Molecular Genetics and Genomics (2023) 298:813–821

https://doi.org/10.1007/s00438-023-02026-0

REVIEW

Understanding the genomic selection for crop improvement: current

progress and future prospects
Rabiya Parveen1 · Mankesh Kumar1 · Swapnil2 · Digvijay Singh3 · Monika Shahani4 · Zafar Imam1 ·
Jyoti Prakash Sahoo5

Received: 29 January 2023 / Accepted: 27 April 2023 / Published online: 10 May 2023
© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023

Abstract
Although increased use of modern breeding techniques and technology has resulted in long-term genetic gain, the pace
of genetic gain must be sped up to satisfy global agricultural demand. However, marker-assisted selection has proven its
potential for improving qualitative traits with large effects regulated by one to few genes. Its contribution to the improve-
ment of the quantitative traits regulated by a number of small-effect genes is modest. In this context, genomic selection
(GS) has been regarded as the most promising method for genetically enhancing complicated features that are regulated by
several genes, each of which has minor effects. By examining a population's phenotypes and high-density marker scores,
genomic selection can forecast the breeding potential of individual lines. The fact that GS uses all marker data in the predic-
tion model prevents skewed marker effect estimations and maximizes the amount of variation caused by small-effect QTL.
It has the ability to speed up the breeding cycle and as a consequence of which superior genotypes are selected rapidly.
Developing the best GS models while taking into account non-additive effects, genotype-by-environment interaction, and
cost-effectiveness will enable the widespread implementation of GS in plants. These steps will also increase heritability
estimation and prediction accuracy. This review focuses on the shift from conventional selection methods to GS, underlying
statistical tools and methodologies, the state of GS research in agricultural plants, and prospects for its effective use in the
creation of climate-resilient crops.

Keywords Genomic selection · Plant breeding · Crop improvement · Genomics

Introduction

The degree of genetic variability present in the germplasm

Communicated by Bing Yang.
is a key feature in plant breeding's ability to successfully
* Jyoti Prakash Sahoo manipulate the genotype's genetic architecture in an artistic
jyotiprakash.sahoo@cgu-odisha.ac.in; and scientific manner. The result of all these breeding tech-
jyotiprakashsahoo2010@gmail.com niques is a cultivar that is better and more widely accepted.
1
Department of Genetics and Plant Breeding, Bihar The methods which were used earlier for the selection of
Agricultural University, Sabour, Bhagalpur 813210, India plants as well as to realize the genetic gain for the desired
2
Department of Genetics and Plant Breeding, traits were solely based on their phenotypes or visual selec-
Centurion University of Technology and Management, tion that might include a few major yield-related attributes.
Paralakhemundi 761211, India Phenotypic selection (PS) based breeding techniques could
3
Department of Genetics and Plant Breeding, Narayan not effectively address the different attributes regulated by
Institute of Agricultural Sciences, Gopal Narayan Singh larger number of minor effects and non-allelic QTLs and
University, Sasaram 821305, India also demonstrating strong genotype × environment (G ×
4
Department of Genetics and Plant Breeding, Maharana E) interactions (Varshney et al. 2012; Moose et al. 2008).
Pratap University of Agriculture and Technology, Numerous varieties of various crops have been created
Udaipur 313001, India
due to the introduction of molecular markers based on
5
Department of Agriculture and Allied Sciences, C.V. Raman DNA and further utilizing them in MAS (marker-assisted
Global University, Bhubaneswar 752054, India

