75 0.59
18 76.5 3.8 140.96 0.64
19 126.7 3.8 193.2 0.4
20 156.1 3.7 122.95 0.42
Total 2,890.6 4.135 2,144.23 0.48
using HighMap strategy (Liu et al. 2014). The Moreover, molecular markers from the
genetic map utilized 6,594 SLAFs from 173 F1 genetic analysis can be used in the estimation of
populations constructed by a cross between ‘Jin- outcrossing rates in mango. Santos and Neto
Hwang’ and ‘Irwin’ (Luo et al. 2016). (2011) demonstrated it by using AFLP and
By comparing the average distance between microsatellite markers in a cross between
these two genetic maps, it shows the potential for ‘Haden’ and ‘Tommy Atkins’. These rates were
constructing a high-density genetic map that calculated using to tackle an outcrossing peren-
allows to implement a fine QTL mapping and nial crops issue. A multi-locus outcrossing rate
MAS in mango. The consensus genetic map of (tm) was estimated by counting number of
mango developed by Kuhn et al. (2017). High markers. The outcrossing rates ranged from 0.85
density map of mango is presented in Fig. 9.2. to 0.87 estimating by 7 AFLP markers and ran-
In addition, the significant association between ged from 0.83 to 0.91 by 3 microsatellite loci.
traits and SNPs markers for several traits was For preservation of these genetic variability of
also explored in this study. Mapped markers mango species, it must be concerned that they are
can be facilitated as anchors for further genetic predominantly open-pollinated. Any biometrical
linkage mapping and genome sequencing models applied to mangoes to estimate genetic
analysis of mango breeding programs in the parameters should consider the deviation from
future. random outcrossing.
Fig. 9.2 High density genetic map of mango (Modified from Luo et al. 2016)
9.2.2 Genes and QTL Mapped The successfully applied of three pairs of
microsatellite markers to identify 82 seedlings
In the past decade, the molecular marker and (14.69%) of 558 seedlings derived from 364
linkage map have not been applied directly to seeds of cultivar ‘Kaew007’ as a hybrid were
mango breeding programs, especially in complex reported. Many mango cultivars also gave a very
characteristics such as quality traits. By the low success of hybrid seedling. By using 14
number of mango germplasm in the Indian and random amplified polymorphic DNA (RAPD)
IndoChinese, this opens a possibility of utilizing primers, only 3% and 5% were recognized as a
GWAS as well as linkage disequilibrium strate- hybrid seedling in cultivars ‘Manila’ and
gies on mango. Moreover, it will lead to an ‘Ataulfo’, respectively. We found the height of a
genetic related traits utilization analysis as a mango seedling ‘Kaew007’ was not associated
next-generation breeding program (Barabaschi with a zygotic seedling (unpublished data). The
et al. 2016; Kang et al. 2016; Can et al. 2019). evaluation of polyembryony in the mango culti-
The mango genetic maps were produced from vars ‘Manila’ and ‘Ataulfo’ was also performed
different populations as basis of QTL analyses. using 14 RAPD primers in 100 seeds of each
But one major drawback of this approach is the cultivar. As a result, more than 80% of ‘Manila’
population size limitation which normally not and ‘Ataulfo’ seeds give two to four embryos
large enough which leads to the limitation of (Ochoa et al. 2012). Polyembryony in mango
recombination rates that can be occurred. Con- was proposed as controlling by only single
sequence in a low efficiency QTL detection. dominant gene (Aron et al. 1998). A significant
There are successful reports between traits and association in two of the three mapping popula-
SNP markers association in branching habit and tions was also reported as a single locus for
some fruit traits which are beak shape, blush polyembryony trait (Kuhn et al. 2017).
intensity, pulp color, and ground skin color. One
of the important mongo characteristics which is
embryo type was also reported by using crosses 9.2.4 Association Mapping Studies
between a monoembryonic maternal parent and a in Mango
polyembryonic paternal parent. The significant
association was shown in a single locus on a In case of mango, association mapping (AM) is
linkage group 8 (LG8) of a consensus map particularly suited to overcome some constraints
(Kuhn et al. 2017). like long generation time, labored trait evalua-
tion, long maturation process as well as the
polyploidy issue which cannot be surpassed
9.2.3 MAS Experiments in Mango during pedigree-based mapping.
Generally, mango requires 5–7 years to
Even though a genetic map is not necessary to become juvenility which is considering as eco-
identification of markers and traits of interest nomic input before phenotypic evaluation
associated in MAS approach, the QTL analysis (Davenport 2007). A full sib crosses from two
can help to increase the chance to identify the outbred is usually used in most of fruit crops
genetic area linked to genes or QTLs of interest. QTL mapping analysis. As a result, there is a low
Unfortunately, there are not many reports in resolution of QTLs detection due to a single
using molecular marker for selecting a progeny meiotic event of maximum four alleles segrega-
in mango breeding program up to date. The tion. Whereas AM utilized a large alleles number
major useful molecular markers especially SNPs distributed over the genomes to be calculated the
up to date can facilitate germplasm identification association with curtain phenotypes to identify
and a hybrid clarification as well as a genetic the significant loci. Hence, AM needs a large set
diversity analysis in various cultivars. of molecular markers to detect any linked to the
Table 9.3 Association mapping studies in mango (Mangifera indica L.)

Study Markers Conclusion References
Resistance gene analogs EST-SSRs 134 unique EST-SSR loci for resistance breeding Lantican
(RGAs) in mango et al.
(2020)
Association of SNPs Marker Mi_0173 associate with polyembryony Kuhn et al.
polyembryony in (2019)
germplasm collection
Association analysis for SSRs A set of five genic-SSR markers associated with six Lal et al.
pomological traits in critical pomological traits like regular bearing, fruit (2017)
mango quality, yield related etc.
Association analysis for SNPs Population structure of Indian mango varieties were Singh
cultivar identification (50 K determined et al.
SNP Chip) (2016)
recombination events within genomes (Khan and breeding program. A web genomic resource
Korban 2012). The utilization of SSRs is wildly MiSNPDb is available at webtom.cabgrid.res.
implemented in many crops such as pear (Ora- in/mangosnps. These web genomic resources
guzie et al. 2010), apple (Cevik et al. 2010), could be utilized to generate high density linkage
peach (Font i Forcada et al. 2013) as well as in map, identification of QTL, differentiation of
mango (Lal et al. 2017). Detail of association closely related varieties, as well as a develop-
studies in mango presented in Table 9.3. Fur- ment of genomic selection SNP chip in the future
thermore, this high density genetic marker using (Iquebal et al. 2017). Presently in October 2020,
in association analysis might reveal new candi- a total of 129 GWAS tools and resources are
date genes associated with interested as either freely available at bioinformaticshome.
major or minor QTLs from the association com/tools/gwas/gwas.html. Some of the bioin-
mapping(Oraguzie et al. 2007). formatics software implemented verities statisti-
cal models to facilitate the association analysis in
GWAS such as PLINK (Chang et al. 2015),
9.2.5 Genome-Wide Association METAL (Willer et al. 2010), GAPIT (Lipka
Studies (GWAS) et al. 2012), and TASSEL (Bradbury et al. 2007).
Additionally, there are improvements of analyt-
The genome-wide association studies (GWAS) ical method, for instance, the development of
overcome several limitations of traditional gene multi-locus and multi-trait, combining of linkage
mapping. It not only provides higher resolution association mapping, etc. (Gupta et al. 2019;
at gene level, but the existing well studied pop- Zhang et al. 2019). The GWAS model numbers
ulations were also can be used in the association are increasing to overcome both computational
analysis as a result in higher number of indi- efficiency and detection power. A few hundred,
viduals in the analysis. Next-generation thousand to multiple millions of sample size are
sequencing technologies provide huge data at required (Zhang et al. 2018). Efficiency of soft-
genomic and transcriptomic level. This infor- ware mainly depends on the availability of
mation provides a useful dataset of SNP which molecular markers and population size, used in
beneficially in the identification of small haplo- the analysis. Increasing a sample size in GWAS
type blocks that significantly associated with is a key feature to explain the heritability better,
QTLs. The GWAS-identified SNPs can be used and it has become a recommendation for great
in combinations with SNP biomarkers in MAS success in GWAS research.
9.3 Concluding Remark and Future Ayala FJ, Coluzzi M (2005)Chromosome speciation:
humans, Drosophila, and mosquitoes. Proc Natl Acad
Prospects Sci USA 102 (Suppl 1): 6535–6542
Bally IS, Lu P, Johnson PR (2009) Mango breeding. In:
There are a very limited number of mango Jain SM, Priyadarshan PM (eds) Breeding plantation
breeding programs worldwide that implementing tree crops: tropical species. Springer, New York,
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molecular genetic information as well as utilizing
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The Genome Sequence
and Transcriptome Studies in Mango 10
(Mangifera indica L.)
Nagendra K. Singh, Ajay K. Mahato,

and Pawan K. Jayaswal
Abstract of 323 Mb of mango variety ‘Amrapali’

(NCBI Accession no. LMWC00000000 v.1).
Mango (Mangifera indica L.) is one of the
The draft genome assembly was updated to a
most important fruits of the world both in reference quality assembly of 403 Mbp with
terms of value and volume. Wild Mangifera 4312 scaffolds anchored to 20 chromosome
species are distributed throughout South and
pseudomolecules (LMWC01000000 v.2). The
South-East Asia, but mango cultivars have latest v.3 Amrapali assembly, assisted by
originated in India which produces more than BioNano optical fingerprinting and Hi-C con-
fifty percent of the world’s mango with more
formation capture sequencing, has 2314 scaf-
than thousand varieties. The genome size of folds with a high N50 value of 11.78 Mpb.
mango estimated by flow cytometry is Mapping sequence reads from 18 different
402 ± 10 Mbp (2n = 40). Here, we present
transcriptome studies showed an average 96%
a brief account of the global efforts for coverage of the gene space, and BUSCO
sequencing of mango genome and transcrip- analysis of 1440 genes showed 93.4% cover-
tome studies for the analysis of trait-related age of the conserved eukaryote orthologs.
differential gene expression. High heterozy- A total of 46,395 protein-coding genes have
gosity of about 2.5% made it difficult to been predicted showing maximum homology
assemble the genome of mango using Illumina with Citrus sinensis. The Amrapali genome
short sequence reads of 100–150 bp because it has 45% repeats and large segmental duplica-
did not permit the assembly of its maternal tions, indicating at least one recent (15.87–
and paternal genomes into an integrated 31.74 Mya) and one ancient (253.96–269.84
mosaic genome assembly. The problem was Mya) whole genome duplication. Mosaic
overcome by using PacBio SMRT long genome assemblies of mango variety ‘Tomy
sequence reads for genome assembly using Atkins’ from USA and ‘Kensington Pride’
long overlaps of 500 bp and high mismatch of from Australia have also been presented at the
15% to take care of the heterozygosity, annual Plant and Animal Genome (PAG) con-
resulting in the first draft genome assembly ferences. Recently, two more mosaic genome
assemblies of mango varieties ‘Hong Jian Ha’
and ‘Alphonso’ have been reported using
PacBio SMRT sequencing with Falcon-unzip
N. K. Singh (&) A. K. Mahato P. K. Jayaswal
and ‘Canu’ software to separate the primary
ICAR-National Institute for Plant Biotechnology,
Pusa Campus, New Delhi 110012, India contigs (P-contigs) and haplotigs (H-contigs).
e-mail: nksingh4@gmail.com However, there is still a need to develop clean

https://doi.org/10.1007/978-3-030-47829-2_10
166 N. K. Singh et al.
phase-separated reference assemblies of the carbohydrate; fat; dietary fiber; protein; and
maternal and paternal genomes of highly minerals (Sodium, Potassium, Calcium, Copper,
heterozygous mango using the recent Iron, Magnesium, Manganese, and Zinc) impor-
trio-binning approach. The reference genome tant for human health (Sogi et al. 2013;
will help accelerate breeding of dwarf, stress Maldonado-Celis et al. 2019; https://fdc.nal.usda.
tolerant, and high-quality mango varieties. gov/fdc-app.html#/food-details/169910/nutrients
). Mango byproducts specifically seeds and peels
generated from the fruit processing industries are
10.1 Introduction a cheap source of food for the tribal population
and also used in the cosmetic and pharmaceutical
Mango (Mangifera indica L.) is known as the
industries for valuable phenolic compounds
‘king of fruits’ for its rich taste, flavor, color,
(Schieber et al. 2003; Coelho et al. 2019).
production volume, and diverse end usage. It
Recent studies have emphasized the utilization of
belongs to the plant family Anacardiaceae and
mango kernel fat as a cocoa butter substitute in
has a small genome size of 439 Mb (2n = 40)
confectionery products, particularly chocolate, as
according to Arumuganathan and Earle (1991).
a rich source of stearic, oleic, palmitic, arachidic,
However, based on flow cytometry a signifi-
behenic, lignoceric, and linolenic acids (Jahurul
cantly smaller genome size of 402 ± 10 Mbp
2014). Despite its huge economic significance
was estimated for the mango variety ‘Amrapali’
genomic resources for mango have been limited
(Singh et al. 2018). Ancient Sanskrit literature
for long and the genetics of useful horticultural
indicates the origin of cultivated mango in India,
and pomological traits are poorly understood.
although wild mango species are distributed
Here, we present a brief account of the global
throughout the South and South-East Asia.
efforts to generate mango genome sequence and
Recovery of Paleocene mango leaf fossils near
its use in the analysis of genetic diversity, pop-
Damalgiri in the West Garo Hills of Meghalaya
ulation structure, and association studies. A ma-
in India points to the origin of genus Mangifera
jor milestone was reached with the publication of
in the peninsular India before the joining of
the draft genome of Indian mango cultivar
Indian and Asian continental plates (Mukherjee
‘Amrapali’ which is a hybrid of popular North
1951; Mehrotra et al. 1998; Singh et al. 2016).
Indian variety ‘Dashehari’ and a regular bearing
India produces more than fifty percent of the
South Indian variety Neelam (Mukherjee et al.
world’s mango and grows more than thousand
1968; Singh et al. 1972). The project was
varieties some of which are commercially viable,
spearheaded by ICAR-National Institute for Plant
e.g., Alphonso, Banganapalli, Bombay Green,
Biotechnology, New Delhi (formerly National
Chausa, Dashehari, Fazli, Gulabkhas, Kesar,
Research Centre on Plant Biotechnology) in
Kishen Bhog, Langra, Neelam, Totapuri among
collaboration with four other ICAR Institutes,
others. India produced 20.8 million tons of
namely Indian Agricultural Research Institute
mango from 2.3 Mha in 2018–19, of which
(IARI), New Delhi; Central Institute for Sub-
46,510 metric tons of fresh mango worth USD
tropical Horticulture (CISH), Lucknow; Indian
60.26 million was exported according to the
Institute of Horticultural Research (IIHR), Ben-
Agricultural and Processed Food Products
galuru and Indian Agricultural Statistics
Export Development Authority (APEDA), India
Research Institute (IASRI), New Delhi. The
(http://apeda.gov.in/apedawebsite/SubHead_
genome assembly has been continuously
Products/Mango.htm).
improved and presented in the annual Plant and
Mango is consumed largely as fresh fruit but
Animal Genome (PAG) Conference at San Diego
now increasingly in processed forms like pulp,
(Singh et al. 2014, 2016b, 2017, 2018, 2019) and
pickles, chutney, juice, etc. Biochemical studies
XIV NAAS Agricultural Science Congress, New
have shown that mango fruit is rich in nutrients
Delhi (Jayaswal et al. 2019). Apart from ICAR,
like vitamins A, C, E, and K; carotenoids (a, b);
10 The Genome Sequence and Transcriptome Studies … 167
four other groups in three different countries have identified 23 genic-SSR markers associated with
also initiated genome sequencing of different 13 traits. Two alleles of the MSSR190 locus
mango varieties, namely ‘Kensington Pride’ in were significantly associated with the fruit
Australia (Dillon et al. 2016), ‘Tomy Atkins’ in diameter, pulp to stone ratio and fruit weight, and
USA (Baruch et al. 2017; Kuhn et al. 2018), and one allele of the MSSR146 locus was associated
‘Hong Xiang Ya’ (Li et al. 2020) and Alphonso with fruit length and width using both GLM and
(Wang et al. 2020) in China. MLM approaches with a high proportion of
phenotypic variance explained (Lal et al. 2017).
Further, the first draft of Amrapali genome was
10.2 Mango Karyotype, Molecular used to identify 122,332 SSR loci and develop
Markers, Genetic Diversity, 8,451 Type 1 and 835 highly variable SSR
Population Structure, (HSSR) markers for high level of polymorphism
and High-Density Linkage (Singh et al. 2016b).
Maps Transcriptome sequence has been used to
identify large number of single nucleotide poly-
Cytological studies on mango and its related morphism (SNP) markers in mango (Sherman
species M. sylvatica, M. caloneura, M. zeylanica, et al. 2015; Mahato et al. 2016). Further,
M. caesia, M. foetida, and M. odorata revealed sequencing of double-digested restriction-site-
that all of them have a diploid chromosome associated genomic DNA (ddRAD) of 84 diverse
number of 2n = 20 (Mukherjee 1950, 1957; Roy mango cultivars identified 1.67 million high-
and Visweswariya 1951). Successful interspeci- quality SNPs, two major sub-populations, and a
fic crosses between M. zeylanica and M. odorata SNP database has been created (Singh et al.
(Mukherjee 1963) showed no sterility problem, 2016b; Iquebal et al. 2017). High-density linkage
and there was uniformity in chromosome kary- maps of mango have been developed using SNP
otypes of these species. First, random amplified markers genotyped using Fluidigm EP-1 plat-
polymorphic DNA (RAPD) markers were used form or specific-locus amplified fragment
for the analysis of intra- and inter-varietal (SLAF) sequencing, which helped in genetic
diversity in mango (Bally et al. 1996; Ravis- anchoring of the mango genome sequence and
hankar et al. 2000), Subsequently, simple quantitative trait loci (QTL) mapping of impor-
sequence repeat (SSR) markers were developed tant traits (Luo et al 2016; Kuhn et al. 2017).
by sequencing of plasmid clones from Recently, SNPs genotyped by ddRAD sequenc-
microsatellite-enriched genomic libraries to study ing were used to study diversity and population
genetic diversity in a limited number (15–36) of structure of 106 mango cultivars (Warschefski
mango varieties (Duval et al. 2005; Honsho et al. et al. 2019). There are two distinct approaches,
2005; Ravishankar et al. 2011). Later on, tran- namely linkage mapping and association map-
scriptome sequence-based 100 genic-SSR mark- ping to identify the markers linked to quantitative
ers were used to analyze 60 diverse mango traits. Linkage mapping explores trait-linked
varieties (Mahato et al. 2006; Lal et al. 2019). markers within a structured bi-parental popula-
Phenotyping of 17 critical pomological traits in tion, whereas association mapping looks for
60 mango varieties was mapped by a genome- marker-trait associations in a set of random
wide association study using generalized linear genotypes without structured population. The
model (GLM) and mixed linear model genetic mapping and molecular characterization
(MLM) approaches. Population structure analy- of complex trait-linked markers have facilitated
sis using the genotyping data from 87 SSR genomics-assisted breeding for the development
markers revealed three distinct sub-populations of high-yielding, disease resistant, and abiotic
corresponding to the geographical origin of these stress-tolerant varieties in rice (Singh et al.
varieties. Association analysis using GLM 2016a; Bhandari et al. 2019).
Fig. 10.1 A snapshot of 100% sample success rate of the mango 80 K genic-SNP chip array designed for Affymetrix
GeneTitan genotyping platform
Singh et al. (2019) reported 10.5 million

