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Chapter
Characteristics of Various Types of

Plant Breeding
Cristian-Radu Sisea
Abstract
Plants have always been integral to human society and their (genetic) improve-
ment has been carried out ever since humans became farmers. Breeders are seeking
to alter plants in a permanent and heritable manner in order to enhance agricultural
production relying on the scientific and technical advancements in molecular biology
and biotechnology. Plant breeding simultaneously creates and exploits biological
diversity (genetic variation), which are the main activities for plant breeders. Both
plant domestication and traditional (conventional or classical) breeding depended
on the natural processes and genetic potential of the species. However, innovations,
such as mutation breeding, various biotechnological tools (e.g. in vitro techniques),
and speed breeding, have been developed to enhance genetic gain and accelerate
the breeding process. Furthermore, to improve selection, molecular markers were
introduced. Strategies, such as molecular-assisted selection and genomic selection,
are part of molecular (modern or nonconventional) breeding, which also includes two
approaches based on genetic engineering: transgenesis and genome editing. The main
characteristics of all these breeding tools — the essential assets for overcoming the
agricultural challenges of modern civilization — and their relation to one another are
presented in this chapter.
Keywords: traditional breeding, mutation breeding, speed breeding, molecular breeding,

marker-assisted selection, genomic selection, transgenic breeding, genome editing
1. Introduction
Plants have always been, and still are, integral to human society because they
provide food, feed, fiber, fuel, raw materials, medicines and other various bioac-
tive compounds, esthetic pleasure, and solutions to various environmental issues.
However, nearly all the plants that are useful today do not occur naturally but exist
only because of human intervention that began thousands of years ago [1].
Early humans gathered what that they could find in the wild, but as their lifestyle
changed from nomadic to sedentary, thousands of years ago, desirable plant species
started to be selected and cultivated. This was the beginning of plant domestication
[2], which represents the earliest form of plant breeding [3]. About 150 years ago,
science revolutionized selection and breeding processes, facilitating and making
them more efficient [4, 5]. To this day, plant traits and characteristics continue to be
1
Beyond the Blueprint – Decoding the Elegance of Gene Expression
changed in order to better serve the needs of modern society [6]. The role of science
and technology in plant breeding has increased continuously [4] and modern breed-
ers rely on more and more sophisticated and efficient methods to create variability,
discriminate among variants, and develop varieties (cultivars) for widespread
cultivation [7].
The last five decades have been the most productive period in world agricultural
history, saving billions of people from hunger and starvation [8]. The enhanced
production has been based on overexploitation of natural resources and changing
the natural environment, essentially entailing the modification of growing condi-
tions [5, 8]. This was possible with the implementation of advanced agricultural
technology, especially the application of production inputs such as fertilizers,
irrigation, and pesticides [4, 5, 8]. However, this progress cannot cater to all the
needs of mankind, and it will be even less sufficient in the coming years because
of the increasing demands of human society [9]. So, for the future, the challenge is
to ensure a sustainable rise in global agricultural production for a growing human
population using finite natural resources and a shrinking agricultural land base due
to industrialization, urbanization, and limiting factors, such as climatic or environ-
mental changes [8–11]. In this context, the genetic improvement of crops is more
important than ever.
In contrast to farmers, whose strategy is to enhance certain traits only temporarily —
without tampering with the genetics of the organism — breeders seek to alter plants in
a permanent and heritable manner so that genetic modifications are transmissible from
one generation to the next [12]. The integration of newly developing technologies, such
as molecular markers, OMICS, transgenesis, genome editing, and RNA interference
into plant breeding, will provide the basic principles for developing modern breeding
methodologies [4, 5, 13]. In this way, genetics coupled with other scientific knowledge
(statistics, biometrics, biochemistry, bioinformatics, biotechnology, etc.) have the
potential to overcome the aforementioned threats and challenges [8].
As an educator, I am concerned first and foremost with the students and the unini-
tiated, for whom understanding of all aspects of plant breeding is difficult to grasp,
particularly because they are at the beginning of a challenging journey. As a result,
it should be noted that this chapter is not intended for expert readers or an advanced
audience as it will only offer a brief overview of the fascinating world of plant breed-
ing, in order to provide up-to-date theoretical background and definitions. The main
characteristics of the various types of plant breeding strategies are presented, starting
with the fundamental principles of classical breeding and all the way to the advanced
technologies of modern breeding, emphasizing approaches such as artificial induction
of mutations, rapid generation advancement, the use of molecular markers, transgen-
esis, and genomic editing.
2. Plant breeding
It should be noted that the terms plant breeding and plant improvement are used
synonymously [5]. One of the best-suited definitions for plant breeding is the one
given by [12]: “the art and science of improving the heredity of plants for the benefit
of humankind.” Other definitions emphasize the changing, altering, or manipulation
of genetic patterns, genetic make-up, genetic information, genome, or genetics of
plants in order to produce desired traits or characteristics, to increase their value, or
to make them a better fit for human purposes. Basically, the plant breeding process
2
Characteristics of Various Types of Plant Breeding
DOI: http://dx.doi.org/10.5772/intechopen.1004008
encompasses techniques for producing, selecting, and fixing superior plant pheno-
types in order to develop new, improved cultivars that better meet the requirements
of farmers and consumers [14, 15].
Many authors state that the scientific basis for plant breeding was established by
the ground-breaking work of Gregor Johann Mendel in the middle of the nineteenth
century. However, the principles put forth by Charles Darwin and Alfred Russell
Wallace during the same period are equally important since breeding is nothing less
than a particular form of evolution. At the beginning of the twenty-first century, the
science of crop improvement is being transformed once again by molecular breeding,
which integrates the latest breakthroughs in biological research — namely molecular
biology and biotechnology — with traditional breeding practices [15–19]. As science
and technology advance, modern breeders are able to make their activities more and
more predictable and precise, with plant breeding becoming indispensable to modern
human society [20]. Thus, the development of a new crop variety is an example of
agricultural biotechnology that includes both traditional breeding techniques and
modern methods [1, 21], such as molecular markers and genetic engineering.
As mentioned before, plant breeding is often likened to evolution [5]. Yet, a crucial
distinction between the two is that evolution is a natural and extremely slow process,
whereas plant breeding is a relatively quick artificial one [2]. Moreover, natural evolu-
tion increases the fitness of the populations or species, whereas plant breeders aim
to direct the population toward specific and predetermined goals — often related to
yield, nutritional value or other commercial traits — that are generally not concerned
with fitness because modern farmers can grow plants under artificial conditions [5]. It
should be noted, however, that in recent years, there has been a shift toward improv-
ing adaptability to abiotic or biotic stress factors in order to make better use of land
resources while also taking climate change into consideration [22].
The development of new cultivars entails two basic activities: assembling genetic
variability and discriminating among variants — selection — in order to identify
and advance desirable genotypes (individuals) that meet the breeding objectives [7].
These two stages are followed by the evaluation and release of the cultivar [5].
Depending on the approaches and techniques employed by breeders, which keep
evolving along with science and technology, there are two basic categories of plant
improvement: traditional (conventional) and molecular (nonconventional) [4, 20].
These two categories and their characteristics will be presented in the remainder of
this chapter.
3. Traditional plant breeding based on selective breeding
Traditional plant breeding, also called classical or conventional breeding, is the

development of crop varieties by using natural processes and conservative, older, sim-
pler, and relatively low-tech tools to modify an organism’s genetic information within
the natural boundaries of its species [1, 5]. The absence of modern developments or
lack in sophistication is not implied here as traditional breeding entails both basic and
advanced methods [23]. In fact, practices used in traditional breeding may include
features of biotechnology such as tissue and cell culture, protoplast fusion techniques
for somatic hybridization, techniques for embryo rescue to overcome incompatibility
barriers, advanced pollination procedures and in vitro fertilization, techniques for
polyploidization a haploidization, and mutation breeding [4, 14, 23]. However, the
fundamental method remains modification through selective breeding [1, 14], also
3
called artificial or phenotypic selection, which is based on phenotype evaluation for

identifying individuals with desirable traits [3, 5, 24]. Consequently, the methods
and techniques used by conventional breeders rely heavily on the species’ mode of
reproduction — self-pollination, cross-pollination, or clonal (vegetative) propaga-
tion — and contrast with the newer and more innovative breeding tools of molecular
breeding [5]. This is why, the initial statement is defining the traditional breeding
approach by actually comparing it to the most cutting-edge breeding technologies.
In much the same manner, EU legislation on genetically modified (GM) organisms
(GMOs) — that is. Directive 2001/18/EC — clearly delineated traditional breeding
from what was, at the time, the most innovative methodology for crop improve-
ment — transgenesis or recombinant DNA technology [23]. This idea was rightly
extended to include other genetic engineering tools – that is. genome editing — which
are considered to have revolutionized crop improvement and biological research and
which will be presented in Subchapter 4.2.2. In conclusion, all genetic engineering
methods that enable the creation and introduction of novel variation into genomes
through genetic engineering should be separated from traditional breeding [25]. This
is especially true from a technical point of view, but the legal implications are more
nuanced; these will be discussed further in Subchapter 4.2.2.
Artificial selection can be performed on naturally occurring individuals, but,
more often, on offspring resulted from controlled crosses, also called matings or
hybridizations. Therefore, in conventional breeding, desirable traits are assembled
into a new cultivar from different but very closely related plants — usually belonging
to the same species [4]. As such, the individuals resulting from conventional breeding
only display characteristics already present in the genetic potential of their species
because new genes (and characteristics) are not introduced [5]. Also, when none
of the individuals on which selection is performed possesses a certain gene variant
controlling a particular trait, it is not possible to select that specific trait [1].
It should also be noted that in a controlled mating all of the genetic material
between the two individuals being bred, which could mean tens of thousands of genes
(maize, for example, has approximately 32,000 genes), is shuffled. The results of
such a mix can be very unpredictable because of the large number of combinations —
that is. genotypes or individuals — it can generate and finding the best one could be
very difficult [1].
Artificial selection is the oldest technique for crop improvement and still remains
widely used [20, 26]. This has actually been the main process through which, over the
years, humans have gradually and systematically favored traits that have increased the
utility of plants [1, 5].
3.1 Mutation breeding
Plant breeding relies on genetic variation — “heritable variation is the lifeblood of

