Definition, Aim, Objectives and Scope of Plant Breeding

Definition :
• Plant breeding can be defined as an art, a science, and technology of
improving the genetic make up of plants in relation to their economic use
for the man kind.
or
• Plant breeding is the art and science of improving the heredity of plants for
the benefit of mankind.
or
• Plant breeding deals with the genetic improvement of crop plants also
known as science of crop improvement.
or
• Science of changing and improving the heredity of plants for benefit of
society
 Plant breeding is a branch of agriculture that focuses on manipulating plant
heredity to develop new and improved plant types for use by society.
 Plant breeding — the science of maximizing plants’ positive genetic traits to produce
desirable effects.
 Plant breeding is a way to modify and improve plant species to achieve the needs and
wants of humankind.
Disciplines Related to the Science of “Plant Breeding”

 Botany

 Genetics and cytogenetics

 Agronomy/Physiology

 Plant Pathology /Entomology /Bacteriology /Virology

 Plant Biochemistry

 Statistics, Biometry, Biometrical genetics

 Plant Biotechnology
 Aims /Objectives of Plant breeding
Plant breeding aims to improve the characteristics of plants so that
they become more desirable agronomically and economically.
• The specific objectives may vary greatly depending on the crop
under consideration.
Objectives of Plant Breeding
1. Higher yield : The ultimate aim of plant breeding is to improve the yield of
economic produce. It may be grain yield, fodder yield, fiber yield, tuber yield,
cane yield or oil yield depending upon the crop species.
2. Improved quality: Quality of produce is another important objective in plant
breeding. The quality characters vary from crop to crop.
3. Abiotic resistance : Crop plants also suffer from abiotic factors such as drought,
soil salinity, extreme temperatures, heat, wind, cold and frost, breeder has to
develop resistant varieties for such environmental conditions.
4. Biotic resistance : Crop plants are attacked by various diseases and insects,
resulting in considerable yield losses.
• Genetic resistance is the cheapest and the best method of minimizing such
losses. Resistant varieties are developed through the use of resistant donor
parents available in the gene pool.
Objectives Cont…
5. Change in maturity Duration/Earliness : Earliness is the most desirable
character which has several advantages. It requires less crop management
period, less insecticidal sprays, permits new crop rotations and often extends
the crop area.
• Breeding for early maturing crop varieties, or varieties suitable for different
dates of planting may be an important objective. Maturity has been reduced
from 270 days to 170 days in cotton, from 270 days to 120 days in pigeon pea,
from 360 days to 270 days in sugarcane.

6. Determinate Growth- Development of varieties with determinate growth is

desirable in crops like Mung, Pigeon Pea (Cajanus cajan ), Cotton (Gossypium
sp.)
7. Dormancy : In some crops, seeds germinate even before harvesting in the
standing.
• A period of dormancy has to be introduced in these crops to check loss due to
germination. In some other cases, however, it may be desirable to remove
dormancy.
Objectives Cont…
8. Desirable Agronomic Characteristics: It includes plant height,
branching, tillering capacity, growth habit, erect or trailing habit
etc., is often desirable. For example, dwarfness in cereals is
generally associated with lodging resistance and better fertilizer
response. Tallness, high tillering and profuse branching are
desirable characters in fodder crops.
9. Elimination of Toxic Substances : It is essential to develop
varieties free from toxic compounds in some crops to make them
safe for human consumption.
10.Non-shattering characteristics: The shattering of pods is serious
problem in green gram. Hence resistance to shattering is an
important objective in greengram.
11.Synchronous Maturity : It refers to maturity of a crop species at
one time. The character is highly desirable in crops like
Greengram, Cowpea, and Cotton where several pickings are
required for crop harvest.
12.Wider adaptability : Adaptability refers to suitability of a variety
for general.
 Plant breeding objectives will depend on:
 Genetics
 Resources available to the breeder
 Sources of germplasm available
 Nature of the transfer of the trait
 Economics – who is going to make decision (the private or
public)
The goals of plant breeding are:
 Addressing world food, feed, and nutritional needs
 Addressing food needs for a growing world population
 The need to adapt plants to environmental stresses
 The need to adapt crops to specific production systems
 Developing new horticultural plant varieties
 Satisfying industrial and other end-use requirements
 ACTIVITIES IN PLANT BREEING
1. Creation of Genetic Variation
1.1 Creation of new variability (man made)
 Hybridization
 Polyploidy
 Somaclonal variation
 Genetic engineering
1.2. Naturally existing variability
2. Selection
3. Evaluation of the selections
4. Multiplication of the variety (the new variety)
5. Distribution to the users
Polyploidy
Polyploid plants possess three or more sets of homologous
chromosomes.
The increase in chromosome number in these plants is the result
of a genome duplication event.
Depending on the origin of the genome duplication:
two Types of polyploid
Autopolyploids- which are derived from multiplication of a
diploid genome (intraspecies),
Allopolyploids- which are the consequence of hybridization
followed by doubling of the two haploid genomes (interspecies)
Genetic variation among cultivars and related species of tomato for fruit characteristics
which includes variation for size, shape, and color
The basic elements of plant breeding strategy are:
1. to identify the morphological, physiological, and pathological
traits in a cultivated plant
2. species that contributes to its adaptation, health, productivity, and
suitability for food, fiber, or industrial products;
3. to search out new genes that encode for desired traits in different
strains of the cultivated species and their close relatives;
4. to combine genes for the desired traits into an improved cultivar
through traditional breeding or new biotechnology procedures;
5. to assess performance of the improved breeding lines in the local
environment in comparison with present cultivars; and
6. to distribute as new cultivars breeding lines superior to cultivars
currently grown.
 Undesirable effects of plant breeding
However, it has the following undesirable effects on crop plants.

1. Reduction in Diversity : Modern improved varieties are more

uniform than land races. Thus plant breeding leads to reduction
in diversity. The uniform varieties are more prone to the new
races of pathogen than land races which have high genetic
diversity.

2. Narrow genetic base : Uniform varieties have narrow genetic base.

Such varieties generally have poor adaptability.