SNPs/Indels by re-sequencing a set of 24 diverse 10.3 Sequencing of the Mango
mango varieties and developed an 80 K genic- Genome
SNP genotyping chip for Affymetrix GeneTitan
platform (Fig. 10.1). The chip was used for 10.3.1 Genome Sequence of cv.
analyzing genetic diversity, population structure, Amrapali
and genome-wide association studies (GWAS) of
fruit quality traits including fruit size, acidity, In January 2014, NK Singh presented the first draft
and pulp percentage in a set of 368 mango cul- genome assembly of the mango variety ‘Amrapali’
tivars (NK Singh et al. unpublished). The popu- using Illumina MiSeq overlapping paired-end
lation structure of cultivars was delineated using reads at San Diego PAG conference (Singh et al.
a subset of 60 genome-wide unlinked SNPs with 2014). However, the assembly size (492 Mbp in
100% call rates revealing two sub-populations 211,141 contigs) was larger than the estimated size
that corresponded to their geographical origin. of mango genome, i.e., 439 Mbp (Arumuganathan
Three different SNPs located on chromosome 5, and Earle 1991), indicating redundancy in the
12, and 19 were significantly associated with assembled contigs. High heterozygosity (about one
mango pulp percentage, and one SNP on chro- SNP/Indel every 40 bp) in the mango genome
mosome 10 was associated with fruit acidity with made it nearly impossible to produce a reference-
very high LOD score of 22. Haplotype-based quality assembly using short sequence reads (100–
phylogenetic analysis revealed the evolutionary 150 bp) of Illumina, because it did not permit
relationship and mutational changes among the integrated assembly of the maternal and paternal
different groups of mango cultivars. Unweighted genomes into an integrated mosaic assembly, par-
Pair Group Method with Arithmetic Mean ticularly in the genomic regions of high heterozy-
(UPGMA) phylogenetic tree of 384 mango gosity. The problem was overcome using 3rd
varieties based on the 60 unlinked SNPs also generation single molecule real-time (SMRT)
clustered them into two major groups, and sequencing on PacBio RXII platform with long
revealed their evolutionary relationships (NK read lengths of 3.5–10 kbp, and the first de novo
Singh et al. unpublished). draft genome assembly of the mango variety
‘Amrapali’ was reported and sequence deposited in assembly with an N50 of 282 kbp, providing
the NCBI public repository with Bio-Project almost complete coverage of the mango genome
no. PRJNA300605, WGS Accession no. size estimated by flow cytometry, i.e., 402 ± 10
LMWC00000000v.1 (Singh et al 2016b). PacBio Mbp. About seventy-five percent of the scaffolds
sequence data of total 70 genome coverage was was anchored to the 20 chromosomes of mango
generated using P4C2 and P5C3 chemistries and with 6,297 (97.5%) of the SLAF markers in the
genome assembly was performed with an experi- high-density linkage map (Luo et al. 2016). Map-
mental version of the PacBio ‘Falcon’ assembler ping of 18 different transcriptome sequence read
using custom assembly parameters of 500 bp archive (SRA) reads on the assembly showed 96%
sequence overlap and 15% mismatch to take care of coverage of the gene space, while BUSCO analysis
the heterozygosity. This produced the first of 1440 conserved eukaryotic genes showed 93.4%
maternal-paternal mosaic genome assembly of 323 coverage of genes (Singh et al. 2019).
Mpb in 9,550 contigs with N50 value of 98.3 Kbp,
the largest contig size of 1.09 Mbp and genome
coverage of 73.2%. Total of 43,247 protein-coding 10.3.2 Genome Sequence of cv.
genes were predicted in the size range of 150– Tommy Atkins
12,102 bp with an average size of 894 bp, and
functional annotation of 33,365 (77.14%) of these A draft genome assembly of mango variety
genes. They also identified 122,332 genomic-SSR ‘Tommy Atkins’ was presented in the PAG con-
of which 8,451 were type 1 SSR and 835 were ference at San Diego (Baruch et al. 2017). The
highly variable SSR (HSSR) markers. Subse- genome assembly was based purely on Illumina’s
quently, a 403 Mbp reference genome assembly of short-read paired-end and mate-pair sequence
‘Amrapali’was produced in 4,312 scaffolds using data, with an assembly size of 760 Mbp, clearly
additional sequence data of 20 genome cover- having phase redundancy due to high heterozy-
age with PacBio P6C4 chemistry (Table 10.1, gosity. It was also obvious from 85% of the
NCBI Accession no. LMWC01000000, v.2, Singh assembly being anchored to 50 linkage groups
et al. 2017, 2018). The present BioNano optical using genetic maps from two different populations.
fingerprint integrated assembly (NCBI Accession An updated version of the Tommy Atkins genome
no. LMWC02000000, v. 3.0) has 2,314 scaffolds assembly was presented in the subsequent PAG
with genome coverage of 408 Mbp and a high N50 conference (Kuhn et al. 2018). For the updated
of 11.78 Mpb as compared to the version 2.0 assembly, they used 100 genome coverage
Table 10.1 Comparison of the main features of the three published maternal-paternal mosaic assemblies of the highly
heterozygous mango genome
Details Amrapalia Hong Xiang Yab Alphonsoc
Sequencing platform PacBio + Illumina + BioNano PacBio + Illumina PacBio + Illumina + Hi-C
Genome size (Mbp) 402±10 389 360
Assembly size (Mbp) 403 371.6 392.9
Sequencing depth (X) 101.98 613.79 240.0
No of sequence contigs 4312 420 672
Repeat sequence (%) 45.02 47.94 40.5
Scaffold N50 (Kbp) 11,780 4820 17,600
No. of predicted Genes 46,395 34,529 41,251
a
Singh et al. (2018)
b
Li et al. (2020)
c
Wang et al. (2020)
Illumina sequence data integrated with 10 mer frequency distribution approach and gener-
Genomics data, assembled using ‘DenovoMagic’ ated sequence data with 225.38 genome cov-
genome assembler of NRGene. The resulting erage on Illumina and 388.41 genome
assembly was of 490 Mpb in 571 super-scaffolds. coverage on PacBio Sequel II platform. The
The assembly was improved by correcting and genome assembly was performed using Falcon
ordering of the scaffolds in pseudomolecules and and Falcon-unzip software to generate primary
incorporation of floating scaffolds into pseudo- contigs (P-contigs) and haplotigs (H-contigs)
molecules using more than 5000 SNP markers assembly of 371.62 Mb in 120 contigs and
from the published genetic maps (Luo et al. 2016; 168.19 Mb in 1,190 contigs, respectively. The
Kuhn et al. 2017). The final assembly is in 20 Primary contigs assembly is having N50 value of
pseudomolecules with a size range of 11–22 Mb 4.82 Mbp, the maximum contig length of 11.46
corresponding to the 20 haploid mango chromo- Mbp, H-contigs N50 value of 458.69 Kbp, and
somes, and 27,000 annotated protein-coding genes the largest contig length of 2.0 Mpb. The pub-
in the genome assembly. lished genetic map of 6500 SLAF markers (Luo
et al. 2016) was used to anchor 112 of the P-
contigs (367.05 Mbp) to 20 pseudomolecules,
10.3.3 Genome Sequence of cv. covering 98.77% of the total assembly
Kensington Pride (Table 10.1). They identified 34,529 protein-
coding genes with an average gene length of
NL Dillon presented the initial draft genome 1,295 bp, average CDS length of 1,143 bp, and
assembly of Australia’s most significant mango 5.6 exons per gene. Overall, 90.71% of the gene
variety ‘Kensington Pride’ in the PAG confer- models were functionally annotated with signif-
ence at San Diego (Dillon et al. 2016). Under the icant similarities in the public databases and
mango genomics initiative of Queensland 284,679 SSRs were predicted constituting 1.1%
Department of Agriculture, Forestry and Fish- (4.066 Mb) of the genome. They have deposited
eries (DAFF), the Horticulture Innovate Australia the genome assembly and sequenced reads in the
(HIA) had led an international collaboration BIG Genome Sequence Archive database under
between DAFF (Australia), Beijing Genomics Accession number PRJCA002248.
Institute (BGI, China), and International Crops
Research Institute for Semi-Arid Tropics (ICRI-
SAT, India) to sequence the ‘Kensington Pride’ 10.3.5 Genome Sequence of cv.
genome. The 407 Mpb assembly was completely Alphonso
based on the Illumina short reads sequencing.
The heterozygosity issue was not addressed in Another genome assembly of mango variety
this assembly, therefore redundancy of the con- ‘Alphonso’ was reported this year by Wang et al.
tigs cannot be ruled out. (2020). Alphonso was selected after a prelimi-
nary screening of 22 mango varieties for having
the lowest level of 1.5% heterozygosity. The
10.3.4 Genome Sequence of cv. Hong estimated genome size of Alphonso based on k-
Xiang Ya mer size distribution was estimated as 360
Mbp. Sequence data with 216 genome cov-
Recently, a genome assembly of mango variety erage was generated using PacBio Sequel II
‘Hong Xiang Ya’ has been reported by Li et al. platform and assembly was performed using
(2020) in the bioRxv preprint repository. They ‘Canu’ assembler and improved further using
estimated a genome size of 389 Mbp using K- paired-end and mate-pair Illumina reads.
Chromosomal level scaffolding was achieved (1187 genes), lipid metabolism (1136 genes),
using 33.77 Gbp of Illumina Hi-C data, and the membrane proteins (1030 genes), structural pro-
scaffolds were arranged in pseudomolecules with teins (998 genes), secondary metabolites (904
the help of 6549 SLAF markers of the genetic genes), uncharacterized (644 genes), miscella-
map (Luo et al. 2016). The final genome neous (584 genes), abiotic stress (567 genes),
assembly size is 392.9 Mbp in 252 large scaf- storage proteins (290 genes), acid metabolism
folds (20 chromosome pseudomolecules, 2 (197 genes), and the largest category of 7884
organelles, and 230 floating scaffolds), with hypothetical genes with no transcript support.
scaffold N50 of 17.6 Mbp and contig N50 of 3.5 Further, the 3603 transcription factor genes,
Mbp, 90.1% of the assembly was anchored to 20 which play very important roles in regulating the
linkage groups with the pseudomolecule size gene expression were divided into 36 categories
rage of 12.2–29.4 Mbp. The Core Eukaryotic with MYB factors (264 genes) other Zf factors
Genes Mapping Approach (CEGMA) analysis (258 gens), NAC factors (213 genes), BHLH
showed 95.1% and the Benchmarking Universal factors (183 gene), and ERF factor (162 genes)
Single-Copy Orthologs (BUSCO) analysis forming the largest five categories. These genes
showed 95.9% genome completeness based on provide important reference points for further
the single-copy orthologous genes, thus con- polymorphism survey and marker-trait associa-
firming the high-quality of assembled genome tion studies for plant breeding applications using
(Table 10.1). Total of 41,251 protein-coding bi-parental or association mapping panels.
genes were predicted with an average gene
length of 3503 bp, of which 37,424 (90.7%)
were placed on the 20 pseudomolecules with a 10.5 Repeat Elements in the Mango
gene density of 105 genes per Mbp and 39,473 Genome
(95.68%) of the genes got functionally annotated.
Further, Wang et al. (2020) have changed the The major proportion of higher eukaryotic gen-
chromosome numbering of mango in their paper omes consists of different types of repetitive
based on descending pseudomolecule size. elements (RE) like transposable elements
(TE) and simple sequence repeats like mini and
microsatellites, which play important role in the
10.4 Gene Content of the Mango genome evolution through cut-paste and copy-
Genome paste mechanisms. Identification and annotation
of REs in the large eukaryotic genomes is a
We predicted total of 46,395 protein-coding challenging task that requires both de novo and
genes in the version 2 assembly of ‘Amrapali’ homology-based approaches (Lerat 2010). De
genome, of which the highest number of 11,349 novo analysis of REs in the mango genome using
genes showed homology with sweet orange Repeat Modeler revealed that Mangifera indica
(Citrus sinensis L.) followed by cacao (Theo- does contain a large proportion of repetitive
broma cacao L.) genome (Fig. 10.2). These DNA. Singh et al. (2018) reported 45.02%
genes were grouped into 21 broad functional interspersed REs (187.75 Mbp) masked in the
categories, namely physiological functions (5363 total 403 Mbp ‘Amrapali’ reference assembly v.2
genes), transportation (4804 genes), protein (Table 10.1). Proportion of different categories
metabolism (4610 genes), transcription factors of sequences in the total REs was long terminal
(3603 genes), phosphatases and kinases (2477 repeat (LTR) (36.72%), DNA transposons
genes), resistance-like and defense response (22.28%), unclassified (33.024%), simple repeats
genes (2267 genes), growth and development (3.034%), low-complexity repeats (0.608%), and
(2247 genes), cell signaling (2178 genes), car- non-LTR (4.34%) (Fig. 10.3). Proportion of
bohydrate metabolism (1451 genes), nucleic acid different categories of REs in the total 323 Mbp
metabolism (1975 genes) unknown function of the Amrapali draft genome (Table 10.2) was
Fig. 10.2 Two-way Venn

diagram of mango (Mangifera
indica L. cv. Amrapai) genes
conserved in 13 other plant
species (shown in red fonts).
Total number of genes in the
respective species are shown
in black fonts. Of the total
46,395 predicted genes,
18,141 were unique to mango
Fig. 10.3 Proportion of

different types of repeat
elements in the Amrapali
mango genome ver.
2 assembly
short interspersed nuclear elements (SINEs) in the mango genome were unique to mango. Li
(0.04%), long interspersed nuclear elements et al. (2020) reported 46.18% TEs in the genome
(LINEs) (0.40%), LTRs (9.04%), DNA trans- of mango variety Hong Xiang Ya, covering
posons (3.58%), unclassified (31.22%), simple 171.58 Mbp out of the total 371.62 Mbp genome
repeats (1.09%), and low-complexity repeats assembly. However, Wang et al. (2020) reported
(0.27%). The largest proportion (31.22%) of REs only 40.54% REs in the Alphonso genome
Table 10.2 Comparison of major repeat elements reported in the genomes of three different mango cultivars
TE Category cv. Amarpalia cv. Hong Xiang Yab cv. Alphansoc
Masked Percent in Masked Percent in Masked Percent in
length (bp) genome length (bp) genome length (bp) genome
SINEs 123,043 0.04 .. .. 7713 0.00001
LINEs 1,282,443 0.40 2,297,579 0.62 3860235 0.98
LTR 29,209,092 9.04 85,763,725 23.08 59676610 15.19
DNA 11,569,382 3.58 16,187,808 4.36 21877011 5.57
elements
Unclassified 100,892,375 31.22 67,335,389 18.12 73881229 18.80
Total 143,076,335 44.28 171,584,501 46.18 159302798 40.54
interspersed
Simple 3,530,710 1.09 5,673,978 1.53 .. ..
repeats
Low 886,364 0.27 906,641 0.24 .. ..
complexity
a
Singh et al. (2016b)
b
Li et al. 2020
c
Wang et al. (2020)
Fig. 10.4 Proportion of

repeat elements in the
Amrapali mango genome ver.
2 assembly in comparison to
some other major fruits and
crop plants
covering 159.30 Mbp of the total 392.9 Mbp

assembly (Table 10.2). In all the three published 10.6 Non-coding RNA in the Mango
mango genomes, LTRs are the most predominant Genome
elements over other class I and II RE. The
reported REs in the mango genome is higher than Most of the higher eukaryotes possess a small
20.5% in sweet orange (Xu et al. 2011), 16.1% in proportion of genes which are transcribed into
Cacao (Argout et al. 2011), 23.90% in grape non-coding RNA (ncRNA), which have very
(Velasco et al. 2007), 25.03% in cucumber important biological functions. The computa-
(Huang et al. 2009), but lower than 53.17% in tional discovery and characterization of novel
papaya (Ming et al. 2008) and 67% in apple ncRNA in plant species enriches our under-
(Velasco et al. 2010) genome (Fig. 10.4). standing of gene regulation in these plants.
Recent studies have described tissue-specific tRNA having the highest copy number
long non-coding RNA (lncRNA), which plays (598) followed by miRNA (n = 235), snRNA
important role in regulating gene expression such (n = 200), snoRNA(n = 47), and ribosomal
as splicing, gene inactivation, and translation RNA (n = 45). Wang et al. (2020) reported in the
(Franco-Zorrilla et al. 2007; Ben et al. 2009; Liu Alphonso genome total of 1893 ncRNA,
et al. 2013). Apart from this, different types of including 599 tRNAs, 459 miRNAs, 560
canonical ncRNAs such as ribosomal RNA snRNAs, and 275 rRNAs). The cultivar specific
(rRNA) and transfer RNA (tRNA) are present in ncRNA are useful to understand the mechanism
all species. Other important ncRNAs, such as of interaction with the coding sequences and may
miRNA, snRNA, and snoRNAs are also present be helpful in defining novel functional networks
in specific cellular locations. Singh et al. (2017, for the genetic improvement of mango.
2018) have reported 1,653 non-coding RNA
elements in the Amrapali genome using Infernal
and tRNAScan software. These belong to ten 10.7 Mango Chloroplast Genomes
different categories such as tRNA (n = 601),
sRNA (n = 12), snRNA (n = 529), rRNA The first chloroplast genome of mango was
(n = 150), ribozyme (n = 51), nodulin (n = 1), reported for variety ‘Langra’ using a combination
miRNA (n = 281), catalytic intron (n = 18), cis- of Sanger and 454-GS FLX sequencing (Azim
regulatory elements (n = 7), and anti-sense RNA et al. in 2014). It was assembled using CLC
(n = 3). Among all identified categories of the Genomics Workbench software (CLC bio, Den-
ncRNA, rRNA, miRNA snRNA, and tRNA are mark) into a cp genome of 151,173 bp in 31
the most dominant over other ncRNAs and contigs with 38.18% GC content. Total of 139
individually make up 9.07% to 36.36% of the genes were predicted of which 119 genes were
total ncRNA (Fig. 10.5). Li et al. (2020) reported single copy, 20 duplicate genes, 29 tRNA genes,
in the Hong Xiang Ya genome total of 1125 four rRNA, and 91 protein-coding genes (NCBI
ncRNAs belonging to six major categories, with GenBank Accession number FJ212316).
Fig. 10.5 Proportions of