plant breeding” [5] — for selecting desired genotypes or traits [27–29].
In nature, mutations — the heritable changes to an individual’s genetic makeup
[14, 30] — represent one of the essential mechanisms for genetic variation and
evolution — individuals with a novel trait may be preferentially selected because of
their superior fitness determined by the novel (mutant) adaptive features [28, 29, 31].
Mutations are in fact the new gene variants (alleles) controlling new traits that are
passed on from parents to offspring [28–30].
Humans have used natural genetic variation since they started cultivating plants
by actually (and also unknowingly) selecting for the alleles that were beneficial and
4
suitable to their needs [9]. The natural rate of mutation is nevertheless very low and
insufficient for generating all the variation that breeders would like to have for their
breeding programs [26], which have to run at a much faster pace than natural evolu-
tion. To overcome this limitation, plant breeders can artificially induce additional
mutations by using physical (i.e. different types of high-energy radiation) or chemical
(e.g. ethyl methanesulfonate and dimethyl sulfate) mutation-causing agents – muta-
gens [28–30, 32, 33]. This way of generating new variation to be exploited in the
breeding process is called mutation breeding. Consequently, the genetic variation
used in plant breeding could be: (1) found in the natural, existing gene pool; (2)
obtained through crossings (hybridizations) that shuffle existing variation into new
combinations without creating novel gene variants; and (3) the result of artificial
mutagenesis which actually means generating new alleles.
Usually, mutation breeding is considered part of conventional or traditional
breeding [23, 28–30, 32, 33], but different opinions can be found as well:
• “Genetic transformation and mutation breeding, as nonconventional breeding

tools for plant improvement, are outlined and selection in vitro against a fungal
toxin isolated from Mycosphaerella fijiensis is presented in more detail.” [34];
• “… nonconventional breeding of banana, more specifically genetic transformation,

protoplast culture, somatic hybridization and EMS-induced mutation …” [35].
EU legislation on GMOs — that is. Article 3(1), in conjunction with Annex I B of

Directive 2001/18/EC — is very clear on this topic: mutagenesis — introducing varia-
tions in the plant genome using radiation or chemicals — is regarded as traditional
breeding and is explicitly exempt from the scope of the Directive 2001/18/EC, on the
basis that it has a long history of safe use [23, 32, 33, 36].
With more than 3000 mutant crop varieties in more than 200 plant species having
been officially released worldwide [28, 29, 31, 37], mutation breeding continues to
be an important tool for today’s plant improvement efforts together with the more
advanced and precise nonconventional techniques [28, 29, 31].
3.2 Speed breeding
Several years are required for developing cultivars using conventional procedures
for generation advancement (to the next breeding cycle). In order to achieve a rapid
generation advancement (RGA) — that is. the shortening of breeding cycles — with
more than three to four generations per year, a relatively unsophisticated and highly
adaptable platform for plant cultivation was perfected [38–42]. Research on this topic
had been reported as far back as 1880 [39, 41], based on the idea of growing plants
under artificial light that was experimented with by botanists [40, 41]. The RGA
approach was first proposed just before World War 2, then modified in the 1960s, and
its most recent form — speed breeding — was introduced only a few years ago [39, 42].
Just like mutation breeding and molecular breeding (Subchapter 4), speed breed-
ing is aimed at accelerating genetic gain [38–40]. For this, plants are cultivated under
fully enclosed environmental conditions, in growth chambers or greenhouses, where
crop-specific optimal light (quality, intensity, and duration), temperature, and
humidity can be artificially controlled [30, 38–40, 42].
The basic and simple procedures of speed breeding can be easily adopted.
However, this approach is much more effective in enhancing genetic gain when
5
integrated with other modern strategies [39]. To produce greatly improved outcomes,
speed breeding can be combined with:
• marker-assisted selection [38]; marker-assisted selection is presented in

Subchapter 4.1.1;
• high-throughput genotyping — that is. genomics-assisted breeding — combina-

tion that represents the most effective strategy for quick variety development
[40]; genomics-assisted breeding is presented in Subchapter 4.1.2;
• genome editing techniques [11, 40], an approach called express edit [40]; genome
editing is presented in Subchapter 4.2.2;
• automated or high-throughput phenotyping [40, 42].
This type of accelerated plant breeding reduces the time, space, and manpower
needed to advance plant generations more rapidly and develop varieties at a quicker
pace, so speed breeding was adopted worldwide, with already well-established proto-
cols in many important staple crops [38–42].
4. Molecular plant breeding
The agricultural challenges of modern society, determined by population growth,

climate change, limited resources, and the constraints of conventional breeding,
require increasingly innovative, modern methodologies to be applied for the genetic
improvement of crops [17, 43, 44]. In the past few decades, due to the progress in
science and technology — that is. the considerable increase of knowledge on genes
and their function at the molecular level — advanced, new tools for plant breeding
have been added to those that have been in use for a long time — that is. traditional
breeding [8, 42]. The various umbrella terms describing these new, advanced breed-
ing methods are nonconventional (or unconventional), modern, and molecular.
Molecular breeding is arguably the most appropriate and commonly used of the
aforementioned terms. The following are some straightforward definitions for
molecular breeding:
• “Application of molecular biology in plant breeding is molecular breeding.” [3].
• “Similarly, the recent integration of advances in biotechnology, genomic

research, and molecular marker applications with conventional plant breeding
practices has created the foundation for molecular plant breeding, an interdisci-
plinary science that is revolutionizing twenty-first century crop improvement.”
[15].
• “Recent progress in biotechnology and genomics has expanded the breeders’

horizon providing a molecular platform on the traditional plant breeding, which
is now known as plant molecular breeding.” [16].
• “Molecular breeding applies molecular biology tools to accelerate the breeding

process.” [17].
6
• “Molecular breeding is a modern technique that refers to the combined applica-

tion of plant biotechnology and breeding for crop improvement.” [18].
• “Modern plant breeding techniques came into being when molecular techniques
were integrated along with conventional breeding techniques in order to achieve
higher genetic gains.” [19].
Taking into consideration the primary components of molecular breeding out-

lined in the previous definitions — that is. molecular biology, biotechnology, molecu-
lar markers, and genomics — it can be concluded that its essential tools are molecular
biology techniques. For better understanding what the concept of molecular breeding
entails it is necessary to consider other, more detailed opinions on this topic, which
are quite heterogeneous. This is due in part to the fact that terms such as genetic engi-
neering, biotechnology, and molecular marker, used to describe molecular breeding
are, in their turn, not always agreed upon by all authors.
Most often, molecular breeding encompasses the use of molecular markers and
genetic engineering, as shown by the following definitions:
• “The areas of molecular breeding include QTL [quantitative trait locus] mapping
or gene discovery, marker-assisted selection and genomic selection, genetic engi-
neering, and genetic transformation.” [3]; here, it should be noted that genetic
transformation is not included in genetic engineering.
• “To this end, recent advances in transcriptome profiling, functional genomics,

proteomics, and metabolomics approaches, coupled with molecular marker-
assisted breeding and transgenic technology have made significant contributions
in enhancing the efficiency of cotton breeding; these methods are collectively
referred as molecular breeding.” [45]; here, the authors do omitted genome edit-
ing; this also applies to the next definition.
• “Molecular breeding in cotton includes traditional cotton breeding supple-

mented with marker-assisted breeding using advances in molecular-marker
technology and QTL mapping (which includes marker-assisted backcrossing and
marker-assisted recurrent selection), genomics (known as genomics-assisted
breeding), and transgenics technology.” [45];
• “Therefore, combination of conventional and modern breeding approaches, such as

backcrossing, foreground and background selection, phenotyping, gene pyramid-
ing, marker-assisted selections, identification of quantitative trait loci, and many
more can be used to have new and improved varieties. Further, biotechnological
approaches such as identification of genes by using markers, genetic transforma-
tion, regulating signal transductions, and different omics approaches (genomics,
transcriptomics, proteomics, and metabolomics) are choice of scientists to develop
next generation crops to tackle the challenge of having sustainable agriculture,
adverse effect of climate change, and to feed the looming population.” [46].
• “Molecular breeding may be defined in a broad sense as the use of genetic

manipulation performed at DNA molecular levels to improve characters of inter-
est in plants and animals, including genetic engineering or gene manipulation,
molecular marker-assisted selection, genomic selection, etc.” [47].
7
There are instances when the authors reference only one of the elements men-
tioned above, either molecular markers or genetic engineering:
• “Molecular breeding is used to describe several modern breeding strategies,

including marker-assisted selection, marker-assisted backcrossing, marker-
assisted recurrent selection and genome-wide selection or genomic selection.” [3].
• “DNA markers are also called molecular markers in many cases play a major role
in molecular breeding.” [47, 48].
• “Marker-assisted or marker-based backcrossing is regarded as the simplest form

of marker-assisted selection, and it is the most widely and successfully used
method in practical molecular breeding.” [47, 48].
• “The use of DNA markers in plant breeding is called marker-assisted selection

and is a component of the new discipline of “molecular breeding.” [49].
• “The classical approach for molecular breeding is heavily dependent on marker-

assisted selection and the trait linked DNA markers as an alternative to support
phenotypic screening.” [50].
• “Molecular breeding uses molecular biology tools in breeding crop plant. It

includes approaches such as marker-assisted selection and qualitative trait loci
mapping.” [51].
• “Single and multigene transgenesis is the current strategy since the past one
decade, which if aptly exercised alongside other molecular breeding strategies,
can yield satisfactorily performing drought tolerant crop plants.” [52].
Other authors present molecular breeding as pertaining either to molecular mark-