3. Danger of Uniformity : Most of the improved varieties have some

common parents in the pedigree which may cause danger of
uniformity.
 Chapter 2:
Crop Evolution Domestication and polyploidy

• The process of evolution has parallels in plant

breeding.
• Darwin’s theory of evolution through natural
selection can be summed up in three principles
that are at the core of plant breeding.
 These are the principles of
1. Variation- Variation in morphology, physiology,
and behavior exist among individuals in a natural
population.
2. Heredity- Offspring resemble their parents more
than they resemble unrelated individuals.
3. Selection- Some individuals in a group are more
capable of surviving and reproducing than others
(i.e., more fit).
 A. Morphological & chemical features changed by
evolution
1. Reduced plant size, determinate growth, dwarfing, associated
usually with favourable partition but not conspicuously with
shorter life cycle:
Sunflower, barley, rice wheats, soybean, pea, beans (Phaseolus),
cowpea (and probably other cereals and pulses), some hemp,
bananas, coconut, apple and pear (rootstocks), peppers, tomato,
potatoes, kola.
2. Reduced plant size and woodiness associated with shorter life
cycle (trend to annuality):
Brassica crops, radish, castor, cassava, rye, pigeon pea, Phaseolus
beans, flax/linseed, cottons, buckwheat.
3. Taller, less branched plants, leading to fewer, larger inflorescences
or fibrous stems:
Grain amaranths, sunflower, maize, flax, hemp, jute.
 ……. changed by evolution
4. Altered photoperiod/vernalization requirements, associated with
latitudinal/climatic adaptation:
Grain amaranths, beets, lettuce, Brassica crops, radish, rice,
sugarcane, rye, sorghum, wheats, maize, pigeon pea, pea,
soybean, Phaseolus beans, cowpea, onion, buckwheat, potato,
carrot.
5. Reduced spininess:
Sisal, pineapple, lettuce, yams, castor, okra, blackberry, eggplant.
6. Reduction of toxic constituents:
Mango (resins), quinoa (saponins), safflower (polyphenolics),
Brassica crops (various compounds), cucurbits (cucurbitacins),
yams (alkaloids), cassava (CN-lycosides), pulses generally (trypsin
inhibitors, haemagglutinins, amino acids, CN-glycosides, eggplant
(bitter principle), potatoes (steroidal alkaloids).
 ……..changed by evolution
7. Development of attractive colours/patterns:
Grain amaranths, sugarcanes, maize, various pulse seeds (e.g.
Phaseolus, Vicia), Capsicum peppers, potatoes, carrot, tomato.
8. Non-shattering infructescences/fruits:
Grain amaranths, quinoa, safflower, lettuce, Brassica crops,
castor, grass-cereals and pulses generally, flax/linseed, hemp,
buckwheat, tobacco.
9. Reduced seed (or tuber) dormancy:
Yams (tuber), oats, rice, rye, wheats, pulses, buckwheat, potatoes
(tuber).
10. Multiple uses, changes of evolutionary direction:
Beets, safflower, Brassica crops, radish, flax/linseed, hemp,
Capsicum peppers, cucurbits.
Chapter 3: Plant genetic resources
conservation and characterization
Origin/Diversity centers
Vavilov considered that “as a rule the primary foci of crop origins were in
mountainous regions, characterized by the presence of dominant alleles.”
• In this he recognizes eight primary centers, as follows.
I. The Chinese Center - in which he recognizes 138 distinct species of which probably
the earlier and most important were cereals, buckwheats & legumes.
II. The Indian Center (including the entire subcontinent) - based originally on rice,
millets and legumes, with a total of 117 species.
IIa. The Indo-Malayan Center (including Indonesia, Philippines, etc.) - with root crops
(Dioscorea spp., Tacca, etc.) preponderant, also with fruit crops, sugarcane,
spices, etc., some 55 species.
III. The Inner Asiatic Center (Tadjikistan, Uzbekistan, etc.) - with wheats, rye and
many herbaceous legumes, as well as seed-sown root crops and fruits, some 42
species.
IV. Asia Minor (including Transcaucasia, Iran and Turkmenistan) - with more wheats,
rye, oats, seed and forage legumes, fruits, etc., some 83 species.
V. The Mediterranean Center - of more limited importance than the others to the
east, but including wheats, barleys, forage plants, vegetables and fruits -especially
also spices and ethereal oil plants, some 84 species.
Origin/Diversity centers
VI. The Abyssinian (now Ethiopian) Center - of lesser importance, mostly a refuge of
crops from other regions, especially wheats and barleys, local grains, spices, etc.,
some 38 species.
VII. The South Mexican and Central American Center - important for maize,
Phaseolus and Cucurbitaceous species, with spices, fruits & fibre plants, some 49
species.
VIII. South America Andes region (Bolivia, Peru, Ecuador) - important for potatoes,
other root crops, grain crops of the Andes, vegetables, spices and fruits, as well
as drugs (cocaine, quinine, tobacco, etc.), some 45 species.
VIIIa. The Chilean Center - only four species - outside the main area of crop
domestication, and one of these (Solarium tuberosum) derived from the Andean
center in any case.
VIIIb. Brazilian-Paraguayan Center - again outside the main centers with only 13
species, though Manihot (cassava) and Arachis (peanut) are of considerable
importance.
• After this brief survey it seems quite clear that out of the very wide range of plant
diversity in the tropical and warm temperate regions of the world our major food crops
have come mainly from high mountain valleys, isolated from each other to a large extent
and with a very great habitat range.
Origin/Diversity centers
.