different kinds of non-coding
RNA in the Amrapali mango
genome ver. 2
Recently, the first full-length cp genome of a blocks were large with duplicated fragment size
wild mango (Mangifera sylvatica Roxb.) has of more than 1 Mbp. Three large blocks each
been reported by Zhang et al, (2020). The short were identified between chromosome pairs 1:20,
read sequence data was generated using Illu- 14:15, and 9:16 while chromosome pair 10:19
mina’s Hiseq 2500 platform, and de novo has two duplicated blocks. Further, seven dif-
assembly was performed using SOAPdenovo ferent chromosome pairs were identified having
software. The full chloroplast genome assembly one duplicated block each, namely chromosomes
of 158,063 bp has a GC content of 37.89% and 11:16, 12:17, 8:13, 9:13, 4:17, 8:18, and 9:19.
total of 112 genes were predicted and annotated Among the eighteen duplicated segments iden-
of which 78 were protein-coding genes, 30 tRNA tified there were at least one recent (15.87–31.74
genes, and four rRNA genes. The sequence is Mya) and one ancient (253.96–269.84 Mya)
available in the NCBI GenBank database under duplication event (Fig. 10.6).
accession number MK790101. Later, Wang et al. (2020) have identified these
duplications in the mango variety Alphonso and
reported that mango diverged from litchi and
10.8 Insights into Mango Genome sweet orange about 70 million years ago.
Evolution by Whole Genome In WGD analysis, Wang et al. reported 41 col-
Duplication linear blocks which were distributed across the
20 chromosomes of mango and also concluded
Exponential increase in the whole genome and that a WGD event may have occurred about 33
transcriptome sequence data provides a valuable Mya. It is broadly accepted that macro-
resource to study the evolutionary consequences evolutionary changes have occurred due to
of gene duplications in different taxa, and unravel whole genome duplications. Singh et al. (2018)
common principles underlying evolution by also reported that a large number of these
genome duplication followed by retention, duplicated segments show collinearity with
diversification, or loss of genes. Singh et al. Citrus sinensis and Theobroma cacao genomes.
(2007) reported the duplication and retention of
conserved single-copy genes between rice and
wheat genomes, after an ancient whole genome 10.9 Transcriptome Studies
duplication (WGD) about 70 million years ago for Identifying Differentially
(Patterson et al. 2004). Studies have shown that Expressed Genes for Mango
genome duplication through polyploidy has led Traits
to increase in the number of species in different
angiosperm lineages like Poaceae, Brassicaceae, During the last decades, RNA sequencing has
Solanaceae, and Leguminosae (Wood et al. 2009; been used extensively for understanding the
Landis et al. 2018). The WGD is one of the most developmental, cellular and physiological pro-
important factors leading to the evolution and cesses as well as domestication, disease resis-
diversification of plant species. In mango gen- tance and alternate bearing in mango and other
ome, two independent studies have reported fruits. The main reason for this is the high
whole genome duplication. Singh et al. (2018) throughput data generation and low cost of RNA
reported at least three ancient whole genome sequencing (Martinelli et al. 2012; Wu et al.
duplication events (a, b and c) in the Amrapali 2014; Dautt-Castro et al. 2015; Mahato et al.
genome. They used SyMAP v4.2 software to 2016; Srivastava et al. 2016; Yadav et al. 2020;
identify the syntenic regions among the 20 Jayaswal et al. 2020). RNA-Seq offers important
chromosomes of mango and reported multiple insights into gene expression under different
recent and ancient WGD in the mango genome. conditions and allows discovery of new genes
The Synteny analysis identified total of 91 non- and pathways. RNA-Seq has demonstrated its
overlapping collinear blocks among which 18 potential in identifying tissue-specific long non-
Fig. 10.6 The time range of whole genome and segmental duplications in the Amrapali mango genome based on
synonymous substitution analyses of 18 large duplicated segment
coding RNA and how do they regulate the gene Flowers become either sterile or the buds abort
expression (Budak et al. 2020). Here, we have shortly after fertilization, causing 80–100% fruit
summarized some of these transcriptome-based yield losses (Nor et al. 2013). Different measures
differential gene expression studies on identifi- are adopted to control the malformation in mango,
cation of candidate genes for important traits in such as fungicides, plantation of pathogen-free
mango. materials, and destruction of the infected branches
of the tree but none of these are effective to control
the disease completely. RNA-seq studies have
10.9.1 Differential Gene Expression been carried out to identify the differentially
During Mango expressed genes (DEGs) between healthy and
Malformation malformed tissues for understanding the molecular
mechanism of mango-F. mangiferae interaction.
Mango cultivation is widely affected by the fungal Liu et al. 2016 analyzed transcriptome profiles of
pathoen Fusarium mangiferae, which is associ- F. mangiferae (strain MG06) infected buds of
ated with deformities in the vegetative and floral mango cv. Keitt, at 45, 75, and 120 days after
organs including shortened internodes and leaves inoculation to generate 99 million sequence reads,
in the mango plant (known as mango malforma- and assembled these into 121,267 unigene contigs,
tion), thus preventing normal fruiting in thousands of which 23,915 unigenes were assigned to 273
of hectares (Chakrabarti 2011; Zhan et al. 2012). KEGG pathways. Variations were seen in the
expression of genes with reference to the control (ACOs) involved in the biosynthesis of JA and ET
sample and three other F. mangiferae infected biosynthesis, respectively (Nascimento et al.
samples, for example, 15,830 DEGs were identi- 2018). There were total of 275 differentially
fied in control vs 45 days, of which 6802 were up- expressed protein kinase genes between healthy
regulated and 9028 were down-regulated. Of the and F. mangiferae infected mango buds. Some of
26,061 DEGs in control vs 75 days, 11,582 were these, e.g., calcium-dependent protein kinases, G-
up-regulated and 14,479 were down-regulated, type lectin, S-receptor-like serine/threonine-
and of the 20,146 DEGs in control vs. 120 days, protein kinases, and proline-rich receptor-like
7222 were up-regulated and 12,924 were down- protein kinase genes were up-regulated, while
regulated. Apart from the DEG between control leucine-rich repeat (LRR) receptor-like serine/
and infected samples, Liu et al. 2016 also studied threonine-protein kinase, and serine/threonine-
plant defense response genes, e.g., (a) Pathogene- protein kinase genes were down-regulated.
sis-related (PR) genes (b) WRKY transcription In another study on mango malformation in
factors (c) phenylpropanoid biosynthesis genes variety Amrapali, Yadav et al. (2020) sampled
(d) signal transduction genes, and (e) protein three infected tissues, namely single swollen
kinase genes. The PR genes play important role in malformed bud stage, multiple malformed bud
plant defenses against pathogen infection. Here, stage, malformed panicle stage together with two
46 PR genes of different categories (PR1, PR2, healthy control samples, namely healthy bud stage
PR4, PR10, PR5, chitinases, peroxidases, pro- (HB-1), and healthy panicle stage (HB-2), to
teinase inhibitors) were affected by infection with generate total of 20.31, 20.77, 20.32, 27.92, and
F. mangiferae. The WRKY transcription factors 18.59 million sequence reads, respectively, using
which regulate the plant immunity via interaction Illumina NextSeq platform. They found higher
with different protein partners like resistance pro- expressions of seven flowering-related genes
tein, histone deacetylases, calmodulin, MAP (MYB30, TPL, bHLH, FTIP1, CDKC2, CPK33,
kinase kinases, MAP kinases, 14-3-3 proteins, and and ATH1) in both healthy buds and panicle as
other WRKY transcription factors can act as acti- compared to the malformed buds and panicle.
vator or repressor in the plant signaling process Among the other differentially expressed flower-
(Pandey et al. 2009; Amorim et al. 2017). The ing genes in six possible combinations, the highly
study indicated that the WRKY genes were dif- up-regulated genes included UBP12, EFS, AGL8,
ferentially expressed in the malformed tissues and AGL14, AGL20, AGL24, KIN10, MYB30, SUS2,
may play crucial role in the mango plant defense. FTIP1, CCT, and LDL2, whereas highly down-
Phenylalanine ammonia-lyase (PAL) has a crucial regulated genes included TIL1, TIC, DCL3,
role in secondary phenylpropanoid metabolism by GA20OX3, CCT, AP1, AGL6, AGL8, MYB30,
thickening of cell walls and activating salicylic AGL8, GCT, and GA3OX1. The data set provides
acid and jasmonic acid defense pathways (Kim and information on transcripts putatively associated
Hwang 2014). Liu et al. (2016) also showed that with embryonic flower, early flowering, flowering
genes for O-hydroxycinnamoyl transferase, chal- time control, and terminal flower in healthy and
cone synthase, isoflavone 7-O-methyltransferase, malformed tissues. Out of the observed DEGs, the
and PALs were induced after Fusarium infection. transcript profiles of GA20OX3, AGL24, and
Total of 93 DEGs were identified that were related LDL2, the key genes regulating floral transition
to hormonal signaling during mango-Fusarium and differentiation, were validated through qRT-
infection. Some of these are lipoxygenase isoform PCR. The study provides a valuable resource for
3, ET-responsive transcription factors (ERFs), exploring the complex molecular mechanisms in
and 1-aminocyclopropane-1-carboxylate oxidases flower development and malformation in mango.
10.9.2 Differentially Expressed Genes (lipoxygenase) and six genes of 13-LOX from
at Different the flavor related pathways were reported show-
Developmental Stages ing differential expression. In addition, other
of Mango transcripts involved in cell wall hydrolysis and
cysteine proteinase inhibition were also reported.
In the early stages of mango fruit development, In another study, Dautt-Castro et al. (2015)
the tissue differentiation occurs for exocarp, reported DEGs of different gene families related
endocarp, and mesocarp. The transcriptome- to fruit ripening. The transcriptome study was
based analysis has enlarged our understanding performed on mesocarp of mature green and ripe
of the gene expression during fruit development. mango cv. ‘Kent’, using 6.7 million reads gen-
Deshpande et al. (2017) reported transcriptome- erated using Illumina sequencing. The differen-
based developmental studies on cv. Alphonso at tial expression analysis showed that between
eight different fruit development stages, includ- mature green and ripe tissues total of 1,178 and
ing flowering, 30 days after pollination, 60 days 1,128 genes were up- and down-regulated,
after pollination, pulp 90 days after pollination, respectively. Several genes of carbohydrate cat-
skin 90 days after pollination, 5 days after har- abolism, sucrose, and ethylene biosynthesis
vest: green stage, 10 days after harvest: mid-ripe among others related to fruit ripening were up-
stage, 15 days after harvest the ripe stage. For regulated. In addition, 327 genes involved in
each tissue, more than 100 million reads were metabolic pathways of fruit ripening were
generated using Illumina sequencing. They reported, namely hormone signal transduction,
reported total of 20,755 unique transcripts starch and sucrose metabolism, galactose meta-
encoding 142 different biological pathways bolism, terpenoid backbone, and carotenoid
including ethylene, flavor-related pathway, biosynthesis. Similarly, Bajpai et al. (2018) has
starch, sucrose, amino acids, and fatty acids reported DEGs involved in anthocyanin biosyn-
metabolism-related pathways. Specifically, the thesis pathway in mango cv. Amrapali. In
comparative analysis of differentially expressed another transcriptome study on mango cv. Zill,
transcripts showed total of 524 genes were down- Wu et al. (2014) reported transcriptome profiling
regulated, including alpha-amylase and subtilisin at four fruit development stages (50 days after
inhibitor-like, carbonic anhydrase, chitinase and flowering: young fruit, 80 days after flowering:
maternal effect embryo arrest 59, whereas 181 young fruit, 100 days after flowering: immature
genes were up-regulated, including stage, and fully ripe fruit), using pooled RNA
homeodomain-like protein, cytochrome P450 sequencing strategy to generate total of 6.8 mil-
like, heat shock cognate 70 kDa protein and lion reads and assembled these into 54,207
inositol-3-phosphate synthase from flower to transcripts of which 23,741 were mapped to 128
fruit to 30 days post-harvest period. Similar dif- different pathways. They reported different genes
ferences in gene expression were observed at like malic enzyme family, aspartate
other stages of development, e.g., in 90 DAP- aminotransferase-like, and phosphoglycerate
skin, 54 transcripts were up-regulated including kinase, which were up-regulated during ripening.
isoflavone reductase, transcription and translation
regulatory proteins, hydrolases, methyl trans-
ferase, etc. while four transcripts related to 10.9.3 Transcriptome Analysis
membrane and cytoplasm were down-regulated. During Post-harvest
Deshpande et al. (2017) also elaborated DEGs and Chilling Injury
from other pathways like terpenes biosynthesis
pathway and reported mono-terpene synthases, Mango is an important tropical fruit rich in
sesque-terpene synthases and di-terpene synthase nutritional constituents with high commercial
genes which were dominant in the flowering and value, however due to short shelf life and quick
30 DAP samples. Further, two genes of 9-LOX softening, mangos are highly susceptible to post-
harvest disease-enabling pathogens to infect and involved transcriptome analysis to explore the
degrade the harvested fruit (Prusky et al. 2001). physiological processes associated with the AB
Post-harvest hot water treatment is widely in mango trees. Recently, Sharma et al. (2020)
adopted for cleaning and disinfecting the freshly have reported a transcriptome-based comparative
harvested fruits, it enhances the storage of fruits gene expression analysis of regular bearing cv.
for 3–4 weeks at 12 °C. Luria et al. 2014, con- ‘Neelam’ and alternate bearing cv. ‘Dashehari’,
ducted transcriptome analysis on the effect of hot and found that among 42,397 assembled tran-
water treatment on mango fruit cultivar ‘Shelly’. scripts, 6453 and 6,104 genes were up- and
They sequenced total of eight libraries of freshly down-regulated, respectively. Transcriptome
harvested and hot water treated mango samples analysis between the two cultivars revealed that
at different time intervals and sequence reads total of 26 DEGs were specifically related to AB,
were generated using Illumina Hiseq 2000 plat- including SPL-like, and GA-20-oxidase genes,
form. The DEG analysis showed that during 0 h suggesting the hormonal regulation of AB. The
of hot water treatment total of 827 genes were reported study emphasized the role of potential
expressed, while after 48 h of heat treatment only genes like gibberellic acid (GA3) which initiates
87 genes were expressed. A significant finding of floral induction from the vegetative buds in
the hot water brushing (HWB) treatment was that mango. Similar role of Gibberellin has been
color index of the fruit skin was comparatively reported in citrus and other fruits (Goldschmidt
increased and the expression of chlorophyll et al. 1997) (Table 10.3).
(LHCIIb, Oxepch, PIRC, and Thl1ch) and
anthocyanin biosynthesis-related genes
(85A2 and Anthocyanin 5) was decreased. Apart 10.10 Conclusions and Way
from this, genes related to sugar and flavonoid Forward
metabolism were also highly up-regulated.
To conclude, attempts have been made over the
last five years to assemble the genome sequence
10.9.4 Differential Expression of five different varieties of mango, namely
of Genes Associated Amrapali (India), Tomy Atkins (USA), Kens-
with Alternate Bearing ington Pride (Australia), Hong Xiang Ya, and
in Mango Alphonso (China). However, it has been difficult
to assemble a high-quality reference genome of
Alternate bearing (AB) is a problem of irregular mango due to high level of heterozygosity and
bearing in the fruit trees where fruit yield is high structural variations in the genome. Recently
in one year (on year) and low in the next year (off published mango genome assemblies have poor
year). Alternate bearing or biennial bearing habit genome coverage even after using various soft-
is prominent in perennial fruits like mango, pis- ware tools to merge the maternal and paternal
tachio, olives, apple, pear, apricot, orange, chromosome sequences into a chromosomal-
jamun, and others (Barranco et al. 1998; Shalom level mosaic genome assembly. Total of 36,000
et al. 2012; Guitton et al. 2012; Khezri et al. to 46,000 protein-coding genes have been pre-
2020). Several parameters have been proposed dicted using ab initio gene perdition software
for the quantitative evaluation of AB, e.g., tools. There is a need to develop bin-separated
biennial bearing index (BBI), which is based on maternal and paternal genome assemblies of the
the mass of fruit on individual branch of the tree, mango genome using the recently devised Trio-
however, the physiological mechanism of alter- Binning (Koren et al. 2018) approach to separate
nate bearing is largely unknown (Wilcox 1944; the maternal and patterns sequence reads based
Bangerth 2009). Recent advancements in on the genome sequence of the two parents and
molecular and genetic studies on synchronization the progeny. A fully annotated bin-separated
of flowering time and seed production have diploid assembly and pan genome of mango
Table 10.3 Chronological list of Bio-Projects of mango (Mangifera indica) registered with the NCBI/EBI/DDJB public repositories for genome and transcriptome sequence
180
data (- indicates information not readily available)

Sr. Accession no. (Registration date) Lead institution Objectives Genotype Sequencing Genomic References
no. technology data
availability
1. PRJNA1935911 (Mar 2013) ICAR-NIPB, IARI, Transcriptome (Leaf) Dashehari AB SOLiD 4 SRA,TSA Mahato et al.
New Delhi, India System (2016), Sharma
et al. (2020)
2. PRJNA193588 (March 21, 2013) ICAR-NIPB, IARI, Transcriptome (Leaf) Neelum AB SOLiD 4 SRA,TSA Mahato et al.
New Delhi, India System (2016), Sharma
et al. (2020)
3. PRJNA2272431 (November 2013) ARO, Israel Transcriptome (Fruit peel, Shelly Illumina SRA,TSA Luria et al. (2014)
hot water treatment)
4. PRJNA1926768 (March 2013) University of Karachi, Transcriptome (Leaf) Langra Illumina SRA,TSA Azim et al. (2014)
Pakistan
5. PRJNA258477 (August 19, 2014) UNAM, Mexico Transcriptome (Ripening Kent Illumina SRA Dautt-Castro et al.
and shelf life) (2015)
6. PRJNA2547719 (July 2014) ARO, Israel Transcriptome (SNP, Tommy Illumina SRA,TSA Sherman et al.
germplasm diversity) Atkins and (2015)
Keitt
7. PRJNA2532722 (June 3, 2014) Cornell University, Transcriptome (fruit peel, Keitt Illumina SRA Tafella-Arellano
USA cuticle) et al. 2017
8. PRJNA2352471 (January 6, 2014) SSCRI, CATAS, China Transcriptome (fruit peel Zill Illumina SRA Wu et al. (2014)
and pulp)
9. PRJNA300605 (October 30, 2015) ICAR-NIPB, New Genome (Bin-separated Amrapali Illumina PacBio SRA, AGP Singh et al. (2016b,
Delhi, India genome assembly) RSII 2017, 2018, 2019)
10. PRJNA3040932 (November 5, ARO-VC, Israel Transcriptome (cold Keitt and Illumina SRA Sivankalyani et al.
2015) storage chilling stress Shelly (2016)
response)
11. PRJNA2887972 (July 2015) Indiana University, Transcriptome (genetic Tommy Illumina SRA Kuhn et al (2016)
USA diversity, SNP markers) Atkins
12. PRJNA286253 (June 2015) CIAD, Sonora, Mexico Transcriptome (ripening Ataulfo Illumina SRA Daut-Castro et al.
due to hot water (2018)
disinfection)
N. K. Singh et al.
(continued)
10
no. technology data
availability
13. PRJNA2798293 (March 2015) ICAR-NIPB, New Leaf Transcriptome (SSR, Amrapali Illumina SRA, TSA Mahato et al. (2016)
Delhi, India SNP, Heterozygosity)
14. PRJNA274728 (February 6, 2015) ICAR-IIHR, Transcriptome (variants, Alphonso Illumina SRA –
Bengaluru, India mutational studies)
15. PRJNA325581 (June 14, 2016) ICAR-IIHR, Transcriptome (Peel – – SRA –
Bengaluru, India color)
16. PRJNA3133402 (February 7, 2016) ICAR-CISH, Lucknow, Transcriptome (Flowering Dashehari Illumina SRA CISH Annual
India pathway) Report (2018)
17. PRJNA3177128 (April 2016) CSIR-NBRI, Lucknow, Transcriptome (Ripening Dashehari Illumina 454 SRA Srivastava et al.
India and aroma) GSFLX (2016)
18. PRJNA3170441 (April 2016) ICAR-CISH, Lucknow, Transcriptome Chausa Illumina SRA Bajpai et al. (2018)
India (transcription regulation)
19. PRJNA3204584 (May 2016) STCRI, CATAS, China Transcriptome F1 population Illumina SRA –
The Genome Sequence and Transcriptome Studies …
20. PRJNA3157912 (March 1, 2016) SATCRI, CATAS, Transcriptomes – Illumina SRA –