ers or genetic engineering:
• “Molecular breeding is the DNA marker-assisted breeding that calls for sophisti-
cated instrumentation and facilities.” [3].
• “Molecular breeding, or MAS, refers to the technique of using DNA markers that
are tightly linked to phenotypic traits to assist in a selection scheme for a particu-
lar breeding objective.” [53]
• “Molecular breeding approaches target on specific regions on the DNA and

therefore are called as marker-assisted breeding. This is often taken from QTL
mapping of the quantitative trait. MAB involves numerous modern plant breed-
ing strategies, comprising marker-assisted selection, marker-assisted backcross-
ing, marker-assisted recurrent selection, and genome-wide selection or genomic
selection. Marker-assisted selection (MAS) is a breeding approach that involves
integration of detection and selection of DNA marker with a conventional breed-
ing program.” [54].
• “Called molecular plant breeding, plant breeders may now access genes from the
animal kingdom for plant improvement, but not without controversy.” [5].
8
Sometimes molecular breeding — potentially referring to molecular markers —

and genetic engineering are seen as two different components of modern breeding
methods:
• “The final part has an excellent discussion of advanced techniques of plant

breeding, such as tissue culture, genetic engineering, molecular breeding, and
application of genomics.” [3].
• “Molecular breeding and [genetic engineering] also have benefits over conven-
tional breeding because they make it tranquil to grow crops with many nutri-
tional traits of interest.” [18].
• “Now, new innovative additional plant breeding tools, including molecular

breeding and plant biotechnology, are available to plant breeders, which have
a great potential to be used along with the conventional breeding methods for
sustainable agriculture.” [55]; here, plant biotechnology most probably refers to
genetic engineering.
• “For introduction of desirable traits molecular breeding and transformation

technique have also been used widely.” [56].
Certainly, there are many other particular definitions for molecular breeding, its
components, and the relations between them.
Conventional techniques are time-consuming, so one of the most important
advantages of molecular breeding is the possibility of reducing the duration of the
crop development process by years [18]. However, due to its complexity, the success-
ful application of molecular breeding requires sophisticated, high-tech infrastructure
and deep knowledge and specialization [44].
4.1 Molecular markers in plant breeding
While significant genetic improvements have been achieved using classical

breeding methods — based on phenotypic selection [3, 24] — the employment of
molecular biology and genomics tools — that is, molecular or DNA markers — has
the potential to enhance genetic gains even more by making selection easier, faster,
and more accurate, which will reduce the generation interval and the costs and
will improve the overall speed and efficiency of the breeding process [57–59]. An
important advantage of using molecular markers is that genotypic evaluation can be
done off-season and the influence of the environment is negligible [60]. Therefore, in
recent decades, the focus shifted from phenotype-based to genotype-based selection
[3], making molecular markers one of the main components of modern breeding. The
two primary types of molecular marker-based strategies used in plant breeding are
presented in the following subchapters.
4.1.1 Marker-assisted selection and breeding
Marker-assisted or marker-aided selection (MAS) is the selection of individuals

with desirable traits based on the direct analysis of their genetic makeup (genotype)
and it can be employed alone or in combination with classical methods [57]. Marker-
assisted breeding (MAB) includes several molecular analysis-based applications
9
intended to enhance mating designs, genetic testing and screening, deployment

strategies and overall quality control in plant improvement programs [57].
Only a few general aspects are addressed here, while the various types of molecu-
lar markers with their features, advantages and drawbacks will not be discussed.
These general aspects, that specialists have different views on, are related to how the
concept of molecular markers should be perceived. One such issue is the influence of
the molecular marker on the target characteristic. In the following examples MAS is
presented as a form of indirect selection — the assumption that the marker closely
associates with one or more genes of interest, due to genetic linkage, but does not
influence the target characteristic:
• “Marker-assisted selection or marker-aided selection (MAS) is a process

whereby a marker (morphological, biochemical or one based on DNA/RNA
variation) is used for indirect selection of a genetic determinant or determinants
of a trait of interest (i.e. productivity, disease resistance, abiotic stress tolerance
and/or quality).” [3].
• “One of the most important methods of molecular breeding is MAS, the use of
DNA markers that are tightly linked to target loci as a substitute to assist pheno-
typic screening.” [17].
• “MAS is an indirect selection process, where individuals for a particular trait of

interest are selected based on the known markers linked to it.” [24].
• “MAS is the process of using morphological, biochemical, or DNA markers as

indirect selection criteria for selecting agriculturally important traits in crop
breeding.” [61].
• “Marker-assisted selection is a strategy to accelerate genetic gain in conventional

breeding programes by selecting plants with a desirable combination of genes
using tightly linked markers.” [62].
However, indirect selection is only one type of MAS, direct selection being also
possible:
• “All forms of indirect selection involve selection for one trait to make improve-
ment in a different trait, called the target trait. A second and developing, form
of MAS is to select directly on the individual alleles at one or more loci affecting
polygenic traits. This form of marker-assisted selection requires knowledge, at
the molecular level, of some or all of the genes controlling the target trait and can
be viewed as direct selection, rather than indirect selection, since selection is for
specific, favorable alleles at those loci.” [57].
• “Marker-assisted selection is a newly emerging approach due to which various

problems of conventional breeding avoid and enhance the selection criteria of
phenotypes with the selection of genes, either indirectly or directly.” [63].
• “Molecular genetic analyses of quantitative traits lead to the identification

of two broadly different types of genetic loci that can be used to enhance
10
genetic improvement programes: causal mutations and presumed non-

functional genetic markers that are linked to QTL (indirect markers). […]
Whereas causative polymorphisms give direct information about genotype
for the QTL, the use of indirect markers for QTL mapping and for selection
is based on the existence of linkage disequilibrium (LD) between the marker
and the QTL” [64].
• “Secondly, some SNPs [single nucleotide polymorphism] are located in coding

regions and directly affect protein function. These SNPs may be directly respon-
sible for some of the variations among individuals in important traits.” [65].
It is also important to understand that molecular markers represent just one of

the several types of markers that can be used in plant breeding. The classification of
markers can vary, but the concept is rather consistent:
• “Genetic markers used in genetics and plant breeding can be classified into
two categories: classical markers and DNA markers. Classical markers include
morphological markers, cytological markers and biochemical markers.” [47].
• “Such variations occurring at different levels, that is. at the morphological,

chromosomal, biochemical, or DNA level can serve as the genetic markers.” [66].
• “Genetic markers are classified: based on visually evaluated traits (morphologi-

cal and productive traits), based on gene product (biochemical markers), and
founded on DNA analysis (molecular markers).” [67].
Usually, genetic markers encompass all of the other types of markers and can be
defined as:
• “… the biological features that are determined by allelic forms of genes or genetic
loci and can be transmitted from one generation to another, and thus they can be
used as experimental probes or tags to keep track of an individual, a tissue, a cell,
a nucleus, a chromosome or a gene.” [47];
• “… any stable and inherited variation that can be measured or detected by a

suitable method, and can be used subsequently to detect the presence of a
specific genotype or phenotype …” [66]; this definition emphasizes only indirect
selection;
• “… a broad term for any visible or assayable phenotype or the genetic basis for
assessing of the observed phenotypic variability.” [67].
The definition of molecular markers also varies between authors, especially when
considering different fields of study and no attempt will be made here to reconcile
them. Below are some appropriate definitions for molecular markers applicable to
plant breeding:
• “The markers revealing variations at the DNA level are referred to as the molecu-
lar markers.” [66].
11
• “Molecular marker is a term used to refer to a specific DNA variation between

individuals that has been found to be associated with certain characteristics.” [67].
• “A molecular or DNA marker is the difference in DNA nucleotide sequence —

between individual organisms or species — that is in proximity or tightly linked
to a target gene that expresses a trait.” [68]; it should be noted that the authors
emphasize only indirect selection.
MAS is probably both the least sophisticated and the most widely used approach
in practical molecular breeding because of its simplicity, especially when compared to
the other molecular breeding strategies.
4.1.2 Genomic selection and genomics-assisted breeding
MAS has demonstrated its practicality and feasibility in the enhancement of