(1) Mexico-Guatemala, (2) Peru-Ecuador-Bolivia, (2A) Southern Chile, (2B) Southern

Brazil, (3) Mediterranean, (4) Middle East, (5) Ethiopia, (6) Central Asia, (7) Indo-
Burma, (7A) Siam-Malaya-Java, (8) China and Korea.
Origin/Diversity centers
 Gene pool concepts
Three categories were defined, primary, secondary, and tertiary gene pools:
1. Primary gene pool (GP1). GP1 consists of biological species that can be intercrossed
easily (interfertile) without any problems with fertility of the progeny.
That is, there is no restriction to gene exchange between members of the group. This

group may contain both cultivated and wild progenitors of the species.
2 Secondary gene pool (GP2). Members of this gene pool include both cultivated and wild
relatives of the crop species. They are more distantly related and have crossability
problems. Nonetheless, crossing produces hybrids and derivatives that are sufficiently

fertile to allow gene flow. GP2 species can cross with those in GP1, with some fertility
of
the F1, but more difficulty with success.
3 Tertiary gene pool (GP3). GP3 involves the outer limits of potential genetic resources.
Gene transfer by hybridization between GP1 and GP3 is very problematic, resulting in
lethality, sterility, and other abnormalities. To exploit germplasm from distant relatives,
tools such as embryo rescue and bridge crossing may be used to nurture an embryo
from a wide cross to a full plant and to obtain fertile plants.
Gene pool concepts
 Why conserve plant genetic resources?
There are several reasons why plant genetic resources should be conserved:
1. Plant germplasm is exploited for food, fiber, feed, fuel, and medicines by
agriculture, industry, and forestry.
2. As a natural resource, germplasm is a depletable resource.
3. Without genetic diversity, plant breeding cannot be conducted.
Genetic diversity determines the boundaries of crop productivity and
survival.
4. As previously indicated, variability is the life blood of plant breeding. As society
evolves, its needs will keep changing.
Genetic erosion
Genetic erosion may be defined as the decline in genetic variation
in cultivated or natural populations largely through the action of
humans.
Loss of genetic variation may be caused by natural factors, and by
the actions of crop producers, plant breeders,
Conservation
Two major approaches are being employed to conserve plant
genetic resources:

1. In situ conservation, i.e. the maintenance of genetic resources in

their natural habitat or on-farm, i.e. in areas where the
germplasm obtained; and
• These protected areas are called by various names (e.g., nature reserves, wildlife
refuges, natural parks).
2. ex situ conservation, i.e. maintaining the collected genetic
resources in especially constructed institutions or genebanks.
• The latter consists of a number of different methods, including
seed storage, in vitro and cryopreservation, the maintenance of
plants in field gene banks and pollen storage.
 Characterization
• A botanical name is a formal scientific name conforming to the
International Code of Nomenclature for algae, fungi, and plants
(ICN)
The levels from highest to lowest classification are as
follows:
 Kingdom
 Phylum
 Class
 Order
 Suborder
 Family
 Genus
 Species
 Subspecies
 International Codes of Nomenclature
 Taxonomists have established several “codes” for scientific
nomenclature.
 These codes are universal and are periodically updated by
consensus.
 The protocol for naming species was invented in the 1700s by
Swedish botanist Carl Linnaeus.
 Linnaeus created the system of “binomial nomenclature,” which
uses only two designations–genus and specific epithet as the
species name.
Common name: These are used locally and may vary by region or country.
Scientific name: These are unique names used by the scientific community to
accurately and universally identify species.
• .
Binomial Name
• The binomial name consists of a genus name and specific
epithet.  The scientific names of species are italicized.
• The genus name is always capitalized and is written first; the
specific epithet follows the genus name and is not capitalized.
Examples
Ensete ventricosum
Allium cepa
Manuhot escculenta
• Landrace - a cultivated crop species that has evolved from wild
populations due to selective pressures from traditional farmers. is
called a
• Landraces, which can be the result of natural forces or
domestication, are plants (or animals) that are ideally suited to a
particular region or environment.
• A clone is a vegetatively propagated population of genetically
identical plants.
The cultivar (agricultural variety) is a group of genetically similar plants, which by
structural features and performance may be identified from other groups of
genetically similar plants within a species.
To understand the concept of the cultivar requires a knowledge of the system of
plant classification. The plant kingdom is divided into taxonomic groups of
similar and closely related plants; in this scheme, families of plants are divided
into genera, which are subdivided into species.
• Within the species, the agronomist and horticulturalist recognize numerous
agricultural varieties, more commonly referred to as varieties or cultivars.
• Variety and cultivar may be used interchangeably, but cultivar is now preferred
in scientific literature. The distinction of being named and distributed
commercially serves to set apart the cultivar from the experimental strain or
breeding line.
• Two essential characteristics of a cultivar are (1) identity and (2) reproducibility.
• Identity is necessary so that the cultivar may be recognized and distinguished
from other cultivars within the species.
 Chapter 4:
Mode of reproduction/mating systems
• Plant Breeding systems:
Breeding system of plants are classified as
 inbreeders,
 outbreeders,
 in-between (in-outbreeds, out-inbreeders) &
 asexually propagated types
Reproduction systems in plants
• Sexual/Seed propagated species
• self-pollinated
• cross pollinated
• self- and cross pollinated
• Vegetatively propagated species
 Sexual reproduction
• In animals: It’s easy because you have separate
male and female individuals.
• In flowering plants: Not so easy, because most
flowers have both male and female parts in them,
called perfect flowers.
• So flowering plants have evolved special ways to
insure out-breeding/out-crossing – and to
prevent inbreeding.
Sexual reproduction
 Advantages of Autogamy
• Insures seed set in absence of pollinators.
• Overcomes sterility.
• Selectively advantageous by transmitting both
sets of genes to offspring.
– Well-adapted genotypes preserved.
• Only single colonizing individual needed.
 Disadvantages of Autogamy
• Decreases genetic variability.
• Inability to adapt to changing conditions.
• Increases inbreeding depression.
– Reduces heterozygosity & increases
- homozygosity of deleterious alleles.
– More uniform populations.
 Cleistogamy
• Flowers never open and only capable of self
fertilization in bud.
• Inconspicuous, bud-like apetalous flowers that
form directly into seed capsules.
• Has evolved independently multiple times
• – throughout the angiosperms, including some
basal lineages.
• 488 species, across 212 genera and 49 families.
– Violaceae, Fabaceae, Poaceae
 Cleistogamy
• Cleistogamy is the condition in which the flower fails to
open. The term is sometimes extended to mean a
condition in which the flower opens only after it has been
pollinated (as occurs in wheat, barley, and lettuce), a
condition called chasmogamy.
• Some floral structures such as those found in legumes,
favor self pollination.
• Sometimes, the stigma of the flower is closely surrounded
by anthers, making it prone to selfing.
– To be classified as self-pollinated, cross-pollination should not
exceed 4%.
– Self-incompatibility does not occur.
 Outbreeding (Cross-pollination)
Advantages:
Increases genetic variability
Strong evolutionary potential
Adaptation to changing conditions
Successful long-term
Disadvantages:
 Can destroy well-adapted genotypes
 Relies on effective cross-pollination, seed
dispersal and establishment
 Strategies to Prevent Self fertilization
Strategies to avoid self-pollination:plants have strategies to avoid
self-pollination:
1. Timing – male and female structures mature at different times
2. Morphological – structure of male and female organs prevents
self-pollination (imperfect flower)
3. Biochemical – chemical on surface of pollen and stigma/style that
prevent pollen tube germination on the same flower
(incompatible)
 Crops Normally Self Pollinated
Some common crop plants that are normally self pollinated are:
• Barley, millet finger, sesame ,bean dry, millet foxtail, soybean ,chickpea,
mung bean tobacco , cowpea, oat, tomato, peanut (groundnut), triticale, flax
(linseed), pea , vetch ,jute, potato, wheat, lentil, rice,