China (Mango/Fusarium
interaction)
21. PRJNA3101932 (January 9, 2016) SSCRI, China Transcriptome – Illumina SRA –
22. PRJNA3944881 (July 4, 2017) King Abdul Aziz Transcriptome – Illumina SRA –
University, Riad, Saudi Chloroplast genome
Arabia
23. PRJNA4501431 (April 3, 2018) USDA-ARS HSRS, Genome (Mosaic Tommy- Illumina SRA Baruch et al. (2017)
Florida, USA assembly) Atkins Kuhn et al. (2018)
24. PRJNA4311252 (January 3, 2018) ICAR-CISH, Lucknow, Transcriptome, Jelly seed Dashehari Illumina SRA –
India development
(continued)
181
182
no. technology data
availability
25. PRJDB4532 (January 10, 2018) NARO Institute of Fruit Genome sequencing DNA Irwin 454 GS FLX SRA Nashima et al.
Tree Science markers. (2017)
26. PRJNA517351SRA Acc. Florida International Origin, Diversity 106 genotypes Illuimna ddRAD SRA Warschefski et al.
SRR8521837– SRR8521844. University, USA (2019)
(January 7, 2019)
27. PRJNA533518 (April 8, 2019) UQ, Brisbane, Gene discovery cv. 1234 Illumina SRA,TSA Chabikwa et al.
Australia (2020)
28. PRJNA5155641 (January 7, 2019) University of Transcriptome (Fruit Chokanan and Illumina SRA Chin et al. (2019)
Nottingham, Malaysia ripening) Golden
Campus Phoenix
29. PRJCA002248 (March 2020) SCAU, Genome (Mosaic Hong Pacbio Sequel II SRA, AGP Li et al. (2020)
Guangzhou, China assembly) ZiangYa Illumina
30. PRJNA4871549 (March 2020) TCGRI, CATAS, Genome (Mosaic Alphonso PacBio SRA, AGP Wang et al. (2020)
Haikou, China assembly) Sequel II
Illumina
N. K. Singh et al.
together with high-quality genome annotations liqueurs (Mangifera indica L.) produced by different
will be helpful in genome-assisted gene discov- methods of maceration. Antioxidants 8(4):102
Chabikwa TG, Barbier FF, Tanurdzic M, Beveridge CA
ery and marker-assisted breeding in mango. (2020) De novo transcriptome assembly and annota-
tion for gene discovery in avocado, macadamia and
Acknowledgements This study was carried out under mango. Sci Data 7:9
the Network Project on Functional Genomics and Genetic Chakrabarti DK (2011) Mango malformation. Springer,
Modification (FGGM) in Crops and Extra-Mural project Berlin
with funding support from Indian Council of Agricultural Chin CF, Teoh FY, Chee MJY, Al-Obaidi JR et al (2019)
Research (ICAR), Ministry of Agriculture and Farmers Comparative Proteomic analysis on fruit ripening
Welfare, Government of India. processes in two varieties of tropical mango (Mangi-
fera indica). Protein J. https://doi.org/10.1007/s10930-
019-09868-x
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The Mango Chloroplast Genome
11
Manish Srivastav, Sanjay K. Singh,
and Nimisha Sharma
Abstract significant role in photosynthesis, cell regula-

tory mechanisms, resistance for herbicides,
Chloroplast is an important cell organelle that
biotic and abiotic stresses. The highly con-
performs photosynsthesis and helps in several served nature of chloroplast genome sequences
cellular processes. Metabolic compounds syn- opened new avenues in phylogenetic and
thesized in chloroplasts help in signal transfer
evolutionary studies on mango, which thus
and play a seminal role in alleviating biotic and offers enormous opportunities for refining our
abiotic stresses. Although chloroplast is smal- insight into its origin, diversity, evolutionary
ler in size and gene number compared to
relationship, and species identification.
nuclear genome, it is equally important for
evolution and molecular ecological studies.
NGS sequencing technologies made it easier to 11.1 Introduction
characterize chloroplast genome in mango.
Chloroplast genome of ‘Langra’ cultivar was Mango (Mangifera indica L.) (Family, Anacar-
first sequenced by using Sanger and GS-FLX diaceae; (n)genome, * 439 Mbp; (cp)genome,
systems which provided insight in new func- 1,57,837 bp) is considered as difficult plant spe-
tional genes in mango. Thereafter, chloroplast cies to handle in improvement programs due to
genome of ‘GuiFei’ cultivar was sequenced certain inherent characteristics including long
using Illumina Hiseq-2000 platform, while in juvenile phase, high level of heterozygosity,
wild mango (Mangifera sylvatica Roxb) it was heavy fruit drop, and lack of knowledge about the
sequenced using Illumina’s Hiseq 2500 which genetics of important agronomic traits. Breeders
are available in the public domain. Genes have been relying on traditional breeding
identified from chloroplast genome are having approaches for understanding the genetics of
mango and utilization of that knowledge for fur-
ther improvement of mango. Despite, its huge
M. Srivastav (&) S. K. Singh N. Sharma economic significance, the researchers paid very
Division of Fruits and Horticultural Technology, late and also little attention to the augmentation of
ICAR- Indian Agricultural Research Institute, genome resources in mango as compared to other
New Delhi 110012, India
fruit crops of temperate origin. This may be due to
e-mail: msrivastav@iari.res.in
the fact that sequencing technologies and their
S. K. Singh
cost was very high initially. Next generation
e-mail: sanjaydr2@gmail.com
sequencing (NGS) technologies offered rapid and
N. Sharma
cost-effective generation of sequencing data by an
e-mail: nims17sharma@gmail.com

https://doi.org/10.1007/978-3-030-47829-2_11
188 M. Srivastav et al.
order of magnitude for a variety of applications. they are actually collected, studied, documented,
Indeed, sequencing of majority of fruit species has and conserved for immediate or long term use by
involved utilization of NGS techniques. Apart the mankind.
from using NGS for whole genome sequencing With the advent of cost and time-efficient
(Lam et al. 2012), these technologies were also NGS techniques and bioinformatics (Metzker
used for whole transcriptome shotgun sequencing 2010; Mariac et al. 2014; Tang et al. 2014),
also known as RNA sequencing (Wang et al. mango genome sequencing got momentum and
2009), whole-exome sequencing (Rabbini et al. the first report of draft nuclear mango genome
2014), targeted or candidate gene sequencing appeared in 2014 during Animal and Plant
(Mardis et al. 2009; Kulski et al. 2014; Leo et al. Genomics Conference at Sandiago, USA (Singh
2015), and methylation sequencing (Pelizzola and et al. 2014). Similarly, genome sequencing of
Ecker 2011). mango chloroplast was also accomplished almost
Cell organelles genome sequencing was once a during the same period (Azim et al. 2014).
tedious job; however, it is now a very commonly Whereas, complete mitochondrial and ribosomal
adopted procedure (Smith 2016). Accumulation of genome sequences have not been attempted in
more number of sequences means more informa- mango. In mango, nuclear and chloroplast gen-
tion for relevant studies and better understanding of omes have been sequenced (Table 11.1 and
genome evolution. Although chloroplast and Fig. 11.1). The quantum of genome data gener-
mitochondrial genomes are smaller in size and ated in the recent past would be highly useful in
gene number, They are equally important for genomic assisted breeding and deciphering the
evolution and molecular ecology studies. Chloro- genetics of important agronomic traits. In this
plast is the site of photosynthesis and mitochondria chapter, information pertaining to mango
is powerhouse of cell, and both have their own chloroplast genome has been discussed.
DNA. Fruit plants cell commonly has one copy of
nuclear and multiple copies of organelle genomes
(Wang et al. 2018). Hence, deciphering the DNA 11.2 Chloroplast Genome
sequences from mitochondria and chloroplast
serve as primary source of data for molecular sys- Chloroplast is the site of photosynthesis process
tematic, phylogeographic, and population genetic in which light energy is converted into chemical
studies on crops like mango to unravel the basic energy for the purpose of synthesis of organic
information which is still not clear. It is more per- compounds in plants. Chloroplast being the most
tinent since out of the 70 plus Mangifera species important organelle of cell also helps in several
hardly one dozen is under cultivation globally, biochemical processes (Daniell et al. 2016). It is
while many are under the constant threat of also suggested by several researchers that meta-
extinction in their regions of origin due to the wrath bolic compounds synthesized in chloroplasts are
of natural calamities, climate change, etc. before helping in signal transfer between different parts
Table 11.1 Details of mango chloroplast genome

Cp genome Size (bp)/Gene Sequencing method Reference
Mangifera sylvatica Roxb. Size-158,063 bp llumina sequencing Zhang et al. (2020)
Total genes-112
Mangifera indica variety ‘GuiFei’ Size-157,837 bp llumina Hiseq 2000 Platform Zhao et al. (2019)
Total genes- 171
Mangifera indica L. Size-157,780 bp Illumina HiSeq 2000 system Jo et al. (2017)
Total genes-112
Mangifera indica variety Size-151,173 bp Sanger and next generation sequencing Azim et al. (2014)
‘Langra’ Total genes-139
11 The Mango Chloroplast Genome 189
Fig. 11.1 Chloroplast

genome map of Mangifera
indica. (Source Azim et al.
2014)
of plant and play a role in stresses caused by www.ncbi.nlm.nih.gov/genome/browse/) (Wang

abiotic and biotic factors (Daniell et al. 2016). et al. 2018).
Chloroplast evolved from endosymbiosis of a Complete chloroplast genome information has
cyanobacterium and during evolution genes of enriched our knowledge of plant cell biology and
the ancestral chloroplasts have been transferred significantly contributed in phylogenetic studies.
into the cell nucleus. However, proteins essential Information pertaining to variation in chloroplast
for the photosynthesis phenomenon remained genome within a species and between species in
with the chloroplast genome. The chloroplast terms of sequences, structure, and organization
genome confers several advantages over nuclear proved highly valuable for understanding the
genome in phylogenetic and population studies. molecular mechanism involved in adaptation of
These includes (i) highly conserved genes and economically important species to different cli-
low mutation rate, (ii) small size, (iii) haploid mates (Wambugu et al. 2015; Brozynska et al.
number, (iv) high copy number, (v) variation in 2016). Variations in chloroplast genomes have also
intergenic regions, (vi) lacks recombination, and helped in understanding the specific gene transfer
(vi) principally maternal inheritance (Schaal et al. from chloroplast to mitochondrial or nuclear gen-
1998). Tobacco (Nicotiana tabacum) (Ohyama omes, and deciphered the relationship among three
et al. 1986) and liverwort (Marchantia poly- valuable genomes in plants. Since, the chloroplast
morpha) were the first plants of which chloro- gene order is comparatively conserved, small in
plast genome was sequenced (Shinozaki et al. size, non-recombinant type, maternally inherited,
1986). Since then, the chloroplasts DNA of more and haploid. Thus, it can overcome the disadvan-
than 3,000 plant species have been deciphered. tages encountered with nuclear DNA markers
Approximately 1,193 chloroplast genomes of analysis. Conservative nature of chloroplast gen-
land plants are available in the National Center ome offers advantage in parentage and taxonomic
for Biotechnology Information (NCBI) (http:// studies (Cheng et al. 2005).
The first draft chloroplast genome sequence of mitochondrial genomes are known to integrate
mango cultivar ‘Langra’ was obtained using a foreign DNA. Jo et al. (2017) completed
combination of Sanger and GS-FLX NGS Sys- chloroplast sequences of plant species including
tem (Roche Inc., USA) and provided insight in mango, fig, guava, pomegranate, cashew, litchi,
the identification of new functional genes in cinnamon, okra, quinoa, and basil. They
mango (Azim et al. 2014). The draft mango observed that most chloroplast have a set of
chloroplast genome size was 1,51,173 bp with conserved coding sequences with size stability
inverted repeats of 27,093 bp. Total 139 and configuration. The phylogenetic tree indi-
chloroplast genes have been detected of which cated grouping of mango with Anacardium
119 were single-copy genes and 20 were dupli- excelsum, A. carymbosum, A. occidentale, A.
cated genes. There were 29 distinct tRNA genes, humile and A. nanum.
four rRNA genes, and seven of which were Chloroplast genome of mango cultivar ‘Gui-
duplicated in the inverted repeats. Azim et al. Fei’ was reported by Chinese researchers using
(2014) described different genes found in mango NGS platform Illumina Hiseq-2000 (Zhao et al.
cpDNA and their involvement in different cel- 2019). The complete genome sequence was
lular processes. Sequence analysis of chloroplast 1,57,837 bp long comprising of inverted repeats
genomes confirmed Citrus sinensis (160,129 bp) pair with small single-copy region of 43,323 bp
as the closest fruit species to mango. and large single-copy region of
Interestingly, M. indica had infA gene coding 59,717 bp. Genes (171) were predicted having
for translation initiation factor was absent in protein coding (118), rRNA (8) and tRNA
Citrus (Bausher et al. 2006). Chloroplast genome (45) genes. Notably, the organization of genome,
map was constructed and a phylogenetic tree of genes, and their relative positions were different
complete cpDNA sequences was accomplished. compared to other fruit species. Interestingly, 32
However, complete sequence could not be genes had more copies, 18 genes were found to
obtained as mango cpDNA sequence of be duplicated in inverted region and 22 genes in
151,173 bp contained 30 gaps, and it was thought single-copy region. Phylogenetic analysis of 41
that only 95% of genome sequences have been (cp)genomes sequences of different species
finally obtained. It was also noted that inverted clearly revealed close relationship of mango with
repeats of mango chloroplast was bigger than C. sinensis, C. paltvmamma and C. aurantifolia.
several previously reported species. The length of This confirmed the fact that mango (cp)genome
mango cpDNA inverted region was 97 bp larger is ideal resource for generation of DNA markers
than C. sinensis (Bausher et al. 2006). This sup- for taxonomic and evolutionary research and
ported the fact that expansion and contraction of provides valuable information on highly variable
inverted region of chloroplast DNA as source of markers for population studies (Zhao et al. 2019).
length variation. The phylogenetic tree indicated In continuation, another research group from
grouping of mango chloroplast sequences with C. China reported complete (cp)genome of wild
sinensis, G. hirsutum and V. vinifera. Along with mango (Mangifera sylvatica Roxb) for the first
two large inverted repeats, i.e., IRA and IRB, time (Zhang et al. 2020). Mangifera sylvatica,
large number of small repeats have also been popularly known as Ban-am or Laksmi-am in
observed and these repeats occur as part of Assam is having close affinity with common
intergenic spacers as well as genes (Azim et al. mango (Mangifera indica). Mangifera sylvatica
2014). This draft sequence of mango chloroplast is having medicinal and nutrition values (Akhter
genome with accession number FJ212316 was et al. 2016). Chloroplast genome was sequenced
submitted in GenBank. using Illumina’s Hiseq 2500. The chloroplast
In plant evolution, intracellular gene transfer genome of M. sylvatica was found to be compa-
is very common and continuous process. rably smaller (158,063 bp) in length than what was
Chloroplast genome generally has resistance for reported by the same group in ‘GuiFei’ cultivar.
foreign DNA incorporation, while nuclear and The large single copy was of 87,008 bp and had 82
genes. However, small single copy was of Noncoding regions which are the hot spots for
18,340 bp and contained 13 genes. The two mutations proved to be an important resource for
inverted repeats were of 26,379 bp. analyzing intra-and-inter specific variations in
The annotation of 78 functional genes ascer- sequences (Intrieri et al. 2007).
tained its similarity with M. indica chloroplast The usefulness of cpDNA intergenic spacer
(Azim et al. 2014; Zhao et al. 2019). trnL-F sequences in phylogenetic relationships
Among the genes coding for protein, atpF, among Mangifera species was demonstrated by
PetB, PetD, ndhA, ndhB, ropC1, rpl2, rpl16, and Fitmawati and Hartana (2010). They compared
rps16 had one intron, however, clpP, rps12, and trnL-F sequences of M. laurina with related spe-
ycf3 had two introns. rRNAs were only restricted cies and found Mangifera sp. Hiku (Mangga hiku)
to inverted region while tRNA genes were located as the main cultivar in the clade as progenitor of
in all the four regions. Comparing chloroplast M. laurina. Similarly, MaturaseK (matK) gene of
genome of M. sylvatica and 29 other species chloroplast DNA has served as appropriate can-
from 10 different families revealed the closest didate for DNA barcoding. Using this DNA mar-
relationship of this wild mango with common ker, phylogenetic relationship among 19
mango (M. indica) and other species of Anacar- Mangifera species collected from Indonesia and
diaceae family, i.e., Spondias bahiensis, Spon- Thailand were analyzed. This study demonstrated
dias tuberose, and Rhus chinensis. that the matK as a barcode classified the Mangifera
into three major groups. Furthermore, matK bar-
code identified species originated in Thailand, and
11.3 Use of Chloroplast Genome it was found that matK gene in M. laurina and M.
Sequences macrocarpa were different in specimens collected
from Indonesia and Thailand (Hidyat et al. 2011).
The recognition that chloroplast has its own Identification of mango cultivar ‘Totapuri’ at
unique DNA has led to intensive investigation molecular level was attempted using chloroplast
about organization of chloroplast genomes, trnL-F region by Jagarlamudi et al. (2011). They
sequence properties, and modes of expression of found that these gene sequences are highly con-
constituent genes. Genes having role in photo- served in nature and remain same in any part of the
synthesis, cell regulatory mechanism, resistance plant. Based on sequence of dominant DGGE
for herbicides and biotic, and abiotic stresses band in tested leaves, cent percent similarity was
have been decoded. The highly conserved noted with chloroplast ITS sequences of M. indica.
cpDNA made it possible to use them for phylo- Dinesh et al. (2015) studied phylogenetic
genetic, evolutionary, and cultivar identification relationships among M. andamanica, M. camp-
studies in mango. Xing-Hua et al. (2007) re- tosperma, M. indica, M. griffithii, and M. odorata
ported high degree of chloroplast DNA poly- using markers designed from chloroplast genome,
morphism and suggested cp base DNA markers viz., petB-petD, rps16, trnL-trnF and nuclear
highly useful in taxonomic studies, genetic markers. The chloroplast and nuclear markers-
diversity analysis, hybridity testing, and analysis based phylogenetic analysis revealed close affin-
of cytoplasm inheritance in mango (Xin-hua ity of common mango M. indica L. with
et al. 2007). Similarly, variations in rpl20-rps12 M. camptosperma and M. griffithii of Mangifera
intergenic spacer of chloroplast genome have sub-genus. However, M. odorata of Limus sub-
been successfully used for taxonomic studies and genus separately grouped with M. andamanica.
identification of cultivars in mango (Khan and Harahap et al. (2017) studied phylogenic
Azim 2011). They compared variations in atp- relationships among Mangifera species in
rbcL and rpl20-rps12 spacers of 12 mango cul- Northern Sumatra using trnLF intergenic spacer.
tivars and found that atp-rbcL region had no They categorized Mangifera species into two
variation, while rpl20-rps12 region variation at clades, first consisting of M. odorata (Aceh
both inter-species and intra-varietal levels. Tengah, Aceh), M. odorata (Rantau Prapat,
Table 11.2 Important chloroplast genes and their functions