qualitative traits — features associated with one or very few major genes — but its
usefulness in improving quantitative traits — polygenic traits controlled by hundreds
or thousands of minor genes, with small effects — is limited [24, 69]. To address this
issue, a powerful new approach called genomic selection (GS) or genome-wide selec-
tion (GWS) was developed [24]. This new approach became feasible only with the
development of new generations of DNA sequencing technologies that revolutionized
biological research and genomics by drastically reducing the costs and duration of
sequencing [59]. High-throughput genotyping enables the routine implementation of
GS to fully benefit crop improvement [59].
Without prior knowledge of relevant QTLs or other molecular markers [69], GS
uses dense single SNPs distributed across the whole genome to estimate the genetic
merit of individuals of a breeding population and to facilitate the selection of candi-
dates for the next breeding cycle [24, 69, 70]. GS shows great potential for resolving
the issue of selection of traits associated with multiple genes [71] because it can
theoretically account for the effect, no matter how small, of every piece of genetic
information — gene or otherwise — from a genome [72], for which conventional
selection and MAS are difficult and time-consuming to apply [71]. Therefore, GS
ensures high accuracy and allows for a substantial reduction in the duration of the
breeding cycle, while also decreasing the costs associated with extensive phenotyp-
ing, and thus accelerating genetic gains and improving the overall efficiency of the
breeding process [60, 73].
The possibility of analyzing individuals through whole genome sequencing has
turned GS and other genomics-assisted breeding (GAB) tools into powerful assets
[3, 60, 72], which enable the integration of genomics with conventional phenotyp-
ing in order to facilitate the prediction of phenotype from genotype [3, 60]. In this
context, the breeder can make a comprehensive characterization of the genetic
variation in order to find the best alleles — that is. to accumulate beneficial alleles
and purge deleterious ones [11] — and combinations of alleles (haplotypes) for
future crop cultivars [3, 11, 60].
Implementation of GS requires that individuals in a fully phenotyped population
v generally called training population — are genotyped using genome-wide markers
instead of selected molecular markers. Available phenotypic and genotypic informa-
tion is employed to build a statistical predictive model that estimates the breeding val-
ues of the alternative alleles of all the markers. The additive sum of all marker effects
is used to calculate the genetic merit of each individual and the genomic estimated
12
breeding value (GEBV) of the training population. GEBV can then be utilized to
estimate the phenotypic value of individuals in a breeding program employing solely
their genotypic data. In this regard, the selection of individuals in subsequent genera-
tions is based purely on GEBVs. This general outline of the genomic selection process
is based on information published by [11, 24, 59, 60, 70, 72, 73].
However, there are certain factors that may influence the accuracy of the genomic
prediction: the size and genetic diversity of the training and breeding populations,
as well as the genetic relationship between the two, the heritability of the target trait,
the influence of the environment on the initial population, the density of markers, the
choice of statistical models used to estimate breeding values, and the accuracy of the
phenotyping [24, 69, 72].
In conclusion, there is great potential in GS and GAB, and overcoming the limita-
tions these technologies are currently facing will make their routine implementation
possible in plant breeding [24, 72, 74], which might lead to replacing phenotypic
selection and MAS, at least in the analysis of complex traits [59].
4.2 Genetic engineering in plant breeding
Due to its most defining attribute — the possibility of direct and highly accurate
manipulation of genetic information — genetic engineering (GE) has transformed
both the way in which biological studies are performed, by becoming an essential
tool for understanding the genetic basis of biological processes and the possibilities
of applying acquired knowledge [9, 75, 76]. The manipulation of genetic material is
intended to induce gene function-level changes — gene inactivation, overexpression
of an already existing (native) gene, or synthesis of a new compound and integration
of a new function after the insertion of a new gene — that will, in turn, alter the phe-
notype. Thus, GE has found numerous applications in all the main sectors of human
activity — industry, medicine, and agriculture — including plant breeding.
GE represents the foremost biotechnological approach that is used in modern
breeding for the genetic improvement of crops, with two basic components: trans-
genesis or transgenic technology and genome or gene editing [77]. Both of them allow
twenty-first-century breeders to alter the genome of an organism and to create new
heritable variability through the direct manipulation of the genes controlling the
traits of interest [16]. There is, however, an essential difference between the two: the
origin of the manipulated genetic material.
In the case of transgenesis, genetic material from two (or more) species is used —
that is. combined. Basically, the transfer of genetic material — that is. a gene, but sev-
eral genes could be transferred as well — from one (or more) species into the genome
of another is carried out. This type of transfer is called horizontal or lateral transfer of
genetic material and cannot take place between the species involved in transgenesis as
they are not capable of sexual reproduction with each other — that is. vertical transfer.
So, in essence, transgenic technology introduces novel genes into an organism in order
to enhance it with new characteristics. On the other hand, most of the gene editing
tools act on the genetic material of a single organism (and species) and their genetic
and phenotypic effects are the same as in the case of naturally, spontaneous occurring
mutations. It should be noted that the transfer of novel genes — just like in the case of
transgenesis — is also possible.
Authors do not always make the same distinction between GE, transgenesis, and
genome editing. Often, GE and transgenesis were used interchangeably, especially
before genome editing became widespread. Today, such an approach can be somewhat
13
confusing — “advancements in genetic engineering and genome editing techniques

draw more attention from conventional plant breeding methods” [78] — and there
are many other examples that may hinder even more the understanding of the differ-
ences between the three concepts mentioned earlier:
• “The process of genetic engineering or gene editing in plants starts with isolation
of the desired gene from a living source, which is then incorporated within a
suitable vector to make a recombinant DNA molecule, and finally this recombi-
nant DNA molecule is inserted into the host’s (plant) genome — thus integrating
a new function within the GM plant. One of the main components of gene edit-
ing tools used for production of GM crops that have the most significant impact
upon the overall process of gene editing is selection of a suitable enzyme.” [79].
• “Gene editing can be defined as a process involving advanced techniques in

molecular biology for site-specific, efficient, and precise modifications within
a genome. The resultant plants can be precisely termed as genetically modified
(GM) plants that occur through the transfer of a transgene (gene) of known
function.” [79].
In the following subchapters, general aspects regarding transgenesis and genome

editing will be presented briefly.
4.2.1 Transgenic breeding
During the past four decades, the asexual transfer of genes employing specific
GE methods has added a new dimension to the genetic modification and improve-
ment of plants [57]. It should be noted that genetic modification is often used to refer
specifically to genetic engineering and transgenesis [14, 80]. However, the term has
traditionally been used to describe any heritable (genetic) improvements in plants
(or animals) irrespective of the methodology employed by the breeders [14, 80].
Modifications — insertions, deletions, or substitutions — can range from small-scale
alterations, such as a single nucleotide affecting a single gene to major changes in the
genetic makeup, affecting numerous genes.
The products of GE — called transgenic plants or crops and commonly referred
to as GM or biotech — became the most rapidly spreading agricultural technology in
history [81, 82]. They contain at least one (foreign or exogenous) gene that has been
artificially inserted into their genome to determine a desired characteristic [49, 77].
The inserted gene is known as a transgene [83] and originates from different sexually
incompatible species or can even be completely artificially synthesized.
Consequently, transgenic technology can overcome the reproductive barriers of
transferring genetic material so that breeding resources are extended to unrelated
species, creating additional genetic variation [49, 77, 84] — characteristics not
available in nature in the plants to be modified are introduced from a variety of
other organisms [3, 57]. In this way, transgenesis is fundamentally different from
traditional, mutation-based, or molecular marker-based breeding [57]. Such an
approach also produces plants with desired characteristics faster than classical
breeding [3], enabling the insertion of the foreign DNA directly into elite cultivars
(genotypes) [49, 83]. The two most popular techniques for plant transformation are
Agrobacterium-mediated gene transfer (plant transformation) and particle bom-
bardment [75, 84].
14
Two particular types of transgenesis have been developed for transferring DNA
that belongs to the same species or to other closely related and sexually compatible
species: cisgenesis employs natural genetic sequences (i.e. genes with their regula-
tory elements) for genetic modification, while intragenesis refers to the use of new
combinations of coding sequences and regulatory elements [77, 85]. There are differ-
ent goals for these types of transfers — for example. Overexpression of genes that are
already present within the crop itself, avoiding linkage drag that occurs when gene
transfer is obtained by crossing — but a very important aspect is that the gene pool
exploited by these approaches is identical to the gene pool available for traditional
breeding. In this way, objections to transgenesis may be overcome more easily [77].
Gene silencing is another important tool used in plant transgenesis [86],
encompassing a series of mechanisms capable of suppressing or inhibiting gene
expression [83, 86].
4.2.2 Genome editing
Several new (plant) breeding techniques (NPBTs or NBTs) — also termed novel
genomic techniques, new genetic modification techniques, etc. — have been devel-
oped over the past few decades [32, 33, 36, 87]. NBTs is an umbrella term, encompass-
ing different biotechnological approaches employed in research and breeding that
are capable modifying an organism’s genetic makeup and that have emerged or have
been created since 2001 [32, 33, 36]. Of these, genome editing or gene editing (GEd),
is a particularly useful strategy for the genetic improvement of crops, allowing much
faster and more precise results than other breeding techniques [32, 33, 77]. Therefore,
GEd has evolved rapidly in recent years, and it has received increasingly more atten-
tion [77, 88, 89], both from researchers and the general public, not only in plant
breeding but also in many other research areas as well.
There are many different molecular (genome) editors available, such as site-
directed nucleases (SDNs), which include meganucleases (MNs), zinc-finger nucle-
ases (ZFNs), transcription activator-like effector nucleases (TALENs) and CRISPR/
Cas or CRISPR-Cas systems — CRISPR is an acronym for clustered regularly inter-
spaced short palindromic repeat, while Cas stands for CRISPR-associated protein,
prime editing (PE), base editing (BE), oligonucleotide-directed mutagenesis (ODM),
transposases, recombinases, chemical (chemistry-based) DNA cutters, and peptide
nucleic acids (PNAs) [90–92]. Although some editing systems have been introduced
since the 1990s, with the first one even earlier, it was the CRISPR/Cas-based platform
that really “revolutionized this revolutionary field.” Introduced only in 2013, the
CRISPR/Cas technology became, by far, the most popular tool for editing the genetic
blueprint of an organism due to its simplicity and versatility — CRISPR/Cas can be
easily adapted and programmed for many different uses — and continues to drive
major breakthroughs in life sciences [90, 93]. The four main classes of CRISPR/Cas-
derived genome editors are nucleases (i.e. SDNs), base editors (i.e. BE), prime editors
(i.e. PE), and transposases/recombinases [90].
In essence, GEd systems generate targeted DNA mutations (at predefined loca-
tions in the genome) [49, 94], ranging from one or a few nucleotides, just like natu-
rally occurring mutations, to inserting or removing one or more entirely functional
genes [9, 36, 37].
Applications of SDNs-based GEd — mainly CRISPR/Cas — are generally grouped
into different types — SDN-1, SDN-2, and SDN-3 — depending on the presence of
exogenous DNA, the cellular response mechanism, and the resulting change in the
15
genetic makeup of the targeted organism [89, 93, 95, 96]. SDN-1 and SDN-2 are some-
what similar, producing plants that contain no exogenous DNA in their genome. The
desired traits result from changes, such as nucleotide substitutions and small dele-
tions and insertions, made exclusively on endogenous DNA and are indistinguish-
able from natural genetic variation or what can be obtained by mutation breeding
[9, 95]. The European Network of GMO Laboratories concluded that without prior
knowledge, it is technically impossible to detect the small DNA changes introduced
by Ged, and thus to distinguish GEd plants from plants selected for certain naturally
occurring mutations or plants that are obtained through mutation breeding [9, 33].
SDN-3, on the other hand, results in the insertion of exogenous DNA into the target
genome at a predefined locus, and such organisms are considered to be GMOs [9, 95].
PE and BE constitute separate categories than any SDN, but the genetic changes they
are producing are similar to SDN-1 and SDN-2 [9].
Breeding has always relied heavily on genetic diversity and modern breeders
have continuously looked for ways to expand it [9]. So, over time, breeding efforts
were augmented by introducing various means — that is. artificial mutagenesis
and trangenesis — for creating new genetic variants in addition to the spontaneous
mutations found in nature [9]. One of the drawbacks of artificially induced mutations
is that it generates many (probably thousands) unknown and uncontrolled muta-
tions in a genome, even deleterious ones, so isolating a desired new trait could still
be time-consuming and, in some cases, virtually impossible [9, 77]. In this context,
a distinction must be made between undirected methods — that is. artificial muta-
tion methods causing random genetic changes — and the more precise site-directed
methods [97] — that is. GEd, also called targeted genome engineering [94]. So, unlike
artificial mutations, the changes produced by GEd are not random, being targeted at
a specific predetermined locus, which gives this technology a high level of precision
while generating new variability [9]. Therefore, GEd increases the efficiency of intro-
ducing single and multiple traits and removing undesirable ones without affecting
genetically linked genes [37].
In many countries, the development, commercialization, and use of GM crops are
severely limited due to the many regulatory, social, and ethical issues and concerns
related to environmental safety and consumer health [9, 77]. As pointed out before,
most GEd technologies work without introducing exogenous DNA fragments in the
targeted genome and their effects on the DNA and phenotype are the same as those of
conventional mutations. It can thus be concluded that “the process is genetic engi-
neering, but the product is not” [97], which should contribute to their acceptance.
Certain authors go as far as calling GEd technology and organisms transgene-free
[76, 98]. In fact, one of the most intriguing aspects related to GEd is its legal status,
especially in relation to transgenesis — whether or not it falls in the same category as
GMOs. Two major rulings applicable GEd were issued in 2018:
1. The US did not regulate “plants that could otherwise have been developed
through traditional breeding techniques” because they are considered “indistin-
guishable from those developed through traditional breeding methods;” so, in
the US, gene editing is not part of the same regulatory oversite as GMOs; a key
point in this regard is the fact that it is nearly impossible to detect whether an
organism’s DNA has been edited [9, 36, 93, 95, 99]. As a result, several countries
worldwide have fully or partially exempted from national biosafety regulations
specific types of GEd organisms [95].
16
2. The ruling of the European Court of Justice (Case C-528/16) was interpreted by
the European authorities to mean that organisms developed through so-called
NBT, including GEd crops are not excluded from the scope of the legislation
on GMOs — Directive 2001/18/EC; this opinion is based on the fact that GEd
techniques alter the genome in such a way that would not occur naturally or by
mating, and they do not have a long safety record [9, 36, 37, 93, 95, 99].
The European regulatory approach regarding GEd crops is considered to be