13
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814
selection), where the desired genes of different crop plants
are tagged with these markers (Collard et al. 2008). Never-
theless, using gene pyramiding, MAS (Servin et al. 2004)
and MARS (marker-assisted recurrent selection) (Crossa
et al. 2010) have been employed to improve the shortcom-
ings of extensively adapted cultivars and further introduce
novel gene(s) into desired parents. However, the characters
which displayed quantitative or complex nature, governed
by a greater number of small-effect quantitative trait loci
(QTLs) are not considerably improved by gene pyramiding
of a small number of genes or alleles (Kearsey et al. 1998).
Furthermore, the application of low density marker sys-
tems limit the efficiency of these approaches in genetically
improving polygenic traits. In this context, the traditional
breeding has been greatly strengthened by precise indirect
choices based on molecular or genomic methods that have
been in frequent use during the past few years. A technique
called genomic (or genome-wide) selection (GS) has the
potential to address the drawbacks of MAS for quantita-
tive traits (Varshney et al. 2012). Instead of pinpointing a
specific QTL, the goal of GS is to evaluate an individual's
genes potential. The core benefit of GS is that it may con-
currently improve numerous phenotypes while also captur-
ing a number of small-effect genetic parameters (Xu et al.
2020a, b). The ability to choose parents solely on the basis of
GEBV (genomic estimated breeding value) is also discussed
in this review, along with a comparison of implementation
alternatives for GS in breeding programmes, making predic-
tions within as well as across breeding cycles. However, GS
was initially created in livestock breeding as a technique to
forecast an individual's breeding value based on markers
that cover up the whole genome and uses simulated data
(Meuwissen et al. 2001).
Drawbacks of conventional marker assisted
selection
In an indirect selection method known as Marker Assisted
Selection (MAS), individuals are chosen based on the known
markers associated with a certain trait of interest (Fernando
et al. 1989). MAS was developed as well as utilized to
choose the characters governed by genes with reasonably
large effects. It utilizes molecular markers associated with
the target characters. Unlike the conventional phenotype-
based selection method in plant breeding, this method has
been found effective for the selection of individuals, but it is
not the best strategy for intricate agronomic traits, because it
typically relies on predictions from a small number of mark-
ers in Linkage Disequilibrium (LD) with QTLs with large
impact on the trait, which overlook the contributions from
small to medium effect QTL [Bernardo 2008, Heffner et al.
2010]. MAS has been widely used for backcross breeding
program, mainly for the introgression of QTLs with major
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Molecular Genetics and Genomics (2023) 298:813–821
effect, desired genes as well as for marker-assisted recur-
rent selection (MARS). Backcross breeding program is a
conventional method of breeding as the recurrent (recipient)
parent is only improved to the degree that the QTLs/intro-
gressed genes stipulate. It doesn't produce any novel gene
combinations that could be anticipated to improve the geno-
type's adaptability and performance potential. The MARS
approach has been criticized for being ineffective because
it also relies on markers that demonstrate a strong correla-
tion with the trait(s). By merging trait phenotypic data and
marker genotype data into a pooled selection index, MARS
aims to account for minor effect QTLs. A new selection
method termed genomic selection (GS), which can help with
selection for such qualities by determining an individual's
net genetic gain by utilizing the impacts of dense markers
spread throughout the genome, has been created to overcome
the drawbacks of both MAS and MARS (Meuwissen et al.
2001).
In essence, GS is a variation of MAS with added benefits
and a wider reach. GS, as opposed to MAS, estimate the
breeding value of an individual solely based on large number
of marker data spread throughout the genome. To determine
the genomic estimated breeding values (GEBVs) for each
individual of the breeding population (BP)/ target popula-
tion, the GS creates a prediction model based on the phe-
notypic and genotypic data of the training population (TP)
(Meuwissen et al. 2001). Since the marker profiles of these
individuals are comparable to those of additional plants of
TP that have been shown to perform more efficiently in a
particular environment, the GEBVs give us the ability to
determine which individuals will perform more effectively
and are appropriate for either their inclusion further in
advanced breeding program or as a parent in hybridization.
According to the GS principle, all population-wide genetic
variants are captured using genome-wide markers, and each
of the QTL determining a particular trait is in LD with at
least one marker. Therefore, the precision of GS depends on
the LD between particular marker alleles and QTLs; which
implies, the larger the LD between the two, the more precise
the genomic predictions (Solberg et al. 2013). The breed-
ing cycle is accelerated via GS by increasing the selection