Gene(s) Function Reference(s)
psaA, psaB, psaC, psaJ, psaI, psbA, psbB, psbC, psbD, psbE, Photosynthetic function Bansal and Saha
psbF, psbH, psbI, psbJ, psbL, psbM, psbN, psbT, cytb6f, ATP (2012)
synthases, rbcL, NAD(P)H, Ycf3a, ycf4 Azim et al.
(2014)
tRNA genes: trnaH, trnK Regulatory role in cell Bansal and Saha
rRNA genes:rrn16, rrn5, rpoA, rpoB metabolism (2012)
rps2, rps3, rps4, rps7, rps8, rps11, rps12, rps14, rps15, Ribosomal proteins Azim et al.
rps16, rps18, rps19, rpl14, rpl16, rpl20, (2014)
rpl22, rpl23, rpl32, rpl33, rpl36
trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, Hypervariable chloroplast DNA Li et al. (2018)
ndhF-rpl32-trnL, ycf1a, ycf1b markers
infA, rpl22, ndh Phylogenetic analyses and Jansen et al.
evolutionary studies (2007)
matK, ycfs Phylogenetic analyses and Carbonell-
evolutionary studies Caballero et al.
(2015)
infA Initiates translation Millen et al.
(2001)
ndhF Stress acclimation Peng et al.
(2011)
PTA (Pinellia ternata agglutinin) Multiple resistances against Jin et al. (2012)
bacteria, insects, and virus
pathogens
CP4EPSPS Glyphosate resistance Ye et al. (2001)
rpl20-rps12 Cultivar identification Khan and Azim
(2011)
ndhA, clpP Cultivar identification Chung et al.
(2019)
trnL, trnF Hybridity testing Muthukumar
et al. (2018)
cemA Gene for inorganic carbon Azim et al.
uptake (2014)
Labuhanbatu, N. Sumatra), M. laurina (Taken- Mango is known to have diverse varieties for
gon, Aceh Tengah, Aceh), M. laurina (Medan, different traits owing to their evolution by open
N. Sumatra), M. indica, M. quadrifida, M. zey- pollination and natural selection and phyloge-
lanica, and second clade consisted of M. foetida netic relationship among cultivars and ascer-
(Aceh Barat, Aceh) and M. foetida (Medan, N. tainment of hybridity of open-pollinated
Sumatra). The intergenic spacer trnL-F with less progenies of mango is very important for trait-
variation in sequences ascertained conserved specific breeding. They also postulated that
nature and low rate of evolution in Mangifera. inheritance of cp genes was not strictly maternal
Muthukumar et al. (2018) affirmed hybridity of but could be paternal or bi-parental in nature
mango cultivars using chloroplast genes trnL and (Muthukumar et al. 2018). A list of chloroplast
trnF localized in large single-copy region. genes and their functions are given in Table 11.2.
11.4 Conclusion analyzing chloroplast DNA diversity in Citrus and

related genera. Tree Physiol 25:661–672
Chung HY, Won SY, Kim YK, Kim JS (2019) Devel-
Advancements in sequencing technologies and opment of the chloroplast genome based InDel
simultaneous development of bioinformatics tools markers in Niitaka (Pyrus pyrifolia) and its applica-
facilitated rapid and cost-effective characterization of tion. Plant Biotechnol Rep 13:51–61. https://doi.org/
10.1007/s11816-018-00513-0
complex cell organelles genomes in different plant
Daniell H, Lin C, Yu M, Chang W (2016) Chloroplast
species in short span of time and in a cost-effective genomes: diversity, evolution, and applications in
way. The complete chloroplast DNA in mango and genetic engineering. Genome Biol 17:134. https://doi.
its wild relatives have been sequenced. Complete org/10.1186/s13059-016-1004-2
Dinesh MR, Ravishankar KV, Nischita P, Sandya BS,
chloroplast genome of Mangifera indica varieties
Padmakar B, Ganeshan S, Chithiraichelvan R,
‘Langra’ and ‘GuiFei’, and wild mango Mangifera Sharma TVRS (2015) Exploration, characterization
sylvatica are now available in public domain. In fruit and phylogenetic studies in wild Mangifera indica
tree like mango, cp genome sequencing would offer relatives. Am J Plant Sci 6:2151–2160. https://doi.org/
10.4236/ajps.2015.613217
unprecedented opportunities for refining our insights Fitmawati F, Hartana A (2010) Phylogenetic study of
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transgenic expression and genome engineering for (1):9–14. https://doi.org/10.4308/hjb.17.1.9
Harahap SP, Fitmawati Sofiyanti N (2017) Phylogenetic
conferring biotic and abiotic stress tolerance, bio- analysis of mango (Mangifera) in Northern Sumatra
synthesis of bioactive compounds and enhancing based on gene sequences of cpDNA trnL-F intergenic
nutritional value of mango. spacer. Biodiversitas 18:715–719. https://doi.org/10.
13057/biodiv/d180239
Hidayat T, Pancoro A, Kusumawaty D, Eiadthong W
(2011) Development matK gene as DNA barcode to
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Mango Functional Genomics
12
Anju Bajpai, M. Muthukumar,
and Sandeep Kumar
Abstract sequencing have been deposited in the NCBI

sequence repository which includes whole
Mango, one of the most relished fruits glob-
transcriptome analysis data of different tissues
ally, has attracted the attention of the global such as flowers, panicles, leaves, fruit pulp,
research community for breeding new vari- peel, and roots pertaining to different com-
eties and hybrids utilizing the naturally exist-
mercial cultivars from various mango func-
ing diverse genetic resources. Functional tional genomics working groups. Despite
genomics approaches are useful in mango non-availability of mango genome sequence
for expediting the trait-specific varietal
in public domain, transcriptomics have pro-
improvement through precision breeding provided leads in marker development and also
grams. This chapter presents the status of for augmentation of genomic resources. Clas-
functional genomics resources in mango that
sical examples and illustrations on the func-
are available in public domain and their tional genomics studies in trait mapping have
applications in trait mapping as well as in also been discussed in detail. Various aspects
breeding for specific target traits such as of functional analysis of genes in terms of
enhanced shelf-life, attractive peel color and full-length cDNAs, EST resources, identifica-
fruit quality traits, regularity in bearing, tion of key candidate genes for specific traits
malformation and abiotic stress tolerance. from transcriptome, proteome and metabolic
The methods, tools, and techniques used in approaches, their cloning and expression
functional genomics, such as transcriptomics, analysis, and genetic transformation have also
proteomics, and metabolomics, are detailed in been summarized. This chapter also highlights
this chapter with examples. The traditional or on the challenges, possible solutions, and
conventional approaches in transcriptional and future prospects of functional genomics in
translational levels of expression profiling are mango.
discussed in this chapter with illustrations. Till
date, 19 transcriptome data sets based on RNA
12.1 Introduction
Mango is an important fruit for the Indian sub-

A. Bajpai (&) M. Muthukumar S. Kumar continent supporting livelihood and nutrition for
Division of Crop Improvement and Biotechnology, many small and marginal farmers besides being a
ICAR-Central Institute for Subtropical Horticulture, part of cultural heritage. Unfortunately, mango
Lucknow 226101, India
breeding and crop improvement are impeded by
e-mail: anju.bajpai@gmail.com

https://doi.org/10.1007/978-3-030-47829-2_12
196 A. Bajpai et al.
Fig. 12.1 Overview of functional genomics based approaches and important target traits of mango
long juvenility, high heterozygosity and poorly fruit quality traits, pulp and peel color, flowering
understood genetics for many important traits and alternate bearing, malformation resistance,
(Bajpai and Muthukumar 2019). Mango func- salinity and chilling injury (Fig. 12.1).
tional genomics offers scope for unraveling
genetic network regulating complex traits, viz,
attractive fruit with delayed ripening, canopy 12.2 Functional Genomics
characteristics, improved rootstock, biotic and Resources
abiotic stress resistance in important cultivars.
The molecular information of mango genome Functional genomics resources pertain to the
would help improvise breeding strategies toward complimentary cDNA sequence information
the development of elite varieties with improved (related to a specific mature mRNA) or protein
agronomic attributes through supplementing tra- sequences that are submitted and stored in the
ditional methods of genetic improvement. Func- public domain database either as a partial or
tional genomics approach encompasses whole complete sequence and are ascribed to genes
genome gene expression profiling through tran- with specific functions. These include either gene
scriptomes to assess transcriptional level changes coding sequences often called expressed
and whole genome proteome profiling to assess sequence tags (ESTs) or amino acid sequences
the translational level changes associated with a that relate to specific peptides or protein
specific trait. In mango, transcriptome analysis sequences. All these sequences should be anno-
especially RNA sequencing has been widely tated and featured with specific exon predictions
explored for understanding several complex for mRNA or motif/domain predictions for a
traits. Limited work has been reported with protein sequence. In mango, as of April 2020
regard to proteomics and metabolomics in mango NCBI data base holds 88,412 nucleotide
with scarce reports on characterization for sequences with 1,231 molecular types repre-
ripening related enzymes and flavor, and aroma senting either genomic DNA or RNA and 2,035
compounds only. The major research efforts by sequences accounting for mRNA contributed by
various working groups are focused on under- 88.411 gene bank source and one from reference
standing the genetic and molecular basis of sequence. Out of 88,412 sequences, about 86,722
important horticultural traits such as ripening and sequences are nucleotide sequences and 1,690
12 Mango Functional Genomics 197
are EST sequences. Although the draft genome transcriptome resources which are available in
has been reported, unavailability on the public the public domain have allowed gene discovery
domain limits the utilization of this genomic and gene expression studies associated with
resource for functional genomics. Yet, consider- complex traits of economic importance like
able amount of SRA submissions pertaining to ripening, shelf-life, pulp traits, etc. These
RNA sequencing datasets of different tissues resources also have potentials for utilization in
from various commercial and popular cultivars or mining genes associated with specific traits in
varieties such as Tommy Atkins, Shelly, Zill, crop improvement programs. Similarly with
Kent, Keitt, Zill, Amrapali, Chausa, and Dashe- respect to protein resources, Uniprot database
hari are available in NCBI database under 19 houses information on 1,197 protein sequences
biosamples as given in Table 12.1. These of Mangifera indica, while the structural
Table 12.1 Transcriptome resources in public domain NCBI database (Information up to April 2020)
S. Bio samples Sequencing SRA Institute
no. platform accession
number (in
relative
order)
1 Mango-Leaves (young:1 Illumina SRX5770298 The University of Queensland,
monthand mature: 5 years) HiSeq 2500 SRX5770299 Brisbane, QLD, Australia
2 Mango—A mixture of roots, Illumina SRX5707082 School of Biological Sciences, The
young and mature leaves, NextSeq 550 SRX5707081 University of Queensland, Brisbane,
stems, axillary buds, flowers, SRX5707080 QLD, Australia
and fruits SRX5707079
3 Dashehari—Pulp Illumina SRX3598947 ICAR-CISH, Lucknow, India
MiSeq
4 Dashehari—Pulp Illumina SRX1687174 CSIR-NBRI, Lucknow, India
HiSeq 2000
5 Chausa—Leaves Illumina SRX1672529 ICAR-CISH, Lucknow, India
NextSeq 500
6 Amrapali—Leaves Illumina SRX1603794 ICAR-CISH, Lucknow, India
NextSeq 500
7 Renong and Uno-bagged and Illumina SRX1645280 South Subtropical Crops Research
unbagged fruits HiSeq 2000 SRX1641640 Institute, China
SRX1641636
SRX1641632
8 Keitt peel Fruit stored—for Illumina SRX1452237 ARO, Volcani Center, Israel
14 days at 12 and 5 °C HiSeq 2000 SRX1452217
—for 7 days at 12 and 5 °C SRX1452216
—for 2 days at 12 and 5 °C SRX1452194
At time of harvest SRX1452149
SRX1452112
SRX1452110
9 Tommy Atkins—mixed organs, Illumina SRX1153795 Monoisolate
seed, mesocarp, Leaf, flower, HiSeq 2000 SRX1149975 Indiana University, USA
exocarp, seed coat SRX1149974
SRX1149973
SRX1149972
SRX1149971
SRX1146011
(continued)

S. Bio samples Sequencing SRA Institute
no. platform accession
number (in
relative
order)
10 Amin Abrahimpur, Burma, M. Illumina SRX1149425 Monoisolate
Casturi “Purple”, Neelum, Thai HiSeq 2000 SRX1149469 Indiana University, USA
Evergreen, Turpentine SRX1149478
SRX1149493
SRX1149504
SRX1149515
11 Ataulfo—Hot water Illumina SRX1058207 CIAD Centro de
disinfection control and treated Genome SRX1058206 InvestigacionenAlimentacion y
fruits’ mesocarp Analyzer IIx SRX1058205 Desarrollo A.C.
SRX1058204
SRX1058203
SRX1058201
SRX1058199
SRX1058169
12 Amrapali—Malformed flower, Illumina SRX3123804 ICAR-NRCPB, New Delhi, India
fruit, and leaf MiSeq SRX3123782
SRX982233
13 Kent—Mesocarp Illumina SRX690486 Universidad Nacional Autonoma de
HiSeq 2000 SRX690439 Mexico, Mexico
SRX690236
SRX689551
14 Keitt—Young leaves, young 454 GS FLX SRX651793 Agricultural Research Organisation,
inflorescences, young fruit, Titanium (ARO), Israel
flesh and peels of mature fruit
15 Keitt—Peel of overripe and ripe Illumina SRX620268 Cornell University, USA
fruits HiSeq 2000 SRX620267
SRX620257
16 Zill—Fruits Illumina SRX434022 South Subtropical Crops Research
HiSeq 2000 Institute, Chinese Academy of
Tropical Agricultural Sciences,
Hongxia Wu
17 Shelly—Control and hot Water Illumina SRX375390 ARO, Israel
Brush treatment at 0, 4,17, and HiSeq 2000
48 h
18 Dashehari-Leaves ABISOLiD SRX553039 ICAR-NRCPB, New Delhi, India
4 System
19 Neelam-Leaves ABISOLiD SRX551448 ICAR-NRCPB, New Delhi, India
4 System
database of protein, i.e., protein data bank wherein such information are available in plenty
(PDB) database has merely one well-predicted because of their well-annotated genomes and
structure of MiGST encoding Glutathione S- huge information on resequencing. Over the
Transferase protein reported through X-ray years, the functional genomic resources flowing
diffraction studies (Chavira et al. 2017). These into the public domain is increasing with the
resources are limited in comparison with other advancements made in next-generation sequenc-
fruit crops such as apple, citrus, and grapes ing (NGS) platforms expediting RNA
sequencing in terms of cost, time as well as 12.3 Functional Genomics

information generation. Strategies, Methods,
RNA-Seq has been widely used by several and Approaches
researchers which not only allows differential
gene expression analysis for understanding Functional genomics strategies of transcrip-
molecular mechanism of complex traits but also tomics, proteomics, and metabolomics have been
identification of simple sequence repeat extensively used for elucidating the molecular
(SSR) and single nucleotide polymorphism mechanisms underlying complex traits in mango.
(SNP) markers. For instance, Iquebal et al. The methods and approaches used in functional
(2017) have used a panel of 84 mango varieties, genomics could be categorized into three gener-
and generated 28.6 Gb data by ddRAD-Seq ations (Table 12.2) based on the technique used,
approach on Illumina HiSeq 2000 platform robustness, and efficiency in understanding
from which 1.25 million SNPs were discovered. gained in a particular trait. Details of the tech-
A web genomic resource MiSNPDb, based on 3- niques and their successful examples have been
tier architecture, was developed using PHP, elaborated in the subsequent sections.
MySQL, and Javascript, which could be exploi-
ted for high-density linkage mapping in mango.
Another database of mango genome called as 12.3.1 First Generation Functional
Mango Genome Database (MGDB) has been Genomics
reported by Qamar-ul-Islam et al. (2018). Simi-
larly, mango genomics resource has been devel- First generation functional genomics involves use
oped at ICAR-Central Institute of Subtropical of tools like northern blotting and polyacrylamide
Horticulture (CISH), Lucknow (www.mangifera. gel electrophoresis (PAGE) for individual tran-
res.in/primer.php) which houses information on script and protein characterization studies. Lim-
genomic and genic SSR markers. A web resource ited work has been done in case of mango and
on cuticle-associated epidermal peel transcrip- much focus was on characterization of full-length
tome data sets generated by RNA sequencing of cDNA related to gene homologs of ripening. The
fruit peel has been documented and is accessi- first report of cDNA encoding alternative oxidase
ble from url: http://bioinfo.bti.cornell.edu/cgi- associated with climateric nature, respiration, and
bin/mango/index.cgi (Tafallo-Aranello et al. ripening processes was isolated and characterized
2017). in mango by Cruz et al. (1995). The gene of 623-
Table 12.2 Classification of different tools and techniques used in mango functional genomics
Time line Techniques for quantification of gene expression and metabolite analysis
Transcriptome Proteome Metabolome
First Northern blot (Specific RNA SDS-PAGE, Native PAGE, Western blot, N- –
Generation detection) terminus Edman sequencing (Specific
protein isolation and analysis)
Second RT-PCR (individual Isoform analysis, Peptide mass fingerprinting –
Generation transcript assays), and Protein sequencing (Specific protein
Differential Display (gene isolation and characterization)
discovery)
Third/Next RNA sequencing (all genes) 2D-GE-MS (few differential proteins), LC- GC-MS (only
Generation and Microarrays (known MS (whole proteome) volatiles)
genes) LC-MS (volatile
and non-volatile
metabolites)
Note The content inside the parenthesis indicates the robustness/limitations of the technique
bp fragment was used as a probe to screen a ripe was isolated from the cotyledon of mango cv.
mango mesocarp cDNA library, from which a Zihua using RT-PCR, and a full-length cDNA
full-length cDNA clone (pAOMI.1), encoding of (2,530 bp) was generated using the 5′ and 3′
mango homolog of the alternative oxidase was rapid amplification of cDNA ends (RACE).
obtained with open reading frame (ORF) yielding Genomic sequence of MiETR1b was 4,116 bp
a polypeptide of 318 amino acids. Gel blot with ORF representing 3,305 bp sequence from
hybridization revealed that pAOMI.1 was likely the start to terminator codon and harboring 6
to be encoded by a single-copy gene. Western exons and 5 introns while the deduced amino
blot analysis using antibodies recognized three acids showed conserved domains of the GAF and
bands of 27, 33, and 36 kDa sizes representing H-ATPase C super-families. MiETR1b was
mitochondrial proteins. The latter two bands were found to be expressed in the proximal and distal
detectable before ripening and the former band cut surfaces throughout the adventitious root
(27 kDa) was accumulated during ripening. formation period which was evident from qRT-
Similarly, Bojorquez and his coworkers (1995) PCR wherein significant up-regulation in roots
characterized a cDNA pTHMF1 encoding for a was ascertained. Unfortunately, proteomics
peroxisomal mango thiolase using differential studies are not much advanced in mango and no
screening of mesocarp cDNA libraries of cv. reports on protein sequencing were reported
Manila and Northern hybridization proved the which could be because of poor specificity in
role of fatty acid metabolism in fruit ripening. In detection while using homologous proteins and
another study, Zainal et al. (1996) have isolated a antibody of relative homologs.
full-length cDNA clone from fruit having
homology to rab11/YPT3 class of small GTPases,
involved in trafficking cell-wall modifying 12.3.3 Third/Next Generation
enzymes through the trans-Golgi network, which Functional Genomics
was found to be expressed in the fruits during
ripening only. The third generation functional genomics
approach includes the latest tools and techniques
that are used in gene expression analysis. This can
12.3.2 Second Generation Functional be grouped as transcriptome analysis techniques
Genomics Approaches such as microarrays and RNA sequencing, pro-
teomics techniques such as 2D-gel electrophore-
The second generation gene expression tools sis and liquid chromatography coupled with mass
include differential display and real-time PCR spectrometry (LC-MS), and metabolomics tech-
techniques for studying expression at transcript niques such as gas chromatography coupled with
level and protein sequencing at translational mass spectrometry (GC-MS) and LC-MS.
level. Luo et al. (2014) have used differential Development of microarray chip for gene
display technique for analyzing differences in expression studies is in infancy stage excepting
gene expression of abiotic stress (cold, drought, for the SNP chips developed for genotyping
salinity, and heavy metal) treatments in mango. (Iquebal et al. 2017). A defined set of well-
Oligo-dT anchored cDNA-SCoT technique was characterized gene probes is essential for devel-
exploited to identify differentially expressed oping gene expression microarrays and without
genes during several stress treatments in mango. the whole genome information this is highly
Ninety-two transcript-derived fragments (TDFs) impractical. Moreover, microarray-based gene
were characterized and their expression patterns expression profiling would be biased because of
were confirmed by quantitative reverse tran- its inherent limitation of characterization of
scription–polymerase chain reaction (qRT-PCR). known genes only. With advancements made in
In a study by Yunhe et al. (2016), a gene NGS platforms, using RNA sequencing for gene
encoding ethyelene response factor (MiETR1b) expression profiling is more rapid, easier, and
efficient owing to the advantages it offers, i.e., 12.4.1 Small RNA Sequencing
studying whole genome gene expression profil- and Identification
ing, understanding minor genes contributing to of MiRNAs for Key Traits
cumulative function, etc. Thus, transcriptome
profiling using RNA sequencing has been widely Small RNA sequencing is a technique for char-
used for gene expression profiling in mango to acterization of miRNAs and is also often quoted
understand different traits. as MicroRNA-Seq which utilizes the NGS or
massively parallel high-throughput sequencing
technologies. This technique differs from RNA-
12.4 Transcriptome Analysis Seq technique because it allows sequencing of
Using RNA Sequencing enriched small RNAs only and is advantageous
in terms of sequence independence and coverage.
Till date, 14 transcriptome data have been well Yet, it has also demerits such as huge costs,
characterized in mango (Table 12.3) which indi- infrastructure, run lengths, and potential artifacts.
cates their potentials in understanding complex Alternately, small RNAs can also be mined from
traits. Perhaps, unavailability of mango genome RNA sequencing transcriptome raw data without
data in the public domain is a critical limitation filtering quality reads. The major idea behind the
that compulsorily forces to opt only for de novo small RNA sequencing is mining of the small
assembly and genomic annotations with related non-coding RNAs and prediction of the targets
genera or family. But if the whole genome gives insights into regulation of complex traits
sequence is made available in open source it which is possible by correlating the target gene
would assist in reference mapping of the tran- expression profiles from transcriptome date with
scripts to the well-annotated genomic regions that miRNA expression profiles of small RNA
facilitates precise gene predictions. Whole gen- sequencing data. As a thumb rule, if miRNA is
ome transcriptome profiling can be performed upregulated, then its corresponding target is
using experimentation and sampling based on expected to be downregulated and vice versa and
(i) case-control that helps in elucidation of mech- thus, it is presumed to play a crucial role in
anisms related to abiotic and biotic stress tolerance regulating downstream genes of a signal trans-
(salinity, drought, cold, malformation, anthrac- duction pathway associated with a complex trait.
nose, wilt) and/or (ii) hypothesis-mechanism Ahmad et al. (2018) used an in silico analysis of
model that allows undermining mechanisms transcriptome data from NCBI database and
behind a specific phenomena such as flowering, identified 18 conserved miRNAs belonging to 15
alternate bearing, peel and pulp coloration. The families. Some important miRNAs identified
transcriptomics work flow is presented in were min-miRNA159, min-miRNA319, min-
Fig. 12.2 which describes the details of the steps miRNA397, min-miRNA160, and min-
involved in RNA-Seq and bioinformatics pipe- miRNA393. Similarly, miRNAs have been
lines. Majority of the transcriptome studies pertain characterized through small RNA sequencing in
to understanding the molecular intricacies of floral and vegetative buds of mango cv. Dashe-
ripening so as to develop varieties with enhanced hari at ICAR-CISH, Lucknow (unpublished),
shelf-life. Most recently, efforts have been made in wherein several known and novel miRNAs were
assessing the gene expression profiles related to identified. A list of known miRNAs and their
other complex traits of mango such as flowering, target transcription factors involved in flowering
anthocyanin pigmentation in peel, chilling resi- that were identified in the study are presented in
lience in peel and hot water treatment for elimi- Table 12.4. Novel miRNAs which are upregu-
nating pathogens as detailed in Table 12.3. lated resulted in its corresponding
Table 12.3 RNA Sequencing based transcriptomics and their utilization in mango functional genomics
202
S. Cultivar Tissue Platform Pathway Prominent genes RT Ref