completely out of line with the regulations existing in other countries [9] and may
constitute an important barrier for GEd-based research and the varieties obtained by
GEd [9, 36]. There is a growing consensus that risk assessment should differentiate
between GEd crops that have DNA changes, which can also occur spontaneously in
nature or as a result of conventional breeding, and Ged crops having genome changes,
which cannot occur in nature or as a result of conventional breeding methods — that
is. the insertion of a foreign gene to a predefined location in the genome (SDN-3).
Despite the tremendous potential and the promising results obtained so far, there
are still enough technical hurdles that need to be overcome so that the utility of GEd can
be exploited as best as possible and with as few negative consequences as possible [97].
There are continuous efforts for streamlining the delivery of editing system components
into cells and for preventing off-target effects — improving the specificity or efficiency of
producing only the desired edits [37, 95]. Nevertheless, it should be taken into consider-
ation that, in plants, the off-target modifications are a relative discussion in the context of
mutation breeding methods, which create many more random changes to the genome [9].
GEd arguably represents the most dynamic and rapidly evolving sector of GE and
biotechnology, with new applications being published almost daily [9]. Researchers
have adopted GEd technology at an unprecedented speed because of its high precision,
time and cost efficiency, simplicity, and versatility that accelerated the plant breed-
ing process — genetic variations determining a certain favorable trait are introduced
in one or two generations of plants [37, 49, 77]. There is a broad consensus that GEd
crops will make a critical contribution to agriculture — and to other areas as well — in
the coming years [9]. But the way GEd crops are regulated internationally — whether
they fall under the scope of GMO legislation or not — will have a significant impact on
the development of GEd technologies and their potential to benefit mankind [77].
5. Concluding remarks
As long as the human population continues to grow, there will also be a high
demand for agricultural products. Increased production can be achieved by expanding
the cultivated land area, using appropriate agronomic practices (e.g. fertilizers, irriga-
tion, and crop rotation) and cultivating superior plant varieties. However, farmlands
are sometimes converted to other uses because an increasing population comes with
higher needs for residential, commercial, industrial, and recreational land uses. There
are also more and more limitations on available resources and protecting the environ-
ment should be taken very seriously in the coming years. In this context, the challenge
is to improve agricultural yields while decreasing the use of resources. The solution to
this challenge rests with the genotypes being cultivated. Developing varieties superior
to the already existing ones is achieved by plant breeding, which, in its modern form,
is a very systematic and highly technological approach.
17
Humans have carried out plant breeding since they first started farming, but its
scientific basis was firmly established only at the beginning of the twentieth century
when Mendel’s work on heredity and variability was rediscovered. Since then, science
and technology have made plant breeding more and more efficient, and spectacular
advances have been made by breeders after the implementation of new molecular and
biotechnological knowledge over the past few decades.
Plant breeding simultaneously enhances and exploits biological diversity — that
is. genetic variation. Therefore, many achievements in plant breeding were based
on phenotypic selection, which is still widely used. However, traditional breeding
is becoming more sophisticated with the addition of modern strategies. The initial
integration of molecular markers in plant breeding — marker-assisted selection
— allowed important progress to be made, and now, due to the availability and
employment of new sequencing technologies, genomic-based approaches are likely to
dramatically change the selection process.
Traditional breeding primarily exploits natural genetic variation, and mutation
breeding and genome editing were designed to extend this type of variation, but
not beyond species limitations. Further expansion of variability beyond the natural
boundaries of sexual reproduction was enabled by other advances in molecular biol-
ogy and biotechnology — transgenesis allows the transfer of genes between sexually
incompatible species. In this way, there is essentially one universal gene pool from
which breeders may obtain variability for crop improvement.
The implementation of the new approaches presented in this chapter has already
made invaluable contributions to overcoming the aforementioned agricultural threats
and challenges. Other possibilities of augmenting breeding methodologies that have
not been discussed here are also available: metabolomics-assisted breeding, high-
throughput or automated phenotyping, RNA and epigenetic editing (i.e. modifica-
tion), etc.
This chapter provided an introduction to plant breeding by presenting the main
types of genetic improvement that were devised to meet the needs of an ever-growing
human civilization. There is a large variety of tools available to breeders, both simple
and complex, with incredible advantages but also drawbacks. The information is,
thus, a vital resource for students interested in this field of agricultural sciences.
Author details
Cristian-Radu Sisea*
Faculty of Horticulture and Business in Rural Development, University of
Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, Romania
*Address all correspondence to: cristian.sisea@usamvcluj.ro
© 2024 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of
the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided
the original work is properly cited.
18
References
[1] Ha M, Schleiger R. Selective Breeding Vol. 1. New York: Macmillan Publishing

and Genetic Engineering [Internet]. Company; 1987. 536 p
Davis, CA, USA: LibreTexts, Inc.;
2023. Available from: https://bio. [8] Bharadwaj DN. Sustainable agriculture
libretexts.org/Bookshelves/Ecology/ and food security: 2050 (future plant
Environmental_Science_(Ha_ breeding). In: Bharadwaj DN, editor.
and_Schleiger)/04%3A_Humans_ Advanced Molecular Plant Breeding:
and_the_Environment/4.03%3A_ Meeting the Challenge of Food Security.
Agriculture/4.3.03%3A_Selective_ New-York: Apple Academic Press; 2018.
Breeding_and_Genetic_Engineering pp. 3-30. DOI: 10.1201/b22473
[Accessed: Sep. 23, 2023]
[9] Dima O, Bocken H, Custers R, Inze D,
[2] Gepts P. A comparison between crop Puigdomènech P. Genome editing for
domestication, classical plant breeding, crop improvement. In: Symposium
and genetic engineering. Crop Science. Summary. Berlin: ALLEA – All European
2002;42(6):1780-1790. DOI: 10.2135/ Academies; 2020. 64 p. DOI: 10.26356/
cropsci2002.1780 gen-editing-crop
[10] Lobato-Gómez M, Hewitt S, Capell T,

[3] Priyadarshan PM. Plant Breeding:
Classical to Modern. Singapore: Springer Christou P, Dhingra A, Girón-Calva PS.
Nature Singapore Pte Ltd; 2019. 570 p. Transgenic and genome-edited fruits:
DOI: 10.1007/978-981-13-7095-3 Background, constraints, benefits, and
commercial opportunities. Horticulture
Research. 2021;8:166. DOI: 10.1038/
[4] Acquaah G. Principles of Plant
s41438-021-00601-3
Genetics and Breeding. 2nd ed.
Chichester, West Sussex, UK: John
[11] Varshney RK, Bohra A, Yu J, Graner A,
Wiley & Sons, Ltd; 2012. 740 p.
Zhang Q , Sorrells ME. Designing future
DOI: 10.1002/9781118313718
crops: Genomics-assisted breeding
comes of age. Trends in Plant Science.
[5] Acquaah G. Conventional plant 2021;26(6):631-649. DOI: 10.1016/j.
breeding principles and techniques. In: tplants.2021.03.010
Al-Khayri JM, Jain SM, Johnson DV,
editors. Advances in Plant Breeding [12] Sleper DA, Poehlman JM.
Strategies: Breeding, Biotechnology Breeding Field Crops. 5th ed. Oxford:
and Molecular Tools. Vol. 1. Blackwell Publishing; 2006. 424 p.
Switzerland: Springer International DOI: 10.1007/978-94-015-7271-2
Publishing; 2015. pp. 115-158.
DOI: 10.1007/978-3-319-22521-0 [13] Voss-Fels KP, Stahl A, Hickey LT.
Q&A: Modern crop breeding for future
[6] Orton TJ. Horticultural Plant food security. BMC Biology. 2019;17.
Breeding. London, United Kingdom: DOI: 10.1186/s12915-019-0638-4
Academic Press; 2020. 397 p.
DOI: 10.1016/C2017-0-03393-1 [14] U.S. Department of Agriculture.
Agricultural Biotechnology Glossary
[7] Fehr WR. Principles of Cultivar [Internet]. Available from: https://
Development. In: Theory and Technique. www.usda.gov/topics/biotechnology/
19
biotechnology-glossary [Accessed: than just GM crops [Internet]. 2014.