crop plants that are normally cross pollinated are:

• alfalfa (lucerne) crested wheatgrass , reed canary grass, bahia
grass , cucumber rye, bermuda grass , safflower birds foot
trefoil, squash, brome grass , johnson grass , sugar beet, cabbage
, sugarcane, carrot , mustard , sunflower. castor , onion, sweet
clover, cassava , orchard grass , sweet potato, clovers, pearl
millet, colocasia, pepper, timothy, corn (maize), wild rice
Crops Both Self and Cross Pollinated
Some crops do not fit neatly in either the self or cross pollinated
categories.
Ex. broad bean, cotton, pigeon pea, and sorghum.
Usually the amount of crosspollination exceeds that of the
normally self pollinated crops, yet does not reach that of the
normally cross pollinated.
In these crops breeding procedures commonly used for self
pollinated crops are modified to accommodate the larger amount
of crosspollination.
Cotton is one of the principal crops in this group. Cotton is largely self
pollinated but crosspollination may range from 5 to 25% or more.
In the flower of the cotton plant, the stigma is exposed and
crosspollination may occur when insects carrying foreign pollen
come into contact with an unpollinated stigma.
 Crops Both Self and Cross Pollinated ..

 In a few cases where insect populations are abundant,

crosspollination in cotton in amounts up to 50% has been
reported.
 Pollen from the cotton plant is heavy and sticky and is seldom
windborne.
 Crosspollination in sorghum by windborne pollen, averages
about 6%; it occurs when a flower opens exposing the stigma
before pollen is shed. Crosspollination in sorghum may be
prevented by bagging heads before flowering to exclude foreign
pollen.
 Breeding procedures utilized for predominantly self pollinating
species may then be practiced.
 Inbreeders vs. Outbreeders
• Self Compatible • Self Incompatible or self
• Small flowers (few) compatible
• Large showy flowers (many)
• Unscented flowers • Scented flowers
• Nectaries & nectar • Nectaries & nectar guides
guides absent present
• Maturation of • Differential maturation of
reproductive parts reproductive parts
– Anthers near stigma – Anthers far from stigma
– Style included – Stigma well-exserted
• All fruits mature • Only some fruits mature
• High pollen/ovule ratio
• Low pollen/ovule ratio
 Asexual propagation
“vegetative reproduction, i.e., multiplication that
does not involve the seed cycle - clonal
propagation.”
• Asexual reproduction may be categorized into
two :
– Vegetative propagation & apomixis.
• Asexual reproduction is also called clonal
propagation because the products are
genetically identical to the propagules.
 Asexual propagation
• Clone - A genetically identical assemblage of individuals
produced from a plant entirely by vegetative means.
• Benefits of clonal Propagation
• Some plants produce few (if any) viable seeds.
• Clonal progeny are highly uniform in all characters.
• Outcrossing plants produce highly variable progeny.
• Plants may have extended juvenile period.
• Cloning allows for combining genotypes in one plant.
• Seeds may have lengthy and complex dormancies.
• Cutting propagation...
• Cutting capable of regenerating roots (or shoots) from
adventitious meristem.
• Cuttings defined by size and location on parent plant:
– stem tip
– nodal
– root
– leaf
• Cuttings also defined by condition of growth:
–soft wood, semihard wood, hard wood
 Conditions required for rooting cuttings
• Hardwood and root cuttings require well drained
medium, but little moisture control.
• Leafy cuttings require high humidity to prevent
excessive dehydration:
– intermittent mist systems.
– poly tents or cold frames.
– fog.
• Medium into which cuttings are stuck must be disease
free, well drained, and light.
• Auxin application now standard treatment.
 Grafting and budding.
‘’The vascular cambium can regenerate the vascular connections between the
scion and rootstock resulting in a complete plant composed of more than one
genotype.”
• Can graft scion cultivar onto size controlling rootstock.
• Many difficult to root plants are graft compatible.
• Grafting defined by season and type of tissue.
– budding (T-budding, inverted T, patch)
– wedge, veneer, whip and tongue, cleft, etc.
• Scion cultivar may be grafted on mature trees (top working)

Grafting
–Segments of different plants are connected and induced to grow together as
one plant.
• Scion - Top section of a graft.
• Rootstock - Bottom section of a graft.
–Successful grafting depends on good contact between the vascular cambium
of the scion and that of the rootstock.
 Layering.
• Air layering - interrupt cambium and cover wound with moistened medium. Ficus elastica,
Magnolia
• Simple layering - low hanging branch covered with soil (with or without wounding) - many
shrubs
• Tip layering - tips of plants (brambles) at certain times of year (rat-tail condition) develop
roots where they touch the soil Blackberries, raspberries
• Mound layering - soil mounded to cover base of specially pruned young tree (also
referred to as stool layering) Apple rootstocks
“Layering involves inducing roots on an intact (or nearly so) plant .”
 Specialized Structures

• Modified Stems
• bulb, corm, tuber, rhizome
• pseudobulb, runner
• Modified Roots
• tuberous root
 Apomixis

• “The development of an embryo within a seed or

flowering structure from a source other than the egg,
resulting in the formation of an embryo (sometimes in
addition to the sexual embryo) that is a clone of the
maternal parent.