No. validation
1 Neelam leaves Sequenced-RNA-sequence Regular bearing SPL-like gene (GBVX01015803.1), Rumani Yes Sharma et al.
and reads and transcript and alternate GA-20-oxidase-like gene (2020)
Dashehari assembly from Mahato bearing (GBVX01019650.1), LOC103420644
et al. 2016 SOLiD total (GBVX01016070.1), and
RNA Seq GBVW01004309.1
2 Zill Fruits Raw transcriptome reads Resistance gene NBS, NBS-LRR, CNL, TNL, CN, TN, RLP, No Lantican
from Hong et al. (2016). analogs (RGAs) RLK, TM-CC, and NBS-encoding proteins et al. (2020)
llumina paired-end with other domains.
sequencing
3 Amrapali Healthy Illumina NextSeq Flowering genes MYB30, TPL, bHLH, FTIP1, CDKC2, Yes Yadav et al.
and in relation to CPK33, ATH1, UBP12, EFS, AGL8, AGL14, (2019)
malformed floral AGL20, AGL24, KIN10, MYB30, SUS2,
floral buds malformation FTIP1, CCT, LDL2, TIL1, TIC, DCL3,
GA20OX3, CCT, AP1, AGL6, AGL8,
MYB30, AGL8, GCT, and GA3OX1
4 Amrapali Leaf Illumina Anthocyanin Alternate spliced variance of CHS, CHI, and Yes Bajpai et al.
NextSeq 500/MiSeq biosynthesis F3H (2018a, b)
pathway related
to fruit peel color
5 Ataulfo Mesocarp Genome analyzer GAIIx II Effect of hot PME, PL, PG, GLB-1, and RG1 Yes Dautt-Castro
water treatment et al. (2018)
on Cv. Ataulfo
6 Keitt Peel Illumina HiSeq 2000 Chilling stress on NADPH Oxidase, MAP Kinase, WRKYs. No Sivankalyani
fruit peel et al. (2016)
7 Zihua – Illumina Hiseq 2500 Adventitious root G1/S-specific cyclin D, CDK inhibitor, Yes Li et al.
formation from Pectate Lyase, Expansin, Xyloglucan (2017b)
cotyledon endotransglycosylase, Endo-1,4-beta-
segment glucanase
(continued)
A. Bajpai et al.
12
S. Cultivar Tissue Platform Pathway Prominent genes RT Ref
No. validation
8 Alphonso Flowers Illumina HiSeq 1000 Fruit CS1, CS2, CTN1, CTN2, CTN3, PL1, PL2, Yes Deshpande
and fruits Development PL3, O3FAd, O6FAD, CFACL, G3PAT1, et al. (2017)
and ripening with G3PAT2, G3PAT3, ADH1, ADH2, ADH3,
respect to aroma ERF1, ERF2, ERF3, ERF4, ERF5, DRP1,
and shelf-life DRP2, MTPS1, MTPS2, MTPS3, MTPS4,
MTPS5, MTPS6,STPS1, STPS2, STPS3,
STPS4, STPS5, DTPS1, DTPS2,DTPS3
Mango Functional Genomics
9 Keitt Fruit Illumina Identification of CD2. SHN1, CER2, CER3, CS2, CS6, LTP3, Yes Tafolla-
HiSeq 2500 system cuticle- LTP1, WBC11, LTP2, LTPG1, CUS1, CUS2, Arellano
associated genes PEL1, NAC, C2C2-GATA, G2-like, CRPK1 et al. (2017)
Like Kinase, HSF, MYB and bHLH
10 Dashehari Fruit 454-GS-FLX Ripening MYB, bHLH, WRKY, HSF, NAC, bZIP, ERF, Yes Srivastava
associated genes SAM Synthase, ACS, ACO, CTR ETR, EIN3, et al. (2016)
Endo-beta-1,4-glucanase, Expansin, Pectate
Lyase, Polygalacturonase
11 Zill Fruits Illumina paired-end Host responses ERFs, NBS-LRR, NPR1 , and PR Yes Hong et al.
sequencing of the mango (2016)
fruit against C.
gloeosporioides
12 Kent Mesocarp Genome Fruit ripening ACO, PME, PG, PL, GLB-1, GUN, GAL-A, Yes Dautt-Castro
Analyzer GAIIx II EXP, RGL, IDI, FPPS, GGPS, SuSy, et al. (2015)
CRTISO, CHYB, BAM, etc.
13 Alphonso Fruit Megabase 100 DNA Fruit IPPI, GPPS, MTPS, GGPPS, FPPS, SqTPS, Yes Pandit et al.
sequencer development and IsoCH, GT, MDHAR, 14-3-3, MT, MeTR, (2010)
ripening sHSP, CHI, CysPI, ERF, UbqPL
14 Dashehari Pulp ABI 373A Ethylene induced Pectate Lyase Normal Chourasia
post-harvest PCR/semi- et al. (2006)
softening quantitative
PCR
203
Fig. 12.2 The transcriptomics work flow describing the details of RNA-Seq and bioinformatics pipelines
Table 12.4 Flowering related known miRNAs identified in flower bud of mango cv. Dashehari
Known miRNAs Gene target Significance and function
miR156 SPL Phase transition V-R, promotes flowering
miR157 SPL Phase transition V-R, promotes flowering
miR172 AP2 Repressor in photoperiod induction
miR159 MYB Promotes flowering
miR171 SCL/LM Promotes/delays flowering
miR319 TCP Promotes flowering
miR390 tasi RNA Promotes juvenility
miR393 TIR Repressor
miR399 PHT2 Temperature, phosphate starvation responsive, Repressor
miR5200 FT Photoperiod induction and promotes flowering
miR169 NF-Y Repress/induce flowering in response to abiotic stress
miR824 AGL Repressor based on environment/genetic background
Fig. 12.3 Novel miRNAs involved in GA signalling in flowering
downregulation of target GRAS family tran-

scription factors involved in GA signaling (GA 12.5 Proteomics Approaches
inhibition-based floral induction) in flowering in Understanding Complex
(Fig. 12.3). Other novel miRNAs identified Traits
targeted SPL and ARF transcription factors.
Unique miRNAs targeting NBS-LRR/Phosphate Proteomics is a study of total proteome configu-
2, S-locus protein kinase were identified in floral ration of the cell or organelle which comes from all
bud. the expressed genes at a given point of time and
tissue. This is a powerful tool that can be used to has developed combinatorial peptide ligand
elucidate the complex traits at the cellular and libraries (CPLLs) for investigating the proteomes
molecular levels. An overall status of protein- of mango peel and pulp as well their peptidome
based studies is presented in Table 12.5. The content (the latter as captured with a C18 resin)
modern proteomics tools include 2D-MS, LC-MS, and used this technique to assess the potential
and HPLC-MS as explained briefly in the earlier presence of allergens and of peptides endowed
classification section. Andrade et al. (2012) have with biological activities. Similarly, Chin et al.
reported on the first comparative proteomic (2019) studied the comparative proteome profiles
investigation between the pre-climacteric and of mesocarps of ripe and unripe fruits of mango
climacteric fruits of mango cv. Keitt to identify cvs. Chokanan and Golden Phoenix using 2-
protein species with variable abundance during dimensional gel electrophoresis (2D-GE) coupled
ripening. In their study, proteins were extracted with MALDI-TOF/TOF. Differentially abundant
from fruits through phenol-extraction protocol proteins identified were found to be involved in
followed by cyanine-dye-labeling and separation ethylene synthesis and aromatic volatiles, cell wall
on 2D gels at pH 4–7. Around 373 proteins spots degradation, and stress-response proteins. Six
were identified from which 47 were consistently differential proteins were validated using qRT-
differentially regulated and were subjected to LC- PCR in which genes encoding glutathione S-
MS/MS analysis. This study helped in the identi- transferase (GST) and alpha-1,4 glucan phospho-
fication of proteins associated with ripening, color rylase (AGP) were found to express in concordant
development, and pulp softening. Fasoli (2013) with differential proteome profiles.
Table 12.5 Brief overview on protein isolation and characterization studies in mango
Time line Approach and technique Protein class Function and trait References
First Individual protein Protein kinase II (PK-II) Phosphorylating casein Frylinck
generation analysis-SDS-PAGE and involved in fruit et al.
ripening (1998)
Second Differential protein Rubisco large subunit 1, carbon fixation, hormone Andrade
generation regulation 2D-DIGE phosphoglycerate kinase, biosynthesis, catabolism, et al.
triose–phosphate stress-response (2012)
isomerase, NADB
Rossmann superfamily
peptides, malate
dehydrogenase, phospho-
glucomutase, enolase,
aldehyde dehydrogenase,
phosphoglycerate kinase,
F1 ATPase family,
transaldolase, electron
transfer flavoprotein–
ubiquinone
oxidoreductase, adenylate
kinase
Second SDS-PAGE and Lewis type a1,3/a1,4- Biosynthesis of Le(a) Okada et al.
generation Western blot analysis fucosyltransferase containing (2017)
glycoconjugates
Second SDS-PAGE and Tau class glutathione S- Cellular detoxification Valenzuela-
generation Zymography transferase Chavira
et al.
(2017)
(continued)

Time line Approach and technique Protein class Function and trait References
Third Protein purification a-amylase iso-enzymes Fruit ripening Ubonbal
Generation using affinity et al.
chromatography, (2017)
Analysis by SDS-
PAGE, Zymography,
and LC-MS/MS
Third 2-dimensional gel glutathione S-transferase Fruit ripening Chin et al.
Generation electrophoresis (2D- (GST) and alpha-1,4 (2019)
GE) coupled with glucan phosphorylase
MALDI-TOF/TOF (AGP)
Third 2-dimensional gel Cytosolic class II small Immunity and defense, Liao et al.
Generation electrophoresis (2D- heat-shock protein oxidation and reduction, (2016)
GE) coupled with HSP17.5, Superoxide and amino acid and
MALDI-TOF/TOF dismutase, Glutamine carbohydrate metabolism
synthetase, Vitamin-b12
independent methionine
synthase, NADP-
dependent malic enzyme,
NAD-malate
dehydrogenase
Third Transcriptome, SDS- 14-3-3, Small heat-shock Signal transduction, Renuse
Generation PAGE, LC-MS/MS protein, Chloroplast apoptosis, cell cycle et al.
chlorophyll A/B binding control, Protein folding, (2012)
protein, Photosynthesis, Citric
Succinate dehydrogenase, acid cycle and electron
3-ketoacyl-CoA thiolase transport chain, Fatty
B: acetyl-CoA C- acid beta-oxidation,
acyltransferase, Glycolysis,
Glyceraldehyde-3- Oxidoreduction
phosphate dehydrogenase,
Glycolate oxidase
chromatography coupled with mass spectrometry

12.6 Metabolomics Approaches commonly called GC-MS and LC-MS, respec-
in Understanding Complex tively. Metabolomics studies in mango are focus-
Traits sed on the characterization of flavor and aroma
compounds in different mango varieties
Metabolomics is a study of metabolome of an (Table 12.6) and mainly using GC-MS technique.
organism’s specific tissue at a given develop- Major flavor and aroma compounds identified
mental stage or pooled stages. It involves studying were mainly falling in the groups of coumarins or
the total metabolite profile which includes both lactones, terpenes, and terpene hydrocarbons. The
primary and secondary metabolites; under a given metabolite studies could also be confirmed by
situation or a developmental stage that defines its transcriptome studies or real-time gene expression
temporal, spatial, and developmentally controlled profiling pertaining to the genes involved in
production. The modern tools for metabolomics specific lactone or terpene or flavonoid biosyn-
approach include gas chromatography and liquid thetic pathways.
Table 12.6 Status of metabolite characterization in different mango varieties using metabolomics approach
S. Technique Cultivar and Metabolite Profile References
no. tissue Total Major Unique metabolites
metabolites metabolites
1 GC-MS Haden, Irwin, 145 Terpene d-3-carene (Haden, Quijano
Manila and hydrocarbons Irwin, Manila and et al. (2007)
Tommy (major Tommy Atkins), a-
Atkins, volatiles) pinene (Hilacha
Hilacha, and Vallenato), a-
Vallenato, Van phellandrene (Van
Dyke, Yulima Dyke), and
(Fruits) terpinolene
(Yulima)
2 GC- Haden, White 54 27 aroma 4-hydroxy-2,5- Munafo
Olfactometry Alfonso, volatiles dimethyl-3(2H)- et al. (2014)
PrayaSowoy, furanone
Royal Special,
and Malindi
(Tree ripe
fruits)
3 GC-MS Shindri, 34 Bicyclo [4.1.0] – Baloch et al.
Langra (Peel) hept-3-ene (2017)
(49%), 3, 7, 7-
trimethyl-,
(1S) (47%)
(Major
essential oils)
4 GC-MS Twenty-five 127 Monoterpenes b-Myrcene Li et al.
mango (Major aroma (Xiaofei, (2017a)
varieties of and aroma Philippines); c-
China, volatile) Octanoic lactone
America, (Guiya, China);
Thailand, Hexamethyl
India, Cuba, cyclotrisiloxane
Indonesia, and (Magovar/Mulgoa,
the Philippines India)
5 GC-MS Ambika, 60 Coumarins Furo-coumarin Unpublished
Arunika, (Major aroma (Arunika, both
Amrapali, volatiles) parents Amrapali
Vanraj, and and Vanraj)
Janardhan dimethoxy-
Pasand flavones (Ambika
and Amrapali
female parent and
absent in Janardhan
Pasand)
12.7 Trait Mapping, Identification, 2014), cv. Kent (Dautt-Castro et al. 2015), cv.
and Functional Dashehari (Srivastava et al. 2016), cv. Keitt
Characterization of Genes (Tafolla-Arellano et al. 2017) were utilized to
Using Functional Genomics divulge insights on genetic resources responsi-
ble for flavor and color of mango fruit.
The transcriptome of mango mesocarp cv. Kent Sequence diversity and differential expression of
identified gene families important for ripening major phenylpropanoid-flavonoid biosynthetic
and captured most of the gene space in mango genes among three mango varieties elucidated
(Dautt-Castro et al. 2015). The expression data characteristic patterns that differed between
obtained by RNA-seq was favorably validated mango peel and flesh of important germplasm
with the data obtained by qRT-PCR. Limited (Hoang et al. 2015). The leaf transcriptome
shelf-life and perishability of mango fruits limit repository was utilized to mine transcript
marketing and global transport, due to posthar- sequences from phenylpropanoid flavonoid
vest desiccation and senescence. Recent studies pathway for elucidating red peel development,
utilizing RNA-Seq analysis (Tafolla-Arellano and anthocyanin genes with MYB, bHLH
et al. 2017) suggested that the pathway lead- transcription factors were upregulated in red
ing to biosynthesis of the cuticle component, peel cultivars (Fig. 12.4; Bajpai et al. 2018a).
cutin, is upregulated during overripening. Genes involved in salinity stress tolerance
RNAseq and de novo assembly of cv. Langra were shortlisted from transcriptome data of
leaf transcriptomic sequences yielded 13,500 salinity tolerant mango cv. 13-1 and these mined
unigenes that could be assigned to 293 KEGG genes such as OLP, ADH, APN, YABBY, FLP,
pathways with emphasis on an array of bio- DREB, DNaseI, WRKY72, LOG, GT were vali-
chemical pathways involved in (a) biosynthesis dated using RT-PCR assay (Bajpai et al. 2018b).
of bioactive flavonoids, flavones and flavonols, Muthukumar et al. (2018) mined leaf transcrip-
(b) biosynthesis of terpenoids and lignins, and tomes (SRA Nos. SRP070908, SRP072727) and
(c) plant hormone signal transduction (Azim shortlisted 6 key genes, viz., STPK, MAPK6,
et al. 2014). Mango fruit transcriptomes of cv. ERF2, MYC2, MDH, and TPS related to salinity
Zill (Wu et al. 2014), cv. Shelly (Luria et al. stress responses and used for expression analysis
Fig. 12.4 Utilization of leaf transcriptome repository for mining anthocyanin pathway genes
Fig. 12.5 Molecular mechanism of salinity tolerance in mango cvs
using salinity tolerant cv. Nekkare and salinity chemistries (Fig. 12.6). Role of F. mangiferae in
susceptible cv. Vellai Colomban. The overall stimulating stress ethylene production and over
strategy used for elucidation of molecular load of “stress ethylene” causing malformed tis-
mechanism of salinity tolerance in mango cvs sue development suggest that cyanide can be an
13-1 and Nekkare is presented in Fig. 12.5. etiological agent (Ansari et al. 2015). Signifi-
Chilling stress in fruit peel of “Keitt” mango was cantly higher levels of cyanide, a by-product of
monitored by transcriptomic, physiological, and ethylene biosynthesis, and corresponding low-
microscopic analyses. Symptoms of chilling ered b-cyanoalanine synthase gene (b-CAS)
injury include red and black spots that start from expression is associated with accumulation of
discolored lenticels and develop into pitting. unmetabolized cyanide in malformed inflores-
Transcriptomic changes in the mango fruit peel cence (Ansari et al. 2019).
were evaluated during optimal (12 °C) and sub- Annual transition of apical meristem from
optimal (5 °C) cold storage (Sivankalyani et al. vegetative to floral is the key feature that deter-
2016). mines regular bearing behavior of mango cultivars
Mango malformation disease (MMD) is under subtropical ecosystems. Characterization of
characterized by symptoms manifested in vege- Constans like gene (Zhang et al. (2005) and role of
tative and floral tissues which includes abnormal, Flowering locus T in inductive conditions were
compact development of shoots, flowers, and established by different workers (Nakagawa et al.
leaves. Metabolite profiles of malformed and 2012; Santos-Villalobos et al. 2012). Expression
non-malformed (normal) panicles of mango were analysis of mango Flowering Locus T (FT) and
obtained by GC-MS that reveal distinct Terminal Flower 1 (TFL1) genes was done in
Fig. 12.6 Metabolite