Sep. 07, 2023] Available from: https://www.isaaa.org/
resources/publications/agricultural_
[15] Moose SP, Mumm RH. Molecular biotechnology/download/agricultural_
plant breeding as the foundation for biotechnology.pdf [Accessed: Sep. 11,
21st century crop improvement. Plant 2023]
Physiology. 2008;147(3):969-977.
DOI: 10.1104/pp.108.118232 [22] Rai GK, Kumar RR, Bagati S, editors.
Abiotic Stress Tolerance Mechanisms in
[16] Koh HJ, Kwon SY, Thomson M, Plants. London: CRC Press; 2021. 370 p.
editors. Current Technologies in Plant DOI: 10.1201/9781003163831
Molecular Breeding – A Guide Book
of Plant Molecular Breeding for [23] van de Wiel C, Schaart J, Niks R,
Researchers. New York. London: Springer Visser R. Traditional Plant Breeding
Science+Business Media Dordrecht; 2015. Methods. Wageningen UR Plant
360 p. DOI: 10.1007/978-94-017-9996-6 Breeding: Wageningen; 2010. 66 p
[17] Khan S, Pandotra P, Gupta AP,
[24] Budhlakoti N, Kushwaha AK,
Salgotra RK, Manzoor MM, Lone SA,
Rai A, Chaturvedi KK, Kumar A,
et al. Plant molecular breeding: Way
Pradhan AK, et al. Genomic selection:
forward through next-generation
A tool for accelerating the efficiency of
sequencing. In: Zargar SM, Rai V,
molecular breeding for development
editors. Plant Omics and Crop Breeding.
of climate-resilient crops. Frontiers in
Waretown, NJ, USA: Apple Academic
Genetics. 2022;13:832153. DOI: 10.3389/
Press Inc.; 2017. pp. 201-234.
fgene.2022.832153
DOI: 10.1201/9781315365930
[18] Mehta DR, Nandha AK. Terminator [25] Breseghello F, Coelho AS. Traditional
technology (GURT technology). In: and modern plant breeding methods
Bharadwaj DN, editor. Advanced with examples in rice (Oryza sativa
Molecular Plant Breeding: Meeting the L.). Journal of Agricultural and Food
Challenge of Food Security. New-York: Chemistry. 2013;61(35):8277-8286.
Apple Academic Press; 2018. pp. 505-534. DOI: 10.1021/jf305531j
DOI: 10.1201/b22473
[26] International Service for the
[19] Anand A, Subramanian M, Kar D. Acquisition of Agri-biotech Applications.
Breeding techniques to dispense higher Pocket K No. 13: Conventional plant
genetic gains. Frontiers in Plant Science. breeding [Internet]. 2006. Available
2023;13:1076094. DOI: 10.3389/ from: https://www.isaaa.org/resources/
fpls.2022.1076094 publications/pocketk/13/default.asp
[Accessed: Sep. 19, 2023]
[20] Chahal GS, Gosal SS. Principles
and procedures of plant breeding. In: [27] Sarsu F, Penna S, Kunter B,
Biotechnological and Conventional Ibrahim R. Mutation breeding
Approaches. Harrow: Alpha Science for vegetatively propagated
International; 2002. 604 p crops. In: Spencer-Lopes MM,
Forster BP, Jankuloski L, editors. Manual
[21] International Service for the on Mutation Breeding. 3rd ed. Rome:
Acquisition of Agri-biotech Applications. Food and Agriculture Organization of
Agricultural biotechnology – A lot more the United Nations; 2018. pp. 157-176
20
[28] Datta SK. Induced Mutation [35] Chen YF, Dai XM, Gong Q , Huang X,
Breeding. Singapore: Springer Nature Xiao W, Zhao JT, et al. Non-conventional
Singapore Pte Ltd.; 2023. 179 p. breeding of banana (Musa spp.).
DOI: 10.1007/978-981-19-9489-0 Acta Horticulturae. 2011;897:39-46.
DOI: 10.17660/actahortic.2011.897.2
[29] Penna S, Jain SM. Mutation
Breeding for Sustainable Food [36] Van der Meer P, Angenon G,
Production and Climate Resilience. Bergmans H, Buhk HJ, Callebaut S,
Singapore: Springer Nature Chamon M, et al. The status under EU
Singapore Pte Ltd.; 2023. 815 p. law of organisms developed through
DOI: 10.1007/978-981-16-9720-3 novel genomic techniques. European
Journal of Risk Regulation.
[30] Ahmar S, Gill RA, Jung KH, 2020;14(1):93-112
Faheem A, Qasim MU, Mubeen M, et al.
Conventional and molecular techniques [37] The Parliamentary Office of Science
from simple breeding to speed breeding and Technology. Genome-Edited
in crop plants: Recent advances and Food Crops [Internet]. Westminster,
future outlook. International Journal of London: The Parliamentary Office
Molecular Sciences. 2020;21(7):2590. of Science and Technology; 2022.
DOI: 10.3390/ijms21072590 Available from: https://researchbriefings.
files.parliament.uk/documents/
[31] Spencer-Lopes MM, Forster BP, POST-PN-0663/POST-PN-0663.pdf
Jankuloski L. Manual on Mutation [Accessed: Sep. 19, 2023]
Breeding. 3rd ed. Rome: Food and
Agriculture Organization of the United [38] Mallikarjuna MG, Veeraya P, Tomar R,
Nations; 2018. 301 p Jha S, Nayaka SC, Lohithaswa HC, et al.
Next-generation breeding approaches
[32] Laaninen T. New plant-breeding for stress resilience in cereals: Current
techniques. Applicability of EU GMO status and future prospects. In:
rules [Internet]. 2019. Available from: Mallikarjuna MG, Nayaka SC, Kaul T,
https://www.europarl.europa.eu/ editors. Next-Generation Plant Breeding
RegData/etudes/BRIE/2019/642235/ Approaches for Stress Resilience in
EPRS_BRI(2019)642235_EN.pdf Cereal Crops. Singapore: Springer Nature
[Accessed: Sep. 19, 2023] Singapore Pte Ltd.; 2022. pp. 1-44.
DOI: 10.1007/978-981-19-1445-4
[33] Laaninen T. New plant-breeding
techniques. Applicability of EU GMO [39] Babu HP, Kumar M, Gaikwad KB,
rules [Internet]. 2020. Available from: Kumar R, Kumar N, Palaparthi D, et al.
https://www.europarl.europa.eu/ Rapid generation advancement and
RegData/etudes/BRIE/2020/659343/ fast-track breeding approaches in wheat
EPRS_BRI(2020)659343_EN.pdf improvement. In: Mallikarjuna MG,
[Accessed: Sep. 19, 2023] Nayaka SC, Kaul T, editors. Next-
Generation Plant Breeding Approaches
[34] Okole B, Memela C, Rademan S, for Stress Resilience in Cereal
Kunert KJ, Brunette M. Non- Crops. Singapore: Springer Nature
conventional breeding approaches for Singapore Pte Ltd.; 2022. pp. 241-262.
banana and plantain improvement DOI: 10.1007/978-981-19-1445-4
against fungal diseases at AECI. Acta
Horticulturae. 2000;540:207-214. [40] Chimmili SR, Kanneboina S,
DOI: 10.17660/ActaHortic.2000.540.23 Hanjagi PS, Basavaraj PS, Sakhare AS,
21
Senguttuvel P, et al. Integrating advanced [46] Mahajan R, Nazir M, Sayeed N,