• Examples include polyembryony in citrus & the

formation of bulbils in garlic.”
 Chapter 5: Characters for Selection
Qualitative traits -
• Classified into discrete classes
• Individuals in each class counted
• Less environmental influence on phenotype
• Controlled by a few (<3) major genes
Quantitative traits
• Express continuous variation (normal distribution)
• Individuals measured, not counted
• Significant environnemental influence on phenotype
• Controlled by many minor (or major) genes, each with small (or
large) effects
Characters for selection as exemplified for potato
POTATO
Crop Breeding characters

Field: strong sprouting, early growth and ground cover; correct maturity;
resistances to late blight, to viruses (Y, X, leaf roll, others), to wart disease, to
eelworms, to insects
Tubers: good yield; shape, smoothness, regularity of size, colour; resistance to
mechanical damage; lack of cracking and second growth; appropriate
dormancy; resistances to tuber diseases (blight, scab, gangrene, skin-spot,
others); good storage characters (delayed sprouting, disease resistance)
Quality: flesh colour; flesh texture: lack of enzymic browning; specific gravity (dry
matter content); lack of after-cooking blackening; texture on cooking; flavour;
chip/crisp colour after frying; reducing sugar content; 'reconditioning' capacity
after cool storage; low glycoalkaloids
 Chapter 6: Breeding Self Pollinated Crops
• Selection involves the Identification and propagation of
individual genotypes from a land race population, or
following designed hybridizations
• Genetic variation must be identified and distinguished
from environment-based variation
• Gamete A mature reproductive cell that is specialized for sexual fusion
• Haploid (n) Containing only one set of chromosomes (n). Each gamete is haploid
• Cross A mating between two individuals, leading to the fusion of gametes
• Diploid (2n) Two copies of each type of chromosome in the nuclei, formed by the
fusion of two gametes
• Zygote The cell produced by the fusion of the male and female gametes
• Gene The inherited segment of DNA that determines a specific characteristic in an
organism
• Locus The specific place on the chromosome where a gene is located
• Alleles Alternative forms of a gene
• Genotype The genetic constitution of an organism
• Homozygous An individual whose genetic constitution has both alleles the same for a
given gene locus (eg. AA)
• Heterozygous An individual whose genetic constitution has different alleles for a
given gene locus (eg. Aa)
• Homogeneous A population of individuals having the same genetic constitution (eg. a
field of pure-line soybeans; a field of hybrid corn)
• Heterogeneous A population of individuals having different genetic constitutions
• Phenotype The physical manifestation of a genetic trait that results from a specific
genotype and its interaction with the environment

Cultivar Is a group of genetically similar plants, which may be identified (by some means)
from other groups of genetically similar plants
Essential Characteristics:
Identity: cultivar must be distinguishable from other cultivars
Reproducibility: the distinguishing characteristic(s) need to be reproduced in the progeny
faithfully
 Types of Cultivars
• Open-Pollinated cultivars O.P. seeds are a result of either natural or human
selection for specific traits which are then reselected in every crop.
• The seed is kept true to type through selection and isolation; the flowers of
open pollinated or O.P. seed varieties are pollinated by bees or wind.
• Synthetic cultivars A population developed by inter-crossing a set of good
combiner inbred lines with subsequent maintenance through open pollination.
• The components of synthetics are inbreds or clones so the cultivar can be
periodically reconstituted.
• Multi-line cultivars A mixture of isolines each of which is different for a single
gene controlling different forms of the same character (e.g., for different races
of pathogens)
• F1 cultivars The first generation of offspring from a cross of genetically
different plants
• Pure-line cultivars The progeny of a single homozygous individual produced
through self-pollination
Breeding Methods of Self Pollinated Crops
Most common techniques include but not only limited
to:
1. Pure line
2. Mass
3. Bulk
4. Pedigree
5. Single Seed Descent (modified pedigree)
6. Backcross
 Population structure of Self-pollinators
In self-pollinated species:
 Homozygous loci will remain homozygous following self-
pollination
 Heterozygous loci will segregate producing half homozygous
progeny and half heterozygous progeny
 Plants selected from mixed populations after 5-8 self generations
will normally have reached a practical level of homozygosity
 In general, a mixed population of self-pollinated plants is
composed of plants with different homozygous genotypes (i.e., a
heterogeneous population of homozygotes)
 If single plants are selected from this population and seed
increased, each plant will produce a ‘pure’ population, but each
population will be different, based on the parental selection
 Pure Line
Pure Line: (Recount Johannsen. 1903)
• usually no hybridization
• Initial parents (IPs) selected from a heterogenous population
(i.e. genetically variable)
• procedure continues until homogeneity is achieved
• last phase is field testing
• A pure line consists of progeny descended solely by self-
pollination from a single homozygous plant
• Pure line selection is therefore a procedure for isolating pure
line(s) from a mixed population
• Pure line cultivars are more uniform than cultivars developed through mass selection
(by definition, a pure line cultivar will be composed of plants with a single genotype)
• Progeny testing is an essential component of pure line selection
• Improvement using pure line breeding is limited to the isolation of the ‘best’ genotypes
present in the mixed population