profiles of malformed and
non-malformed panicles
mango cultivars Alphonso and Ratna in Inida

(Vyavahare et al. 2017). RNA-seq data has also 12.8 Discovery, Tagging, Isolation,
allowed identification of key differentially regu- and Characterization of Genes
lated genes (DEGs) coding for transcription fac- for Specific Traits
tors related to vegetative growth, ABA and auxin
hormonal changes, sugar metabolism and dor- Gene tagging methods are traditional approaches
mancy related genes (Bajpai et al. 2019), that for mapping traits which are done through acti-
indirectly influence flower induction. vation tagging or transposon tagging methods.
Using mapping populations and mutants in tag- 12.9 Functional Validation of Key
ging the genes are cumbersome in perennial Genes for Specific Traits
systems like mango and therefore, such approa-
ches have limited scope. Alternately techniques All 3-omics components of functional genomics
for gene discovery are i. using genomic infor- such as transcriptomics, proteomics, and meta-
mation and identification of gene homologs in bolomics in mango have helped in short-listing
wild species of Mangifera, ii. full-length cDNA several key genes associated with the specific
isolation and characterization using 3′-rapid traits as discussed earlier in the trait mapping
amplification of cDNA ends (RACE) and 5′- section. These key genes are ideal candidates for
RACE. Some successful examples are available functional validation and utilization in mango
related to ripening related genes such as ETR1, breeding or trait improvement programs. At first,
ERS1, Rab5, anthocyanin synthesis, and flow- these genes need to be confirmed if they are
ering pathway genes (Table 12.7). governing the trait. This could be ascertained by
Table 12.7 Molecular cloning and expression of key genes for specific traits toward functional validation
S. Gene (s) Function Full- Cloning Trait Reference
No. length vector and
clone Expression
system
1 ETR1 and ERS1 Ethylene RACE pMD18-T Ripening Li et al.
biosynthesis (2019)
2 SOC1 Flowering 3′ and 5′ pGEM-T Flowering Wei et al.
pathway RACE Easy (2016)
Vector
3 F3’5’H Flavonoid 3′ and 5′ – Peel Zhao
pathway RACE coloration et al.
(2016)
4 Rab5 GTP-binding 5′ pET-30a Fruit Liu et al.
Protein RACE ripening and (2014)
stress
response
5 ANS Anthocyanin 3′ and 5′ – Peel Zhichang
biosynthesis RACE coloration et al.
(2014)
6 ETR1b Ethylene 3′ and 5′ pMD18-T Ripening Yunhe
biosynthesis RACE vector et al.
(2013)
7 ERS1 Ethylene DNA – Ripening Contreras-
biosynthesis walk- Vergara
ing et al.
(2012)
8 ACC, ACO1, ACS1, ACS3, Ethylene From – Fruit de Godoy
AMY, AOX, APX, BGAL, enzymes, NCBI softening, et al.
CHS1, CHS2, EXP, FFT, Starch database cell wall (2009)
FGT, UDP glucose: mobilization, integrity,
flavonoid 3-O- Ascorbate peel and
glucosyltransferase; PG, metabolism pulp color
PME, PHO, Alpha 1,4-
glucan phosphorylase; R1,
Starch debranching enzyme
either using knock-out mutant analysis or genetic (2019) have first reported successful functional
transformation using Agrobacterium-mediated validation of eukaryotic translation initiation
transformation system using the gene associated factors (eIFs) associated with abiotic stress, viz.,
with the trait. Functional validation is usually MieIF1A-a, MieIF5, and MieIF3sB that were
done through knock down mutant screens in most strongly expressed under salinity, osmotic,
Arabidopsis models or through induced mutation and low temperature (2 °C) stress, respectively.
created by site-directed mutagenesis followed by Overexpression of MieIF1A-a in Arabidopsis
screening the mutants in subsequent generations. resulted in enhanced seedling growth and sur-
This need to be further confirmed in native host vival rates, higher chlorophyll content, increased
plant, i.e., mango through transgenics approach. ROS scavenging enzyme activities (superoxide
But owing to the reasons such as perenniality, dismutase, peroxidase, and catalase), and
heterozygosity, and heterogeneity in mango, the decreased malondialdehyde accumulation under
mutant screening seems to be highly imperative salt treatment compared to the wild-type Ara-
and thus mutant screening studies are not bidopsis. This study provides new insights into
advisable. Next best choice for functional vali- the MieIF genes that could be applied to the
dation is molecular cloning of the candidate breeding of salt-tolerant mango varieties. With
genes and expression in model organisms such as all these challenges to be resolved, presently only
tobacco, tomato, or Arabidopsis system through resort could be Agrobacterium-mediated in-
Agrobacterium-mediated transformation. Both planta transformation and thus efforts are
for mutant screen assays and genetic transfor- underway in different laboratories. There are so
mation, the first and foremost requisite is an many constraints in developing transgenic man-
efficient protocol for regeneration and generation goes and in the present scenario, functional
of large number of tissue culture plants for genomics approaches would aid in smart breed-
functional characterization and validation. ing through using functional genomics for min-
Unfortunately, limited success has been reported ing functional markers, i.e., SSR or SNP markers
in mango regeneration systems and only few co-located within the genes for specific traits and
sporadic reports are available on successful using these markers for genome-wide association
regeneration of tissue culture mango plants studies would help in molecular breeding
(Mishra et al. 2010; Busaidi et al. 2016). Li et al. (Fig. 12.7).
Fig. 12.7 Global research organizations and their research priorities

12.10 Global Mango Functional and the Clustered Regularly Interspaced Short
Genomics’ Working Groups Palindromic Repeats (CRISPR-Cas/) systems,
called as genome editing techniques. Unlike the
Globally several research organizations have Agrobacterium-mediated transformation which
research priorities (Fig. 12.7) that address mango integrates the gene into any location, the genome
genetic resources management, genomic resour- editing tools offer scope for engineering the plant
ces augmentation and their utilization through genome directly through targeting the location of
functional genomics tools such as transcrip- the gene to specific genomic locations and
tomics, proteomics, and metabolomics. An Aus- making minimum alternations in the genome. As
tralian group comprising of Frank Wise Institute of now, genome editing approaches have not
of Tropical Agriculture, Agriculture Western been initiated in mango yet, it has ample scope in
Australia, Kununurra Queensland Horticulture near future. Similarly, a new area of genomics
Institute Mareeba, Queensland Northern Terri- tool called genetical genomics has evolved which
tory Department of Primary Industries and integrates the genetics and gene expression
Fisheries and Darwin CSIRO Plant Industry, analysis. The identification of the causal genes
Darwin have a major focus on molecular breed- and markers underlying quantitative trait loci
ing and genomics. CIRAD, France has emphasis (QTLs) would help in effective marker-assisted
on “genomics and effectomics”. CGIAR insti- breeding in mango. So far, paucity of markers
tutes such as ILRI, Kenya; ICRISAT, Hyderabad and genotyping were presumed to be a major
in collaboration with USDA, USA and CIAD, challenge in mango improvement. But with the
Mexico has been concentrating efforts on geno- latest developments in NGS and genotyping by
mics and genomic resources. IITA, Nigeria sequencing (GBS) platforms, genotyping costs
another CGIAR institute has been working on have been curtailed to a large extent and the
disease resistance and functional genomics available mapping populations at ICAR-CISH,
aspects related to disease resistance. In India, ICAR-IIHR, and ICAR-IARI could be geno-
CSIR and ICAR institutes are major contributors typed and used for genome-wide association
of functional genomics in mango. ICAR- studies. ICAR-CISH, Lucknow, is a national
NRCPB, New Delhi, is a global leader in germplasm active repository of mango with more
sequencing mango genome in collaboration with than 800 mango germplasm accessions and sev-
ICAR-CISH, Lucknow; ICAR-IARI, New Delhi; eral hybrid progenies and thus has enormous core
and ICAR-IIHR, Bengaluru. The same team is and mapping populations for selection of asso-
involved in functional genomics with specific ciation panels. Efforts are made in this direction
focus expression profiling of different mango by different working groups including ICAR-
varieties and hybrids as well as the molecular CISH for utilizing these “omics” technologies,
genetics of key straits such as flowering, mal- viz., transcriptomics, metabolomics, and pro-
formation, peel and pulp color. teomics for developing markers and utilizing
them in molecular breeding and developing more
superior hybrids.
12.11 Conclusion and Future
Prospects Mango Functional Genomics
Research Working Groups
Precision functional genomics tools have been
developed in the recent past due to technological ARO VC Agricultural Research Organization,
advancements made in tailored editing of specific Volcani Center, Israel
genomic regions using engineered nucleases BGI Beijing Genomics Institute, China
such as zinc finger nucleases (ZFNs), transcrip- CDRI Central Drug Research Institute,
tion activator-like effector nucleases (TALENs), Lucknow, India
CGIAR Consultative Group on International USDA US Department of Agriculture,

Agricultural Research Washington, USA
CIRAD The French Agricultural Research
Centre for International
Development. Montpellier, France.
CISH Central Institute for Subtropical References
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Mango Genomic Resources
and Databases 13
Sarika Jaiswal, Mir Asif Iquebal, UB Angadi,
Sunil Kumar, Anil Rai, Nagendra
K. Singh, and Dinesh Kumar
Abstract tome based and SNP marker based. Linkage

Map genomic resource describes how two
Web resources are the archival repository for
distinct varieties, i.e., Jin-Hwang and Irwin
data and also a research accelerator tool for have been used to make the very first
global community, economizing cost of data high-density genetic map of mango. This is
along with the advantage of rapidity, and ease
based on 156,368 polymorphic specific-locus
of accessibility. Recently, the mango genome amplified fragments (SLAFs) with total length
has been sequenced but very limited web of 3,148.28 cM and 20 linkage groups with an
genomic resources of this crop are available.
average marker distance of < 0.50 cM. Whole
This chapter covers mango web genomic genome-based genomic resources covers latest
resources under four sub-heads, viz., linkage whole genome sequence (WGS) data accessi-
map based, whole genome based, transcrip-
bility at NCBI (BioProject: PRJNA487154). It
also provides INSDC ID of all 12 chromosome
for download. Transcriptome-based genomic
resources describe existing genomic resource
S. Jaiswal M. A. Iquebal U. Angadi S. Kumar
A. Rai D. Kumar (&) MGdb based on four mango varieties, viz.,
Centre for Agricultural Bioinformatics, ICAR-Indian langra (Pakistan), zill (China), shelly (Israel),
Agricultural Statistics Research Institute, New Delhi, and kent (Mexico). This section also tabulates
India
transcriptome resources available in GenBank
e-mail: dinesh.kumar@icar.gov.in
with varieties, types/treatment of tissues, Bio-
S. Jaiswal
project number with country and organiza-
e-mail: sarika@icar.gov.in
tional details. The last section of this chapter
M. A. Iquebal
e-mail: ma.iquebal@icar.gov.in
describes how such web genomic resources
can be used for DNA-based varietal signature
U. Angadi
supplementing distinctness, uniformity and
e-mail: ub.angadi@icar.gov.in
stability (DUS) test, quantitative trait locus
S. Kumar
(QTL) detection, gene discovery, variety
e-mail: sunil.kumar7@icar.gov.in
improvement for better biotic and abiotic
A. Rai
e-mail: anil.rai@icar.gov.in
stresses management, traceability, adulteration
issues in mango product or origin or protection
N. K. Singh
in terms of intellectual property (IP) of geo-
ICAR-National Institute for Plant Biotechnology,
New Delhi, India graphical indication (GI) law. More such
e-mail: nksingh4@gmail.com resources are warranted not only for

https://doi.org/10.1007/978-3-030-47829-2_13
220 S. Jaiswal et al.
knowledge discovery but also for better pro- 13.2 Mango Genome Resources
ductivity and profitability of mango growers as Linkage Map
with better consumer interest protection.
Genetic maps are important resources used in
mapping if simply inherited and quantitative trait
13.1 Introduction
loci (QTLs) and thereby in marker-assisted
selection (MAS) for improvement in target
Web resources or databases have become not
traits. In mango, a genetic map has been prepared
only an archival space for data, but are also a tool
by the crossing of two distinct varieties, Jin-
for organizing voluminous biological data which
Hwang and Irwin, by researchers at the Key
can be used by global researchers to access and
Laboratory of Tropical Fruit Biology, Ministry of
retrieve customized information. Users can easily
Agriculture; South Subtropical Crops Research
access and share/use the data in minimum time
Institute, Chinese Academy of Tropical Agricul-
and in a user-friendly manner, economizing cost
tural Sciences, Zhanjiang, China. This was
of data and also with advantage of rapidity
achieved by genomic and phenomic data of 173
(Lathe et al. 2008). Though mango is the ‘king of
F1 plants and high-throughput sequencing and
fruits’ of tropical and subtropical ecological
specific-locus amplified fragment (SLAF) library
region of the world with relatively smaller
construction. This very first high-density genetic
allotetraploid genome size of < 450 Mb made of
map of mango was constructed by 66.02 GB
20 pairs of chromosome, still genomic resources
genomic data having 330.64 M reads, 156,368
of mango are very limited. Very recently, in the
polymorphic SLAFs (out of 318,414 SLAFs).
year 2020, chromosome-wise whole genome
This map has a total length of 3,148.28 cM, with
sequence assembly of mango genome has
an average marker distance of <0.50 cM by use
become available (Wang et al. 2020). Unless
of 6,594 SLAFs distributed on 20 linkage groups
more and more genomic resources are available,
(Table 13.1). The single nucleotide polymor-
the germplasm improvement using genomics-
phism (SNP) distribution and transition/
based approach can never be able to see the light
transversion numbers are shown in Table 13.2.
of the day.
The mango crop is highly sensitive to diver-
sity of both, soil and tropical ecology. This has
led mango crop to evolve with diverse varieties 13.3 Whole Genome-Based
having unique appearance, taste, and aroma in Genomic Resources of Mango
different geographical regions of the world.
Hence their genomic resources are equally Though cytogenetic, transcriptome and genetic
diverse. The web genomic resources as a source map data had been available in mangoes, whole-
of knowledge discovery can be used to under- genome resources were publically available only
stand the crop with better management of in the year 2020. The popular traditional Indian
germplasm. The following mango genomic mango variety Alphonso was sequenced by
resources are available in the public domain for China in collaboration with the USA. This was
the global community: done by using the PacBio Sequel II platform
1. Mango genomic resources as linkage map along with paired-end, mate-paired short reads
2. Whole genome-based mango genomic and Hi-C sequencing for scaffolding. De novo
resources assembly having 20 chromosomes (pseudo-
3. Transcriptome-based genomic resources molecules) were made by anchoring scaffolds
4. SNP marker-based genomic resources. over genetic maps having 20 linkage groups
13
Table 13.1 Basic characteristics of the 20 linkage groups of mango. (Luo Chun et al. 2016)
Linkage Total number of markers Total distance (cM) Average distance (cM) Gap <5 (cM) Max. gap (cM) Number of markers
group with segregation
distortion
Female Male Integrated Female Male Integrated Female Male Integrated Female Male Integrated Female Male Integrated Integrated map
map map map map map map map map map map map map (%) map map map
(%) (%)
LG1 230 145 362 161.96 113.72 168.04 0.71 0.79 0.47 96.51 92.36 98.06 22.148 22.188 9.612 17
LG2 170 111 272 180.35 165.48 173.21 1.07 1.50 0.64 94.67 93.64 97.05 21.295 23.033 12.019 8
LG3 245 67 299 198.74 104.87 170.13 0.81 1.59 0.57 96.31 90.91 98.32 13.030 14.758 10.450 28
LG4 390 162 526 188.39 137.92 184.04 0.48 0.86 0.35 99.23 95.65 99.43 13.548 31.201 10.715 1
LG5 209 80 262 144.75 88.97 150.23 0.70 1.13 0.58 95.67 93.67 97.70 10.940 17.055 10.940 22
LG6 207 76 255 146.29 108.31 119.44 0.71 1.44 0.47 98.06 92.00 96.85 16.249 38.316 13.690 3
LG7 195 49 224 125.31 116.33 121.40 0.65 2.42 0.54 96.39 91.67 97.76 12.290 39.192 10.311 9
Mango Genomic Resources and Databases
LG8 191 74 219 167.78 105.03 175.09 0.88 1.44 0.80 97.37 91.78 96.79 28.000 45.865 12.075 15
LG9 202 171 368 182.83 258.06 198.19 0.91 1.52 0.54 95.02 93.53 97.28 20.624 45.959 18.734 3
LG10 192 130 287 119.61 122.70 122.33 0.63 0.95 0.43 96.86 96.12 99.30 9.610 34.369 5.144 0
LG11 392 235 480 178.46 189.62 184.04 0.46 0.81 0.38 98.21 96.58 99.37 9.523 19.466 5.388 12
LG12 160 108 231 136.15 106.60 126.40 0.86 1.00 0.55 93.71 93.46 98.70 12.401 21.295 5.245 9
LG13 264 160 371 160.10 141.03 150.57 0.61 0.89 0.41 97.72 93.08 98.92 16.249 21.295 6.088 17
LG14 219 86 272 116.84 109.00 123.21 0.54 1.28 0.45 96.33 96.47 98.89 6.143 46.874 8.047 14
LG15 183 98 262 140.72 85.10 141.19 0.77 0.88 0.54 95.05 92.78 96.17 9.926 16.249 6.801 4
LG16 477 223 591 206.09 169.13 205.69 0.43 0.76 0.35 98.74 96.40 99.49 11.665 31.035 6.967 1
LG17 174 80 228 132.75 116.64 133.93 0.77 1.48 0.59 95.38 86.08 95.15 45.959 24.032 13.799 0
LG18 158 160 266 140.96 192.00 170.57 0.90 1.21 0.64 93.63 96.23 98.11 21.026 33.952 12.696 11
LG19 359 294 520 193.20 258.51 206.90 0.54 0.88 0.40 98.04 95.22 98.27 38.932 27.908 17.809 0
LG20 249 76 299 122.95 58.87 123.68 0.50 0.78 0.42 97.18 88.00 97.99 10.227 6.705 8.827 0
Total 4866 2585 6594 3144.23 2747.89 3148.28 0.65 1.07 0.48 96.50 93.28 97.98 45.959 46.874 18.734 174
*“Gap < 5” indicates the percentages of gaps in which the distance between the adjacent markers was less than 5
221
Table 13.2 Distribution Linkage group SNP number Transition/transversion number