intensity as well as precision (Crossa et al. 2017) and facili-
tating the quick selection of high-performing genotypes.
This accurate selection is necessary for more rapid genetic
advancement during breeding for complex traits.
Population used in genomic selection
The process of GS involves two distinct but inter-related
populations. The Training Population (TP) (Reference Popu-
lation) is the first, and other one is the Breeding Popula-
tion (BP) (Testing Population) (Heffner et al. 2009). The TP
is utilized to train the GS model and to predict the associated
Molecular Genetics and Genomics (2023) 298:813–821
marker effects required to determine the GEBVs of particu-
lar genotype in the BP. On the other hand, the BP is the
one that undergoes GS to accomplish the required progress
and select superior lines to be used as parents or new vari-
eties of fresh, improved hybrids. The estimated breeding
values for each genotyped line in BP are calculated using the
data from TP to rank the lines without phenotyping and to
assess the effect of each assayed marker. Additionally, these
reserved individuals can be used as parental lines that could
mate with one another to introgress advantageous alleles
for the upcoming selection cycle (Jonas et al. 2013, Desta
et al. 2014; Heffner et al. 2010). To estimate the BVs of the
lines being tested, only marker data and statistical models
created in a TP are used in the basic GS process (Meuwis-
sen et al. 2001).
A TP is a population for which complete genotypic and
phenotypic data are available and from which the GS model
parameters are obtained. The BVs of the lines in the BP, also
called as the genomic estimated breeding value (GEBV) on
the basis of the genotypic data, are then evaluated using the
GS models. The breeding population must be represented by
a set of lines that are closely associated, and whose ancestry
is well-known, such as half-siblings or closely linked popu-
lations. However, a diagram of basic scheme of genomic
selection process is illustrated in Fig. 1. Furthermore, a
generalized process for genomic selection can be explained
as, (i) Creation of a TP appropriate for the concerned BP,
(ii) The TPs individuals are genotyped for the large set
of markers that are uniformly distributed throughout the
whole genome, (iii) Individuals are then subjected to exten-
sive phenotypic evaluation in replicated trials over loca-
tions and preferably over years, (iv) GS model parameters
are computed using marker genotypic and phenotypic data,
which is called model training, (v) BP is then assessed for
Population
Training Population Breeding Population
Phenotype
+ Genotype
Genotype
GS Model GEBVs
Fig. 1  Basic scheme of Genomic Selection process
815
the similar set of markers that are used to estimate model
parameters, and no phenotypic evaluation, (vi) GEBVs of BP
lines are then estimated using information on their marker
genotype data and related effects derived from the TP, and
(vii) Based on their GEBV estimates, the superior genotypes
or lines are chosen from the BP.
The breeder’s equation and genetic gain
The following well-known breeder’s equation predicts
genetic gain in a plant breeding programme:
ΔG = ih𝜎a ∕L
where i = selection intensity, h = narrow sense heritability,
σa = additive genetic variance, L = length of breeding cycle
interval or generation
To achieve higher genetic gains in breeding programs,
strategies that allow quick increases in genetic diversity in
the breeding population, selection intensity, and/or heritabil-
ity of characters are required (Krishnappa et al. 2021). These
approaches also need to allow for a decline in the number of
breeding cycles (Xu et al. 2016). The breeding cycle inter-
val can be shortened to enhance the genetic gain per unit
of time, significantly by raising period of breeding per unit
of time as well as decreasing the expense of phenotyping
(Crossa et al. 2010), particularly for plant species with long
breeding cycles (Wong et al. 2008; Sahoo et al. 2018a). GS
quickens the breeding cycle and makes it possible to identify
superior genotypes quickly (Crossa et al. 2017; Heffner et al.
2010; Sahoo et al. 2018b).
Design of training population
By fostering high levels of prediction accuracy or enhancing
BP diversity in the context of precise and effective breeding
initiatives, TP design plays a significant role in GS (Isidro
et al. 2015, Zhang et al. 2017). The BP composition is the
primary factor to be taken into account when developing a
test procedure, thus it is necessary to establish BP before
developing a TP design that focuses on maximizing candi-
date prediction accuracy while minimizing expenses related
to phenotyping and genotyping. For high GEBV accuracy,
the training population should contain members of the BP
(Rutkoski et al. 2011). A TP could be made up of historical
data or could be an actual population made up of existing
individuals (Singh et al. 2015; Sahoo et al. 2019). Ideally,
for each BP, a fresh TP should be created. Since the breeding
population and training population would be interconnected,
this strategy will result in high accuracy in prediction of
GEBV. As a result, QTL effects, the genetic background,
moderate allele frequencies, etc., will be similar in the two
populations. However, this will call for a precise phenotypic
13
816 Molecular Genetics and Genomics (2023) 298:813–821