• More effective than MS in development of selfpollinated cultivars

• However, leads to rapid depletion of genetic variation
• Genetic variability can be managed through directed cross hybridizations
• Essential to progeny test selections
 Pure-line Selection-Steps
 Select desirable plants
• Number depends on variation of original population, space and
resources for following year progeny tests
• Selecting too few plants may risk losing superior genetic variation
• A genotype missed early is lost forever
 Seed from each selection is harvested individually
 Single plant progeny rows grown out
• Evaluate for desirable traits and uniformity
• Should use severe selection criteria (rogue out all poor, unpromising and
variable progenies)
 Selected progenies are harvested individually
 In subsequent years, run replicated yield trials with selection of highest
yielding plants
 After 4-6 rounds, highest yielding plant is put forward as a new cultivar
Advantages
1. ID of best pure line reflects maximum genetic advance from a
variable population; no ‘poor’ plants maintained
2. Higher degree of uniformity
3. Selection based on progeny performance is effective for characters
with relatively low h2

Dis advantage

1. Requires relatively more time, space, and resources for progeny

testing than MS to develop new cultivar
2. High degree of genetic uniformity; more genetically vulnerable and
less adaptable to fluctuating environments
3. ID and multiplication of one outstanding pureline depletes available
genetic variation; leads to fast genetic erosion
 Mass Selection
 May or may not include hybridization
 Make IP selections based on single, ideal or desirable phenotype
and BULK seed
 May repeat or go directly to performance testing
 Mass Selection has 2 important functions:
1. Rapid improvement in land-race or mixed cultivars
2. Maintenance of existing cultivars (sometimes purification)

Many pb’ers of self pollinated crops believe that combining closely

related pure lines imparts “genetic flexibility” or buffering capacity
and so are careful to eliminate only obvious off types
 Mass selection
 Success depends on extent of variation and h2 of the traits of
interest
 Land races make an ideal starting source
• High genetic variability accumulated over generations of
mutation and natural hybridization
 Initial selection Can be either a positive or a negative selection
 Negative screening: A screening technique designed to identify
and eliminate the least desirable plants.
 positive screening: which involves identifying and preserving the
most desirable plants.
 Mass Selection - 1st Year
• Select plants with respect to height, maturity, grain size, and any
other traits that have ‘production’ or ‘acceptability’ issues
• Bulk seed (may ‘block’ these bulks if wide variation is present for
certain traits; e.g. height)
• May be able to use machines to select
• Harvest only tall plants, or save only large seed passed through a
sieve
 Mass Selection - 2nd Year
• MS really only takes 1 yr because selected seed represents a
mixture of only the superior pure lines that existed in the original
population
• However, additional rounds of selection and bulking will allow for
evaluation under different environments, disease and pest
pressures.
• Also, multiple years will allow you to compare performance with
established cultivars over years and environments.
 Advantages of Mass Selection
1. To increase the frequency of superior genotypes from a
genetically variable population
2. Purify a mixed population with differing phenotypes
3. Develop a new cultivar by improving the average performance of
the population
Disadvantages
1. Selection based on phenotypic performance; not effective with
low h2 traits
2. Without progeny testing, heterozygotes can be inadvertently
selected
3. Population cannot realize maximum potential displayed by the
‘best’ pure line, due to bulking
4. Final population is not as uniform as those developed through
pure-line selection
Bulk Method
 Bulk method
 The bulk method is a procedure for inbreeding a
segregating population until a desired level of
homozygosity is reached.
 Seed used to grow each selfed generation is a sample
of the seed harvested in bulk from the previous
generation.
 In the bulk method, seeds harvested in the F1 through
F4 generations are bulked without selection; selection
is delayed until advanced generations (F5-F8).
 By this time, most segregation has stopped.
 Advantages
1. Less record keeping than pedigree
2. Inexpensive
3. Easy to handle more crosses
4. Natural selection is primarily for competitive ability
5. More useful than pedigree method with lower h2 traits
6. Large numbers of genotypes can be maintained
7. Works well with unadapted germplasm
8. Can be carried on for many years with little effort by the
breeder
 Disadvantages
1. Environmental changes from season to season so adaptive
advantages shift
2. Most grow bulk seed lots in area of adaptation
3. Less efficient than pedigree method on highly heritable traits
(because can purge non-selections in early generations)
4. Not useful in selecting plant types at a competitive disadvantage
(dwarf types)
5. Final genotypes may be able to withstand environmental stress,
but may not be highest yielding
6. If used with a cross pollinated species, inbreeding depressionmay
be a problem
 Pedigree Method
• Most popular Essentially a plant to row system to
develop near pure lines
• Followed by performance testing of resulting strains
• This method and its variants require a lot of record
keeping
 Pedigree Method
Genetic Considerations:
• 1.Additive genetic variability decreases within lines and
increases among lines, assuming no selection recall the
movement toward homozygosity following the hybridization