of SNP loci on the 20
linkage groups of mango LG1 750 487/263
(Luo et al. 2016) LG2 575 371/204
LG3 691 439/252
LG4 1112 692/421
LG5 592 404/189
LG6 561 389/172
LG7 512 340/172
LG8 443 278/165
LG9 775 497/279
LG10 596 421/176
LG11 971 578/393
LG12 474 312/162
LG13 788 523/265
LG14 562 355/207
LG15 506 319/188
LG16 1139 726/414
LG17 515 351/164
LG18 549 329/221
LG19 1105 705/400
LG20 628 397/231
Table 13.3 Whole Total sequence length : 392,983,452

genome data of mango at
NCBI (BioProject: Total ungapped length : 392,900,608
PRJNA487154) Gaps between scaffolds : 0
Number of scaffolds : 252
Scaffold N50 : 17,652,500
Scaffold L50 : 10
Number of contigs : 421
Contig N50 : 3,579,047
Contig L50 : 35
Total number of chromosomes and plasmids : 22
Number of component sequences (WGS or clone) : 252
(Wang et al. 2020). These genomic resources are Table 13.3. The entire 20 chromosomes can be
freely accessible at NCBI (BioProject: downloaded using INSDC ID as shown in
PRJNA487154). The assembly statistics reflect- Table 13.4 along with their respective size and
ing the quality of assembly are shown in GC content.
13 Mango Genomic Resources and Databases 223
Table 13.4 Mango Sl. no. Type/name *INSDC ID Size (Mb) GC%
chromosome-wise data
(Wang et al. 2020) 1. Chromosome 1 CM021837.1 29.46 32.5
2. Chromosome 2 CM021838.1 24.4 32.5
3. Chromosome 3 CM021839.1 23.14 32.9
4. Chromosome 4 CM021840.1 21.51 32.7
5. Chromosome 5 CM021841.1 21.08 33.1
6. Chromosome 6 CM021842.1 18.81 32.4
7. Chromosome 7 CM021843.1 20.62 32.5
8. Chromosome 8 CM021844.1 18.24 33.5
9. Chromosome 9 CM021845.1 18.23 32.5
10. Chromosome 10 CM021846.1 17.65 32.4
11. Chromosome 11 CM021847.1 17.14 32.9
12. Chromosome 12 CM021848.1 16.03 32.8
13. Chromosome 13 CM021849.1 15.46 32.5
14. Chromosome 14 CM021850.1 14.81 32.7
15. Chromosome 15 CM021851.1 14.77 32.3
16. Chromosome 16 CM021852.1 13.82 32.4
17. Chromosome 17 CM021853.1 13.51 32.4
18. Chromosome 18 CM021854.1 13.37 32.6
19. Chromosome 19 CM021855.1 13.09 32.5
20. Chromosome 20 CM021856.1 12.29 32.3
21. Mitochondria CM021857.1 0.87 44.4
22. Plasmids CM021858.1 0.15 37.8
23. Unplaced – 34.52 33.5
*INSDC: International Nucleotide Sequence Database Collaboration
are available online in GenBank. In Table 13.5,

13.4 Transcriptome-Based Genomic such transcriptome resources are described with
Resources of Mango variety, type/treatment of tissue, Bioproject
number of GenBank, and country with organi-
Qamar-ul-Islam et al. (2018) have reported the zational details.
mango web genomic resource MGdb, based on
comparative transcriptome analysis of four
mango varieties, viz., Langra (Pakistan), 13.5 SNP Genomic Resources
Zill (China), Shelly (Israel), and Kent (Mexico). of Mango
This was based on limited public domain sec-
ondary transcriptome data which were already World’s first web-based genomic resources based
published. These transcriptome resources were on 84 distinct mango varieties was reported from
pooled from mango varieties, viz., Langra (Azim India (Iquebal et al. 2017). This was based on
et al. 2014), Zill (Wu et al. 2014), Shelly (Luria 1.25 million SNPs, discovered from 28.6 Gb
et al. 2014), and Kent (Dautt-Castro et al. 2015). data, generated by ddRAD-Seq approach using
Though Mango Genome Atlas as web geno- Illumina HiSeq 2000 platform. The developed
mic resource for this particular plant is yet to be web genomic resources MiSNPDb is freely
developed, considerable transcriptomic resources accessible at http://webtom.cabgrid.res.in/
Table 13.5 Transcriptomic resources of different mango varieties

Sl. Variety Tissue BioProject Organization with country
no. number
1 Dashehari Floral and vegetative PRJNA610491 ICAR-Central Institute for
buds of mango Subtropical Horticulture,
Lucknow, India
2 Wild Mango Six sets PRJNA533518 University of Queensland,
Australia
3 Dashehari Jelly seed stage PRJNA431125 ICAR-Central Institute for
Subtropical Horticulture,
Lucknow, India
4 Dashehari Fruits with various stage PRJNA317712 ICAR-Central Institute for
of ripening and aroma Subtropical Horticulture,
Lucknow, India
5 Chausa Various stages of fruits PRJNA317044 ICAR-Central Institute for
Lucknow, India
6 Zihua Stages of root formation PRJNA316542 Chinese Academy of
in cotyledon segments Tropical Agricultural
of mango Sciences, Zhanjiang, China.
7 Dashehari Fruits stages for PRJNA317712 CSRI-National Botanical
ripening and aroma Research Institute, Lucknow,
India
8 Keitt Tissue bud with stages PRJNA315791 South Asia Tropical Crop
of infection with Research Institute, CATAS,
Fusarium mangiferae China
9 Amrapali various stages of flower PRJNA313340 ICAR-Central Institute for
Lucknow India
10 Ono and Renong No.1 Pericarp PRJNA310193 South Subtropical Crops
Research Institute, Chinese
Academy of Tropical
Agricultural Sciences
11 Keitt fruit peel with chilling PRJNA304093 Agricultural Research
stress Organization, Volcani
Center, Israel
12 Tommy Atkins with other six mixed organs, seed, PRJNA288797 Keithanne Mockaitis,
varieties viz Turpentine’ ‘Thai seed coat, mesocarp, Indiana University,
Everbearing’ ‘neelum’ M. casturi leaf, flower, exocarp for Bloomington
“Purple”‘ ‘Burma’ ‘Amin marker discovery
Abrahimpur’
13 Ataulfo hot water treated fruits PRJNA286253 CIAD: Centro de
for insect control Investigacion en
Alimentacion y
Desarrollo A.C. Mexico,
Mexico
14 Amrapali Malformed flower, PRJNA27982 ICAR-Indian Agricultural
Mango healthy fruit, Research Institute, New
Amrapali leaf Delhi, India
(continued)

Sl. Variety Tissue BioProject Organization with country
no. number
15 Kent Mesocarp for fruit PRJNA258477 National Autonomous
ripening University of Mexico
(Universidad Nacional
Autonoma de Mexico),
Mexico
16 Tomy Atkins and Keitt Different fruit stages PRJNA254771 Agricultural Research
Organization, Volcani center,
Israel
17 Keitt Fruit peel PRJNA253272 Cornell University, Ithaca,
New York
18 Zill Fruit development and PRJNA235247 South Subtropical Crops
ripening in mango Research Institute, Chinese
Academy of Tropical
Agricultural Sciences
19 Shelly Fruit stress Hot water PRJNA227243 Agricultural Research
treatment Organization, Israel
20 Dushehari leaves PRJNA193591 ICAR-National Research
Centre on Plant
Biotechnology, Pusa
Campus, New Delhi, India
21 Neelam leaf PRJNA193588 National Research Centre on
Plant Biotechnology, IARI
Pusa Campus, New Delhi,
India
22 Langra leaves PRJNA192676 International Center for
Chemical and Biological
Sciences, University of
Karachi, Karachi, Pakistan
mangosnps/. Table 13.6 describes type of SNP development of varietal DNA signature, trace-
variation, their number and percentage of the ability, genome finishing and SNP chip devel-
SNP type in MiSNPdb. Table 13.7 describes opment for future genome-wide association
number of SNP available in 84 different mango studies (GWAS) in genomic selection programs
varieties in MiSNPdb. (Iquebal et al. 2017). It can be used for other non-
model species which are genetically close to this
species. These SNPs can be mapped in latest
13.6 Utility of Mango Web Genomic genome assembly of mango and such location
Resources specific SNP can be of much greater value.
Markers of Mango SNP database can be used
Mango genomic resources are required to over present linkage map of mango. This can
improve the germplasm for resistance against increase marker density further over chromo-
various biotic and abiotic stresses. They are also some. The database has markers from non-genic
required to accelerate the DNA-based varietal regions also thus ultra-dense genetic map is
differentiation, phylogeographic studies, QTL feasible covering entire chromosome region. It
detection, and gene discovery in germplasm can be used for mango throughput SNP arrays
management and improvement. It can be used in (SNP chip) development where MAF
Table 13.6 Type of SNP variation, their number and percentage of the SNP type (Iquebal et al. 2017)
Type of variation Number Percentage of the SNP type
A/G 427968 34.00
C/T 429349 34.11
A/T 118403 9.40
A/C 98811 7.85
C/G 83914 6.66
G/T 100260 7.96
Total 1258705 100.00
Table 13.7 Number of SNPs detected in each of the 84 varieties of mango (Iquebal et al. 2017)
Variety Number of Variety Number of Variety Number of
SNPs SNPs SNPs
Afeam 17749 Fazri Kalam 11889 Mohanbhog 8980
Alphan 16439 Gilas 8132 Mombosa 18388
Alphanso 12305 Gola Bhadaiya 19057 Mulgoa 18270
Amin Prince 13929 Gourjeet 9891 Mundappa Black 8955
Amrapali 14002 Gulab Khas Green 11236 Neelum 15352
Arka Aruna 18636 Hardil Aziz 10045 Nekkare 16946
Arunika 8913 Heraswania 26619 Prabhashankar 5018
Baganapalli 19227 Himsagar 31479 Primor de 9979
Amoreira
Banganpalli 16458 Hyb. 165 13375 Pusa Arunima 22087
Banglora 13851 Irwin 9889 Pusa Lalima 16964
Baramasi 19290 Iturba 18228 Pusa Peetamber 13154
Baramasi 13286 Janardan Pasand 15850 Pusa Pratibha 11330
Ajholi
Bathui 11030 Kala 13867 Pusa Shersth 12922
Bhadaiya 15080 Kalapahar 8873 Pusa Surya 14123
Sukul
Bhadauran 11122 Karishad 9704 Ramkela 16380
Bombay 7440 Kesar 19130 Rataul 17558
Bombay 13236 Khasulkhas 14202 Ratna 14419
Green
Bombay 9793 Kothapalli Kobbari 13768 Rosari 16491
Yellow
Bride of 22978 Kurukkan 11571 Safdar Pasand 14382
Russia
Carabao 15576 Langra 30131 Samar Bahist 7946
Alibagh
Chandrakaran 13538 Langra Gorakhpur 14260 Seipia 17643
Chinku 12245 Machhli 15548 Sensation 13110
Creeping II 15272 Malda 15530 Sonatol 9698
(continued)

Variety Number of Variety Number of Variety Number of
SNPs SNPs SNPs
Dushehari 15095 Malihabad Safeda 13653 Sukul 18788
Edward 13431 Mallika 19592 Suvarnarekha 37688
Elaichi 9243 Manipur dwarf 11064 Tatoul 3122
Extrema 15042 Manorajan 33248 Willard 26827
Fazri 13350 Mohammada 19862 Zardalu 4936
Vikarabad
(minorallele frequency) information is critically discovery such resources also play a critical role
required for selection of SNPs for array devel- in terms of better profitability to mango growers
opment to be used in GWAS and genomic and also ensuring consumer interests protection
selection programs. as envisaged in GI law of countries.
Use of mango SNPs and mango genomic
resources is very useful in DNA-based trace-
ability in establishing the origin of mango
products. In case of varietal dispute for intellec- References
tual property (IP) or sovereignty issues, few
selected SNPs can be used as DNA signature of Azim MK, Khan, I, Zhang Y (2014) Characterization of
mango variety. SNPs offer advantages by their mango (Mangifera indica L.) transcriptome and
ability of high-resolution power and objectivity. chloroplast genome. Plant Mol Biol 85(1–2):193–
208. https://doi.org/10.1007/s11103-014-0179-8
It can easily be achieved by taking any sample in Dautt-Castro M, Ochoa-Leyva A, Contreras-Vergara1
form of live germplasm or any tissue of pro- CA, Pacheco-Sanchez MA, Casas-Flores S, Sanchez-
cessed products with rapidity and cost- Flores A, Kuhn DN, Islas-Osuna MA(2015) Mango
effectiveness (Iquebal et al. 2017). Such DNA- (Mangifera indica L.) cv. Kent fruit mesocarp de novo
transcriptome assembly identifies gene families impor-
based tests are legally admissible while estab- tant for ripening. Front Plant Sci 6:62. https://doi.org/
lishing varietal identity during dispute resolution. 10.3389/fpls.2015.00062
Online availability of such resources to the glo- Iquebal MA, Jaiswal S, Mahato AK, Jaiswal PK,
bal community can accelerate the development of Angadi UB et al (2017). MiSNPDb: a web-based
genomic resources of tropical ecology fruit mango
a specific assay for varietal identification as and (Mangifera indica L.) for phylogeography and varietal
when required for group of mango varieties differentiation. Sci Rep 7:14968 (2017). https://doi.
having adulteration issues in their product or org/10.1038/s41598-017-14998-2
origin or protection in terms of GI (geographical Lathe W, Williams J, Mangan M, Karolchik D (2008)
Genomic data resources: challenges and promises. Nat
indication) protection. The phylogenetic tree Educ 1(3):2
using 749 common SNPs across 84 mango Luo C, Shu B, Yao Q, Wu H, Xu W, Wang S (2016)
varieties has revealed three major lineages Construction of a high-density genetic map based on
among the Indian mango varieties, which were large-scale marker development in mango using
Specific-Locus Amplified Fragment Sequencing
superimposed over geographical map of India (SLAF-seq). Front Plant Sci 7:1310. https://doi.org/
(Iquebal et al. 2017). It has clearly demonstrated 10.3389/fpls.2016.01310
the ability of such genomic resources to protect Luria N, Sela N, Yaari M, Feygenberg O, Kobiler I,
intellectual property given to mango growing Lers A, Prusky D (2014) De-novo assembly of mango
fruit peel transcriptome reveals mechanisms of mango
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tection. Besides research and knowledge (1):957. https://doi.org/10.1186/1471-2164-15-957
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Genetic Resources in Mango

Chapter · March 2021

Shailendra Rajan Manish Srivastav

SEE PROFILE SEE PROFILE

Farmers' FIRST Project View project

Mango Functional Genomics View project

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Chittaranjan Kole Editor

More information about this series at http://www.springer.com/series/11805

The Mango Genome

ISSN 2199-4781 ISSN 2199-479X (electronic)

© Springer Nature Switzerland AG 2021

As expected, sequencing of chromosomal regions would have led to too

physiology, pathology, entomology, nematology, crop production, bio-

New Delhi, India Chittaranjan Kole

The development of molecular tools in mango is extremely limited, and

in high-end mango research. I personally congratulate the authors and the

New Delhi, India K. L. Chadha

The chapters of this book have been contributed by 47 authors precisely

New Delhi, India Chittaranjan Kole

1 Mango: The King of Fruits . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

12 Mango Functional Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . 195

K. Abirami ICAR-Central Island Agricultural Research Institute, Port Blair,

Sarika Jaiswal Centre for Agricultural Bioinformatics, ICAR-Indian

Nimisha Sharma Division of Fruits and Horticultural Technology, ICAR-

2,4-D 2,4-dichlorophenoxyacetic acid

ITS Internal transcribed spacer

Abstract 1.1 Introduction

© Springer Nature Switzerland AG 2021 1

1.2 Voyages to Different Buddhist monks during the fourth-ﬁfth centuries

Fig. 1.1 Area under cultivation in different countries

Name Amount Unit Min Max

1.5 Usage yogurts, soups, meat, ﬁsh curry, spices, etc.

Abstract M.sylvatica, M.odorata, M.zeylanica and M.

© Springer Nature Switzerland AG 2021 13

Table 2.3 Mangifera species as donors

Though there is a growing awareness about 3. Rare: M. andamanica

2.3.1 Description of the Mangifera 2.3.2 Botanical Descriptions

M.andamanica M.camptosperma M.grifithii

Fig. 2.1 Fruits of different Mangifera species

Fig. 2.2 Types of shoots and inflorescence in mango (Davenport 2007)

Fig. 2.3 Filament

Fig. 2.4 Pollen grain size

2.3.4 Pollen Characteristics 2.3.4.1 Floral Biology

2.4.2 Polyembryony preference as edible varieties. Hence, the

Abstract polyembryonic mangoes as rootstocks.

© Springer Nature Switzerland AG 2021 31

3.3 Substrates for Mango 3.4 Monoembryonic Versus

have a full air porosity (FAP) value between 15

success in grafting by cutting the petioles exchange of germplasm started to be practiced

areas of India and also for mild weather in

3.6.5 Care and Maintenance

For improving success of mango grafting it is

Fig. 3.6 Mango graft after removal of protection

white paper bag to reduce heat stress. All the

hard plastic (about 80 mm long 60 mm width)

3.6.6 Other Techniques

Mango can be also propagated through cuttings

3.6.7 Micropropagation through direct somatic embryogenesis. The con-