molecular, genomic, and speed breeding Rai V, Mushtaq R, Masoodi KZ, et al.
methods for genetic improvement Unraveling the abiotic stress tolerance
of stress tolerance in rice. In: in common bean through omics. In:
Mallikarjuna MG, Nayaka SC, Kaul T, Zargar SM, Rai V, editors. Plant Omics
editors. Next-Generation Plant Breeding and Crop Breeding. Oakville: Apple
Approaches for Stress Resilience in Academic Press; 2017. pp. 313-368.
Cereal Crops. Singapore: Springer Nature DOI: 10.1201/9781315365930 311-365
Singapore Pte Ltd.; 2022. pp. 263-284.
DOI: 10.1007/978-981-19-1445-4 [47] Jiang GL. Molecular markers and
marker-assisted breeding in plants. In:
[41] Singh H, Janeja HS. Speed breeding Andersen SB, editor. Plant Breeding from
a ray of hope for the future generation Laboratories to Fields. London, United
in terms of food security: A review. Kingdom: IntechOpen; 2013. pp. 45-83.
Plant Archives. 2021;21(1):155-158. DOI: 10.5772/52583
DOI: 10.51470/plantarchives.2021.v21.
s1.028 [48] Jiang GL. Molecular markers
and marker-assisted breeding in
[42] Wanga MA, Shimelis H, Mashilo J, plants. In: Al-Khayri JM, Jain SM,
Laing MD. Opportunities and challenges Johnson DV, editors. Advances in
of speed breeding: A review. Plant Plant Breeding Strategies: Breeding,
Breeding. 2021;140(2):185-194. Biotechnology and Molecular Tools. Vol.
DOI: 10.1111/pbr.12909 1. Switzerland: Springer International
Publishing; 2015. pp. 431-472.
[43] Malik B, Pirzadah TB, DOI: 10.1007/978-3-319-22521-0
Qureshi I, Tahir I, Murtaza I, Rehman RU.
Phenomics science: An integrated
[49] Gaur RK, Verma RK, Khurana SMP.
inter-disciplinary approach for crop
Genetic Engineering of Horticultural
improvement. In: Zargar SM, Rai V,
Crops: Present and Future. In: Rout GR,
editors. Plant OMICS and Crop Breeding.
Peter KV, editors. London: Academic
Oakville: Apple Academic Press; 2017.
Press; 2018. 444 p
pp. 201-234. DOI: 10.1201/9781315365930
[44] Tripodi P. Crop breeding. In: [50] Rai R, Singh AK, Zargar SM,
Methods in Molecular Biology. Singh DB. A recap on quantitative trait
New York, NY, USA: Springer loci associated with disease resistance
Science+Business Media, LLC; 2018. in food legumes. In: Zargar SM,
282 p. DOI: 10.1007/978-1-0716-1201-9 Rai V, editors. Plant Omics and Crop
Breeding. Oakville, ON, Canada: Apple
[45] Boopathi NM, Sathish S, Academic Press Inc.; 2017. 495 p. DOI:
Kavitha P, Dachinamoorthy P, 10.1201/9781315365930
Ravikesavan R. Molecular breeding
for genetic improvement of cotton [51] Kaur L, Meena MR, Lenka SK,
(Gossypium spp.). In: Al-Khayri JM, Appunu C, Kumar R, Kulshreshtha N.
Jain SM, Johnson DV, editors. Advances Molecular approaches for improving
in Plant Breeding Strategies: Breeding, abiotic stress tolerance in sugarcane.
Biotechnology and Molecular In: Shanker AK, Shanker C, Anand A,
Tools. Vol. 1. Switzerland: Springer Maheswari M, editors. Climate Change
International Publishing; 2015. and Crop Stress. Molecules to Ecosistems.
DOI: 10.1007/978-3-319-22521-0 London, United Kingdom: Academic
22
Press; 2021. pp. 465-492. DOI: 10.1016/ [58] Koh HJ, Kwon SY, Thomson M,
C2017-0-03584-X editors. Current Technologies in Plant
Molecular Breeding. A Guide Book
[52] Nataraja KN, Madhura BG, of Plant Molecular Breeding for
Parvathi MS. Omics: Modern tools Researchers. New York. London: Springer
for precise understanding of drought Science+Business Media Dordrecht; 2015.
adaptation in plants. In: Zargar SM, p. 360. DOI: 10.1007/978-94-017-9996-6
Rai V, editors. Plant Omics and Crop
Breeding. Oakville, ON, Canada: Apple [59] Bhat JA, Ali S, Salgotra RK, Mir ZA,
Academic Press Inc.; 2017. pp. 263-294. Dutta S, Jadon V, et al. Genomic selection
DOI: 10.1201/9781315365930 in the era of next generation sequencing
for complex traits in plant breeding.
[53] Jaradat AA. Breeding oilseed crops Frontiers in Genetics. 2016;7:221.
for climate change. In: Jaradat AA, DOI: 10.3389/fgene.2016.00221
editor. Breeding Oilseed Crops for
Sustainable Production. London, [60] Leng PF, Lübberstedt T,
United Kingdom: Academic Press; Xu ML. Genomics-assisted breeding–a
2016. pp. 421-472. DOI: 10.1016/ revolutionary strategy for crop
B978-0-12-801309-0.00018-5 improvement. Journal of Integrative
Agriculture. 2017;16(12):2674-2685.
[54] Lodhi SS, Maryam S, Rafique K, DOI: 10.1016/S2095-3119(17)61813-6
Shafique A, Yousaf ZA, Talha AM,
et al. Overview of the prospective [61] Ashraf M, Akram NA, Foolad MR.
strategies for conservation of genomic Marker-assisted selection in plant
diversity in wheat landraces. In: breeding for salinity tolerance. In:
Climate Change and Food Security Walker J, editor. Plant Salt Tolerance:
with Emphasis on Wheat. London, Methods and Protocols. Totowa, NJ:
United Kingdom: Academic Press; Humana Press; 2012. pp. 305-333
2020. pp. 293-309. DOI: 10.1016/
B978-0-12-819527-7.0021-2 [62] Kang M, Ahn H, Rothe E,
Baldwin IT, Kim SG. A robust genome-
[55] Al-Khayri JM, Jain SM, Johnson DV. editing method for wild plant species
Advances in Plant Breeding Strategies: Nicotiana attenuata. Plant Biotechnology
Breeding, Biotechnology and Molecular Reports. 2020;14:585-598. DOI: 10.1007/
Tools. Vol. 1. Switzerland: Springer s11816-020-00634-5
International Publishing; 2015. 656 p.
DOI: 10.1007/978-3-319-22521-0 [63] Hasan N, Choudhary S,
Naaz N, Sharma N, Laskar RA. Recent
[56] Agnihotri A, Kumar M, Kilam D, advancements in molecular marker-
Aneja JK. Genomic and transcriptomic assisted selection and applications in
approaches for quality improvement in plant breeding programmes. Journal of
oilseed brassicas. In: Plant OMICS and Genetic Engineering and Biotechnology.
Crop Breeding. Oakville, ON, Canada: 2021;19(1):1-26. DOI: 10.1186/
Apple Academic Press Inc.; 2017. s43141-021-00231-1
pp. 31-48. DOI: 10.1201/9781315365930
[64] Dekkers JC, Hospital F. The use of
[57] White TL, Adams WT, molecular genetics in the improvement
Neale DB. Forest Genetics. Cambridge: of agricultural populations. Nature
CABI Publishing; 2007. 702 p. Reviews Genetics. 2002;3(1):22-32.
DOI: 10.1079/9781845932855.0000 DOI: 10.1038/nrg701
23
[65] Beuzen ND, Stear MJ, Chang KC. [71] Visioni A, Al-Abdallat A,
Molecular markers and their use in Elenien JA, Verma RPS, Gyawali S,
animal breeding. The Veterinary Journal. Baum M. Genomics and molecular
2000;160(1):42-52. DOI: 10.1053/ breeding for improving tolerance
tvjl.2000.0468 to abiotic stress in barley (Hordeum
vulgare L.). In: Rajpal V, Sehgal D,
[66] Yadav AK, Tomar SS, Jha AK, Kumar A, Raina S, editors. Genomics
Singh J. Importance of molecular markers Assisted Breeding of Crops for Abiotic
in livestock improvement: A Stress Tolerance, Vol. II, Sustainable
review. International Journal of Development and Biodiversity. Vol. 21.
Agriculture Innovations and Research. Cham, Switzerland: Springer Nature
2017;5(4):614-622 Switzerland AG; 2019. pp. 49-68.
DOI: 10.1007/978-3-319-99573-1_6
[67] Singh U, Deb R, Alyethodi RR, Alex R,
Kumar S, Chakraborty S, et al. Molecular [72] Skøt L, Kelly R, Humphreys MW.
markers and their applications in cattle Genomics assisted approaches for
genetic research: A review. Biomarkers improving abiotic stress tolerance in
and Genomic Medicine. 2014;6(2):49-58. forage grasses. In: Rajpal V, Sehgal D,
DOI: 10.1016/j.bgm.2014.03.001 Kumar A, Raina S, editors. Genomics
Assisted Breeding of Crops for Abiotic
[68] Amiteye S. Basic concepts and Stress Tolerance, Vol. II., Sustainable
methodologies of DNA marker systems Development and Biodiversity. Vol. 21.
in plant molecular breeding. Heliyon. Cham, Switzerland: Springer Nature
2021;7(10). DOI: 10.1016/j.heliyon.2021. Switzerland AG; 2019. pp. 91-103.
e08093 DOI: 10.1007/978-3-319-99573-1_6
[69] Chaudhary HK, Badiyal A, [73] Chaudhary J, Alisha A, Bhatt V,

Hussain W, Jamwal NS, Kumar N, Chandanshive S, Kumar N, Mir Z, et al.
Sharma P, et al. Innovative role of DH Mutation breeding in tomato: Advances,
breeding in genomics assisted-crop applicability and challenges. Plants.
improvement: Focus on drought 2019;8(5):128. DOI: 10.3390/
tolerance in wheat. In: Rajpal V, plants8050128
Sehgal D, Kumar A, Raina S, editors.
Genomics Assisted Breeding of [74] Okada T, Whitford R. Hybrid
Crops for Abiotic Stress Tolerance, wheat and abiotic stress. In: Rajpal V,
Vol. II., Sustainable Development Sehgal D, Kumar A, Raina SN, editors.
and Biodiversity. Vol. 21. Cham, Genomics Assisted Breeding of Crops
Switzerland: Springer Nature for Abiotic Stress Tolerance. Vol. II.
Switzerland AG; 2019. pp. 91-103. Cham, Switzerland: Springer Nature
DOI: 10.1007/978-3-319-99573-1_6 Switzerland AG; 2019. pp. 211-224.
DOI: 10.1007/978-3-319-99573-1_6
[70] Kumar S, Muthusamy SK,
Mishra CN, Gupta V, Venkatesh K. [75] Agarwal S, Grover A,
Importance of genomic selection in crop Khurana SMP. Plant molecular biology:
improvement and future prospects. Tools to develop transgenics. In:
In: Bharadwaj DN, editor. Advanced Khan MS, Khan AI, Barh D, editors.
Molecular Plant Breeding: Meeting the Applied Molecular Biotechnology.
Challenge of Food Security. New-York: The Next Generation of Genetic
Apple Academic Press; 2018. pp. 505-534. Engineering. Boca Raton, FL, USA: CRC
DOI: 10.1201/b22473Oakville Press; 2016. pp. 33-60
24
[76] Lawrenson T, Atkinson N, Forner M, Current Opinion in Biotechnology.