of unlike and homozygous parents

• 2.Dominant genetic variability complicates pedigree selection
homozygous and heterozygous individuals look alike and
therefore you may continually select the heterozygote
• THUS, selection can be discontinued with phenotypic
uniformity within a line is obtained
 Pedigree Method
Advantages
• 1. Eliminates unpromising material at early stages;
• 2. Multi-year records allow good overview of inheritance, and more effective
selection through trials in different environments;
• 3. Multiple families (from different F2 individuals) are maintained yielding
different gene combinations with common phenotype
• 4. Allows for comparison to other breeding strategies
Disadvantages
• 1. Most labor, time and resource intensive method; usually compromise
between # crosses and population sizes;
• 2. Very dependent on skill of breeder in recognizing promising material;
• 3. Not very effective with low h2 traits;
• 4. Slow; can usually put through only one generation per year, and the right
environmental conditions must be at hand for accurate selection.
• 5. Upper ceiling set by allelic contents of F2; can not purge selections of
undesirable alleles once ‘fixed’.
Single Seed Descent
 Single Seed Descent
Advantages
• 1. Rapid generation advance; 2-4 generations/yr
• 2. Requires less space,time and resources in early stages, therefore
accommodates higher # crosses;
• 3. Superior to bulk/mass selection if the desired genotype is at a
competitive disadvantage; natural selection usually has little impact on
population.
• 4. Delayed selection eliminated confusing effects of heterozygosity; more
effective than pedigree breeding when dealing with low h2 traits;
• 5. Highly amenable to modifications and can be combined with any method
of selection.
 Single Seed Descent
Disadvantages
• 1. May carry inferior material forward
• 2. Fewer field evaluations, so you lose the advantage of
natural selection
• 3. Need appropriate facilities to allow controlled environment
manipulation of plants for rapid seed production cycles (day
length, moisture and nutrient control)
 Backcross
• The plan of the backcross is to cross an adapted and productive
cultivar, yet one that lacks a desirable allele (or alleles)
controlling a superior character, to a breeding line or cultivar in
which the desirable allele is present.
• Beginning in the F1 and continuing for several generations,
hybrid plants containing the dominant allele are selected and
successively crossed back to the adapted parent cultivar.
• The adapted parent, to which the allele is being added, enters into
each backcross and is called the recurrent parent.
• Same form whether self or cross pollinated species
• Goal is to move 1 to a few traits from a donor parent (deficient in
other traits) to a recurrent parent (deficient in the trait of interest)
Backcross
 Chapter :
Breeding Methods with cross-pollinating crops
• Mass Selection
• Bulk Breeding Method
• Single-seed Descent
• Pedigree Breeding
• Hybrid Breeding Methods
 GENOTYPE BY ENVIRONMENT
INTERACTION
• Variation in performance among certain genotypes
when evaluated in different environments is known
as G x E interaction.
• This interaction is part of the behavior of the
genotype and confounds its observed performance
with its true value.
• Assessing any genotype without including its
interaction with the environment is incomplete and
thus limits the accuracy of yield estimates.
• Genotype by Environment Interaction
P = G + E + GE
 GENOTYPE BY ENVIRONMENT
INTERACTION
• Every factor that is a part of the environment of a
genotype has the potential to cause differential
performance that is associated with genotype x
environment interaction.
• In view of the plant improvement, environment is a
general term that covers conditions under which
plants grow and may involve locations, years,
management practices or a combination of these
factors.
 GENOTYPE BY ENVIRONMENT
INTERACTION
• Knowledge of the extent of G x E interaction and
stability of the performance of genotypes across
environments is absolutely essential to breeders.
• The former helps to decide whether the breeder will
aim at widely adapted genotypes or the specifically
adapted ones while stability is used in recommending
the final release.
 Methods of Estimating GxE
• The most commonly used
statistical methods to compute
genotype-environment interaction
are:
– relative ranking,
– graphic methods
– conventional analysis of variance
– regression analysis and
– principal component analysis (AMMI) .
 Methods of Estimating GxE
• Ranking
• In this method, the performance of genotypes
across environments is ranked at each
environment.
• If all genotypes follow the same ranking (the best
genotype at one environment maintains its rank
throughout the test environment) then there is no
genotype by environment interaction. In such cases
it is easy to pick the best genotype based on its rank
like genotype four (Table 1).
 Methods of Estimating GxE
Table 1. Genotypic ranking across environments

Environment ____________________________
Gen E1 E2 E3 E4 E5
1 5 5 5 5 5
2 3 3 3 3 3
3 2 2 2 2 2
4 1 1 1 1 1
5 4 4 4 4 4
 Ranking
• If on the other hand the relative ranking for
one genotype changes from environment to
environment then there is genotype by
environment interaction. In this kind of
situation, the best genotype is selected
based on its relative ranking, which is most
frequently appearing genotype in the best
ranking like genotype three (Table 2).
 Ranking
Table 1. Genotypic ranking across environments
Environment
____________________________
Genotype E1 E2 E3 E4 E5 RR
1 5 2 3 5 5 4.0
2 4 3 4 3 2 3.1
3 2 1 1 2 1 1.4
4 1 5 2 4 3 3.0
5 3 4 5 1 4 3.4
 Average yield versus
average rank
Ge Yield Rank Yield Rank Avg Avg
n Yield Rank
A 9.5 1 1.5 3 5.5 2

B 7.5 2 2.5 1 5.0 1.5

C 6.0 3 2.0 2 4.0 2.5

 Graphical Method
• Performance on the y-axis
• Environmental effects on the x-
axis
 Figure 1. No GxE

80

60

G1
Trait

40
G2
20

E1 E2
Environment
 Figure 2. Genotype-environment interaction

80

60

G1
Trait

40
G2

20

E1 E2

Environment
 Figure 3. Effect of altitude on the height of different species

150
Plant height (cm)

100

50
S1

S2
0

S3
1 2 3
Altitude (1= 100, 2 = 1500 and 3 = 3000 m.a.s.l.)
 Figure 4. Genotype x environment interaction

3000

2500
Mean yeild (kg/ha)

2000 G1
G2
1500 G3
G4
1000 G5

500

0
E1 E2 E3 E4 E5 E6
Environment
 Conventional ANOVA method
Table. Mean yield (kg/ha) of five genotypes tested at six envts
Environments Total Gi
---------------------------------------------------------------------
Genotype E1 E2 E3 E4 E5 E6
G1 702 1498 583 2140 1454 2262 8639
G2 770 1266 614 2071 1194 2187 8102
G3 833 1429 723 2115 1276 2137 8513
G4 527 1557 718 2056 1098 2133 8089
G5 905 1482 626 2074 1454 2399 8940

Ej 3737 7232 3264 10456 6476 11118 42283

 Conventional ANOVA method
• Individual location analysis of variance is the first
step towards combined analysis of variance.
• In order to combine the data the error with which
each mean is measured should be tested for
homogeneity which is one of the basic assumptions
of analysis of variance.
• A quick test of homogeneity of variance is provided
by the ratio of the largest mean square error to the
smallest mean square error
• If the ratio is < 3, then we combine.
 Conventional ANOVA method
Table. Preliminary analysis of variance

Sources DF MS E(MS)