assessment of distinct TP for each BP in the desired set of
environmental condition. This will hindered the growth and
will also add to the cost in the running program.
As an alternative, the entire breeding effort might use a
single training population. This population would be made
up of samples of genotypes or lines taken from all the BP
being considered in a particular breeding program. GS mod-
els trained based on the populations as per second approach
would allow to precisely estimate GEBVs of individual
genotypes from each BP represented in TP. Numerous sim-
ulation experiments show that GS models trained on these
populations are quite accurate in predicting the GEBVs of
the populations in consideration, especially when extremely
greater marker densities are employed. This strategy would
shorten selection cycles and cut their cost (Singh et al. 2015;
Sahoo et al. 2020a). The breeding population's allelic fre-
quencies and LD structure would change as a result of selec-
tion; hence the TP should be revised to include genotypes
or lines chosen from the BP. The GS model should also be
retrained with every revision of the training population. To
reach the highest level of prediction accuracy, the GS model
should actually be trained over the course of more than one
generation.
Cross validation
The level of prediction accuracy is crucial for the effective
use of GS in regular plant breeding operations, hence it's
crucial to cross-validate the trained model to ensure a high
level of prediction accuracy. The most accurate prediction
model in the TP is trained and developed via cross-vali-
dation, and it can then be used to assess the GEBV of BP
(Perez-Cabal et al. 2012; Sahoo et al. 2020b). The K-fold
cross-validation that is most frequently used cross-valida-
tion, in which the sample is divided into K nearly equal
parts. Using variables calculated from the other K-1 parts,
each part is predicted (sample without the predicted part).
Eventually, all parts are estimated using samples that exclude
the parts to be estimated. This is accomplished by first creat-
ing a prediction model using a large portion of the training
population, and then utilizing solely genotypic information
to find out the GEBVs of the remaining members of the TP.
This enables scientists to "test" and improve the prediction
model to ensure that the forecast accuracy is good enough
that upcoming predictions may frequently be relied upon
(Robertson et al. 2019).
at genotypic level. The amount of prediction accuracy in
various GS models is determined by the assumptions and
approaches taken to marker effects (Liu et al. 2018; Wang
et al. 2018; Samal et al. 2021). However, the most commonly
used models in genomic selection are illustrated in Fig. 2.
Since stepwise regression (SR) methods are necessary
for traditional MAS as it treats marker effects as fixed, fit-
ting markers separately or in small groups and resolves the
issue of lack of degrees of freedom. Only those markers
are retained that displayed significant effect on the character
after this process, and the rest are discarded. The markers
with significant effects are estimated, while the markers with
non-significant effects are given "zero" effect values, which
is essential for maintaining model estimability (Lande et al.
1990; Priyadarshini et al. 2020). Though effects preserved
in the model can be significantly exaggerated (Beavis 1998;
Hayes 2007; Sahoo et al. 2021a), when only substantial
marker effects are estimated, only a percentage of the genetic
variance will be detected (Goddard et al. 2007; Hayes 2007;
Sahoo et al. 2021b). This is especially true when several
effects are assessed.
As suggested by Meuwissen et al. (2001), SR in GS sim-
ulation showed low GEBV accuracy as a consequence of
limited QTL detection. The two frequently utilized models
for prediction in different GS research in crop plants are RR-
BLUP i.e., ridge regression best linear unbiased prediction
Stepwise
Regression
G-BLUP
(Genomic
BLUP (Best BLUP)
Linear
Unbiased RR-BLUP
Predictor) (Ridge
Regression
BLUP)
Bayes A
Whole genome
regression models
for Genomic Bayes B
Seletion
Bayesian
Approach
Bayes Cπ
Bayes Dπ