Harwood W. Highly efficient gene 2006;17(2):174-178. DOI: 10.1016/j.
knockout in medicago truncatula copbio.2006.02.009
genotype R108 using CRISPR-Cas9
system and an optimized agrobacterium [82] James C. Global Status of
transformation method. In: Yang B, Commercialized Biotech/GM Crops.
Harwood W, Que Q, editors. Plant Brief 44. ISAAA: Ithaca; 2012. 329 p
Genome Engineering: Methods
and Protocols. 2023. pp. 221-252. [83] Singh Y, Prajapati S. Status of
DOI: 10.1007/978-1-0716-3131-7_15 horticultural crops: Identifying the
need for transgenic traits. In: Rout GR,
[77] Marone D, Mastrangelo AM, Peter KV, editors. Genetic Engineering
Borrelli GM. From transgenesis to of Horticultural Crops. London, United
genome editing in crop improvement: Kingdom: Academic Press; 2018. pp. 1-22
Applications, marketing, and legal
issues. International Journal of Molecular [84] Joung YH, Choi PS, SY K,
Sciences. 2023;24(8):7122. DOI: 10.3390/ Harn CH. Plant transformation
ijms24087122 methods and applications. In: Koh HJ,
Kwon SY, Thomson M, editors. Current
[78] Shackira AM, Sarath NG, Veena M, Technologies in Plant Molecular Breeding
Johnson R, Jeyaraj S, Aswathy Raj KP, – A Guide Book of Plant Molecular
et al. Resistance identification and Breeding for Researchers. New York.
implementation. In: Shah T, Nie L, London: Springer Science+Business
Teixeira Filho MCM, Amir R, editors. Media Dordrecht; 2015. pp. 296-344.
Cereal Crops: Genetic Resources and DOI: 10.1007/978-94-017-9996-6
Breeding Techniques. Boca Raton, FL,
USA: CRC Press; 2023. pp. 141-156. [85] Espinoza C, Schlechter R, Herrera D,
DOI: 10.1201/9781003250845 Torres E, Serrano A, Medina C, et al.
Cisgenesis and intragenesis: New tools
[79] Ahad A, Jan US, Rafique K, Zafar S, for improving crops. Biological Research.
Ahmad MA, Abbas F, et al. Climate 2013;46(4):323-331. DOI: 10.4067/
change and cereal modeling. Impacts S0716-97602013000400003
and adaptability. In: Shah T, Nie L,
Teixeira Filho MC, Amir R, editors. [86] Choudhary S, Jain D, Meena MR,
Cereal Crops: Genetic Resources and Verma AK, Sharma R. Gene silencing
Breeding Techniques. Boca Raton, FL, in horticultural transgenic crops. In:
USA: CRC Press; 2023. pp. 239-272. Rout GR, Peter KV, editors. Genetic
DOI: 10.1201/9781003250845 Engineering of Horticultural Crops.
London, United Kingdom: Academic
[80] U.S. Food and Drug Administration. press; 2018. pp. 47-62
Voluntary Labeling Indicating Whether
Foods Have or Have Not Been Derived [87] Eckerstorfer MF, Engelhard M,
from Genetically Engineered Plants: Heissenberger A, Simon S,
Guidance for Industry [Internet]. 2019. Teichmann H. Plants developed by new
Available from: https://www.fda.gov/ genetic modification techniques -
media/120958/download?attachment Comparison of existing regulatory
[Accessed: Sep. 19, 2023] frameworks in the EU and non-EU
countries. Frontiers in Bioengineering
[81] Raney T. Economic impact of and Biotechnology. 2019;7:26.
transgenic crops in developing countries. DOI: 10.3389/fbioe.2019.00026
25
[88] Cohen J. With its CRISPR [95] Rostoks N. Implications of the

Revolution, China Becomes a World EFSA scientific opinion on site directed
Leader in Genome Editing. [Internet] nucleases 1 and 2 for risk assessment
Washington, DC, USA: American of genome-edited plants in the EU.
Association for the Advancement of Agronomy. 2021;11(3):572. DOI: 10.3390/
Science; 2019. Available from: https:// agronomy11030572
www.science.org/content/article/
itscrispr-revolution-china-becomes- [96] Kawall K, Cotter J, Then C.
world-leader-genome-editing [Accessed: Broadening the GMO risk assessment in
Sep. 19, 2023] the EU for genome editing technologies
in agriculture. Environmental Sciences
[89] Kuiken T, Kuzma J. Genome Editing Europe. 2020;32(1):106. DOI: 10.1186/
in Latin America: Regional Regulatory s12302-020-00361-2
Overview. Washington, DC, United
States: Inter-American Development [97] Wünschiers R. Genetic Engineering:
Bank; 2021. DOI: 10.18235/0003410 Reading, Writing and Editing Genes.
Wiesbaden, Germany: Springer
[90] Anzalone AV, Koblan LW, Liu DR. Fachmedien Wiesbaden GmbH; 2021.
Genome editing with CRISPR–CAS 39 p
nucleases, base editors, transposases and
prime editors. Nature Biotechnology. [98] Ma X, Li X, Li Z. Transgene-
2020;38(7):824-844. DOI: 10.1038/ free genome editing in Nicotiana
s41587-020-0561-9 benthamiana with CRISPR/Cas9
delivered by a rhabdovirus vector. In:
[91] Liu Z, Dong H, Cui Y, Cong L, Yang B, Harwood W, Que Q , editors.
Zhang D. Application of different types Plant Genome Engineering: Methods
of CRISPR/Cas-based systems in and Protocols. 2023. pp. 173-185.
bacteria. Microbial Cell Factories. DOI: 10.1007/978-1-0716-3131-7_11
2020;19(1):1-4. DOI: 10.1186/
s12934-020-01431-z [99] Schleissing S, Pfeilmeier S,
Dürnberger C. An introduction: Between
[92] Xu Y, Li Z. CRISPR-Cas systems: precaution and responsibility.
Overview, innovations and applications In: Schleissing S, Pfeilmeier S,
in human disease research and Dürnberger C, editors. Genome Editing
gene therapy. Computational and in Agriculture: Between Precaution
Structural Biotechnological Journal. and Responsibility. Baden-Baden,
2020;8(18):2401-2415. DOI: 10.1016/j. Germany: Nomos; 2019. pp. 9-22.
csbj.2020.08.031 DOI: 10.5771/9783845296432-9
[93] Gocht A, Consmüller N, Thom F,

Grethe H. Economic and environmental
consequences of the ECJ genome editing
judgment in agriculture. Agronomy.
2021;11(6):1212. DOI: 10.3390/
agronomy11061212
[94] Kim H, Kim JS. A guide to genome

engineering with programmable
nucleases. Nature Reviews Genetics.
2014;15(5):321-334. DOI: 10.1038/nrg3686
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Characteristics of Various Types of

Keywords: traditional breeding, mutation breeding, speed breeding, molecular breeding,

3. Traditional plant breeding based on selective breeding

Traditional plant breeding, also called classical or conventional breeding, is the

called artificial or phenotypic selection, which is based on phenotype evaluation for

3.1 Mutation breeding

Plant breeding relies on genetic variation — “heritable variation is the lifeblood of

• “Genetic transformation and mutation breeding, as nonconventional breeding

• “… nonconventional breeding of banana, more specifically genetic transformation,

EU legislation on GMOs — that is. Article 3(1), in conjunction with Annex I B of

3.2 Speed breeding

• marker-assisted selection [38]; marker-assisted selection is presented in

• high-throughput genotyping — that is. genomics-assisted breeding — combina-

• automated or high-throughput phenotyping [40, 42].

4. Molecular plant breeding

The agricultural challenges of modern society, determined by population growth,

• “Application of molecular biology in plant breeding is molecular breeding.” [3].

• “Similarly, the recent integration of advances in biotechnology, genomic

• “Recent progress in biotechnology and genomics has expanded the breeders’

• “Molecular breeding applies molecular biology tools to accelerate the breeding

• “Molecular breeding is a modern technique that refers to the combined applica-

Taking into consideration the primary components of molecular breeding out-

• “To this end, recent advances in transcriptome profiling, functional genomics,

• “Molecular breeding in cotton includes traditional cotton breeding supple-

• “Therefore, combination of conventional and modern breeding approaches, such as

• “Molecular breeding may be defined in a broad sense as the use of genetic

• “Molecular breeding is used to describe several modern breeding strategies,

• “Marker-assisted or marker-based backcrossing is regarded as the simplest form

• “The use of DNA markers in plant breeding is called marker-assisted selection

• “The classical approach for molecular breeding is heavily dependent on marker-

• “Molecular breeding uses molecular biology tools in breeding crop plant. It

Other authors present molecular breeding as pertaining either to molecular mark-

• “Molecular breeding approaches target on specific regions on the DNA and

Sometimes molecular breeding — potentially referring to molecular markers —

• “The final part has an excellent discussion of advanced techniques of plant

• “Now, new innovative additional plant breeding tools, including molecular

• “For introduction of desirable traits molecular breeding and transformation

4.1 Molecular markers in plant breeding

While significant genetic improvements have been achieved using classical

4.1.1 Marker-assisted selection and breeding

Marker-assisted or marker-aided selection (MAS) is the selection of individuals

intended to enhance mating designs, genetic testing and screening, deployment

• “Marker-assisted selection or marker-aided selection (MAS) is a process

• “MAS is an indirect selection process, where individuals for a particular trait of

• “MAS is the process of using morphological, biochemical, or DNA markers as

• “Marker-assisted selection is a strategy to accelerate genetic gain in conventional

• “Marker-assisted selection is a newly emerging approach due to which various

• “Molecular genetic analyses of quantitative traits lead to the identification

genetic improvement programes: causal mutations and presumed non-

• “Secondly, some SNPs [single nucleotide polymorphism] are located in coding

It is also important to understand that molecular markers represent just one of

• “Such variations occurring at different levels, that is. at the morphological,

• “Genetic markers are classified: based on visually evaluated traits (morphologi-

• “… any stable and inherited variation that can be measured or detected by a

• “Molecular marker is a term used to refer to a specific DNA variation between