Envt, E 5 2152871.07** σ2e + rσ2GxE+ rgσ2E

Blocks/E 30
Gen, G 4 22124.89** σ2e + rσ2GxE+ reσ2G
GxE 20 10710.42** σ2e+ rσ2GxE
Pooled Error 120 1012.12 σ2e

**, significant at 0.01 level of probability

 Causes of GEI
• Environmental stresses
– Biotic
– Physical
– Chemical
 Causes of GEI cont.
• Different plants have different
levels of responces to
environmental stresses.
• The extent of adaptability to the
environmental stresses reflects
the inherent capacity of those
plant species.
 Causes of GEI cont.
• Adaptability is a quantitative trait
of a particular genotype and is
determined by the extent and
sophistication of its plastic traits.
Implications of GEI in Crop Breeding

• GEI has a negative impact on

heritability.
• The lower the heritability of a
trait, the greater the difficulty in
improving that trait via selection.
Implications of GEI in Crop Breeding

• Understanding the nature of GEI

is important in plant breeding
because a significant GEI can
seriously impair efforts in
selecting superior genotypes
realtive to new crop introductions
and cultivar development
program.
Implications of GEI in Crop Breeding

• Moreover, GEI is useful to

breeders as it can help determine
if there is a need to develop
cultivars for all environments or
specific cultivars for target
environments
 Components of Variability
Phenotypic value of quantitative traits in this commonly used expression:
P (phenotype) = G (genotype) + E (environment)
• Total variance of a quantitative trait may be mathematically expressed as
follows:
VP = VG + VE
where VP = total phenotypic variance of the segregating population, VG
= genetic variance, VE = environmental variance,
The genetic component of variance may be further partitioned into three
components as follows:
VG = VA + VD + VI
where VA = additive variance (variance from additive gene
effects), VD = dominance variance (variance from dominance gene action),
and VI = interaction (variance from interaction between genes).
 Heritability

• Heritability is a property of the trait, the population, and the

environment. Changing any of these factors will result in a
different estimate of heritability.
• Heritability is the proportion of the observed variation in a
progeny that is inherited.
H = Vg / Vp
Vp = Vg+Ve Where Vp = phenotypic variance
Vg = genotypic variance
Ve =environmental variance
• This is valid when homozygous lines are studied.
• But when segregating generations are studied genotypic variance
consists of (a) additive variance (b) dominance variance (c) and
variance due to epistasis.
 Types of heritability
There are two different estimates of heritability.
1 Broad sense heritability.
It is expressed mathematically as: H = VG/VP
Some use the symbol H2 instead of H.
2 Narrow sense heritability. Because the additive -component of genetic variance
determines the response to selection, the narrow sense heritability estimate is more
useful to plant breeders than the broad sense estimate. It is estimated as:
h 2 = VA/VP
• However, when breeding clonally propagated species (e.g., sugarcane, banana), in
which both additive and non-additive gene actions are fixed and transferred from parent
to offspring, broad sense heritability is also useful.
• The magnitude of narrow sense heritability cannot exceed, and is usually less than, the
corresponding broad sense heritability estimate.
 Difference between additive and dominance variance

Additive Dominanace

It refers to difference between It refers to deviation of Aa from the

homozygotes (AA/aa) mean of AA and aa
Genes show lack of dominance Genes show incomplete, complete or
over dominance
Associated with homozygosity and is Associated with heterozygosity and is
more in inbreders more in outbreeders
It is fixable It is non-fixable

Selection is very effective as it is fixable Selection is ineffective as it is non-

fixable
it is the chief cause of transgressive
It is the chief cause of heterosis
segregation
Genetic Advance (GA)
GA is the difference between the mean of the selected plants in
the original population and the mean of the progeny raised
from the selected plants in the next generation.
It can be predicted by the following formula.
Genetic advance (GA) = P * H * K
K = selection intensity 2.06 when 5% of the population
is selected
P = phenotypic standard deviation of the character in
the
population
H = heritability in broad sense
Correlation Among Traits
• Association between traits
– Importance
– Breeding implication
• Drought
• Low N
Correlation Among Traits
• The genetic correlation is a
measure of the extent to which
the same gene, or closely linked
genes, cause simultaneous
variation in two different traits.
Correlation Among Traits
• The two possible causes of a
genetic correlation are attributed
to pleiotropism and/or linkage
disequilibrium (Allard, 1960).
 Correlation Among Traits
• Pleiotropism occurs when one gene
affects simultaneously several
physiological pathways, resulting in
influence over several observed
traits
Correlation Among Traits
• Linkage disequilibrium refers to
genes that show a tendency to
being transmitted together within
a population.
Correlation Among Traits
• If linkage is important, the
genetic correlation should
become smaller over time as
crossing over reduces the linkage
disequilibrium causing correlation
Correlation Among Traits
• The major use of correlation
estimates for plant breeding is to
predict correlated response to
selection.
Correlation Among Traits
_______________________________
x y x2 y2 xy
_______________________________
2 5 4 25 10
1 3 1 9 3
5 6 25 36 30
0 2 0 4 0
________________________________
Total 8 16 30 74 43

∑x ∑y ∑x2 ∑y2 ∑xy

  xy   n 
( x)( y )
r
=___________________________
( x 
2  ( x) 2
)( y 
2  ( y)2
)
n n
8 x16
43 
4
= 82 162
(30  )(74  )
4 4

= 0.93
Correlation Among Traits
• The observation that two traits
tend to simultaneously vary in a
certain direction does not imply
the presence of a direct
relationship between them.
Correlation Among Traits
• It is a matter of common sense
than of statistical reasoning to
determine if an observed
correlation has a practical
interpretation or is spurious.
Correlation Among Traits
• Therefore, when using the
correlation coefficient as a
measure of relationship among
traits, it is important to be very
careful to avoid the possibility
that external variable is affecting
any of the variables under
consideration.
• Reading Assignment
In the book ‘‘Principles of plant genetics and
breeding” take special note and read critical
chapter 20 & 21
Focus on 1. breeding for disease resistance
2. breeding for drought resistance
Again do not forget that
term papers are part of your course
Share information each other and read.