Statistical model for genomic selection RR-BLUP

Penalized
Approach
A proper statistical model must be chosen to accomplish LASSO
a significantly greater prediction capacity and, in turn, the
effectiveness of GS, despite the fact that numerous GS mod-
els have been designed to forecast performance of the crops Fig. 2  Most commonly used Models in Genomic Selection

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Molecular Genetics and Genomics (2023) 298:813–821
and G-BLUP i.e., genomic best linear unbiased prediction.
The RR-BLUP model presupposes that each marker have
minor effects and similar variances. Each marker possesses
different effects, despite the assumption of equal variance
(Bernardo et al. 2007). When the character is regulated by
numerous loci with minor effects, RR-BLUP produces good
prediction accuracy (Burgueno et al. 2012). Another popular
model that may determine the additive genetic qualities from
a genomic association matrix is the G-BLUP, which is equal
to the RR-BLUP (Wang et al. 2015; Sahoo et al. 2022a).
RR-BLUP and G-BLUP are better appropriate for quantita-
tive attributes that are regulated by a huge number of small
genes since they share the same presumption that all loci's
effects have a common variance (Sahoo et al. 2022b). The
majority of the markers have minimal or no effects, and only
a small number of markers have big impacts, therefore the
presumptions of RR-BLUP and G-BLUP are seldom met.
Both the models assume that every marker adds the
equal amount of variance, which is not true for all traits. As
a result, it is necessary to predict the variation of the markers
depending on the genetic makeup of the trait (Sahoo et al.
2022c). Several Bayesian models that assume the existence
of a prior distribution of marker effects have been put forth
for this purpose. Additionally, conclusions regarding the
model's parameters are drawn from the posterior distribu-
tions of marker effects. For genomic prediction, Bayesian
models are available in a number of forms, including Bayes
A, Bayes B, Bayes Cπ, and Bayes Dπ (Meuwissen et al.
2001; Habier et al. 2011), as well as other derivatives such
Bayesian LASSO (Least Absolute Shrinkage and Selection
Operation). Given that the shrinkage level is lower than that
of Bayes B and Bayes A and Cπ is most appropriate for
characters controlled by a several genes. Most markers are
not considered in the model because the Bayes B model pre-
sumes that the majority of loci have no influence on the char-
acter. If large-effect QTLs that account for a considerable
portion of the genetic variance control how a trait manifests,
Bayes B fits well (Munkvold et al. 2009). In contrast, the
parameter in Bayes Cπ can be determined from experimental
data, allowing for the estimation of the shrinkage level. As
a result, it is better suited than Bayes B for the examination
of actual data.
Since Bayesian models capture large-effect QTLs, they
will typically have more accurate predictions. These Bayes-
ian models are sensitive to the number of QTLs; as the
number of QTLs rises, so does the predictive ability (Wang
et al. 2015). On the other hand, it is more likely for plant
traits controlled by a greater number of minor genes because
the predictive ability of RR-BLUP and G-BLUP frequently
remains almost constant regardless of the number of QTLs.
The number of markers (p) exceeds the number of observa-
tions (n), i.e., genotype/lines, and it causes the difficulty of
over-parameterization (large "p" and small "n" problem (p
817
>> n), which is the major challenge in linear models using
abundant of markers throughout the genome. As a result,
this challenge is successfully addressed by the penalized
regression-based technique known as ridge regression (RR)
(Meuwissen et al. 2001). The least absolute shrinkage and
selection operator (LASSO), which is a form of penalized
regression similar to RR, penalizes estimate to get a sparse
solution. Ridge regression compelled all the coefficients
to decrease to zero, but LASSO can set some coefficients
to zero that are not related to the phenotype. Hence, if the
phenotype is governed by numerous markers with minute
effects, ridge regression will detect such effects (Heffner
et al. 2009), while LASSO will considers major effects with
few markers (van Eeuwijk et al. 2018).
The markers are omitted from the model and their geno-
typic information is not needed in the breeding phase if the
coefficients of the markers are set to zero or a low value
during the training phase. A non-parametric technique for
making genetic predictions is reproducing kernel Hilbert
space (RKHS). In comparison to parametric techniques,
non-additive genetic effects can be easily captured by non-
parametric models in genomic prediction (Gionala et al.
2006). By combining an additive genetic model with a ker-
nel function (Gionala et al. 2006) and transforming predic-
tor variables into a set of distances between observations,
RKHS produces a definite matrix for use in a linear model.
However, the factors affecting GEBVs accuracy are illus-
trated in Fig. 3.
Population size
Whether using traditional MAS or GS, population size, par-
ticularly the TP, has a considerable impact on prediction pre-
cision. It is evident that a decline in accuracy is anticipated
if the TP size is minimal since the model would inaccurately
predict the marker effects and subsequently the prediction
Population Size
Marker Density
Gene effects and
GEI
Heritability
Linkage
Disequilibrium (LD)
Fig. 3  Factors affecting GEBVs Accuracy
13
818
accuracy. When TP and BP had a closer genetic link, pre-
diction accuracy in GS was noticeably greater (Calus et al.
2007). Additionally, as the number of the effective breeding
population grows, so too should the size of the TP (Nakaya
and Isobe 2012).
Marker density
Meuwissen discovered that accuracy in prediction rises as
marker density does. The ideal number of markers is such
that at least one marker is in strong LD with the largest num-
ber of QTLs impacting the trait. Therefore, the extent of LD
in the species in consideration will determine the marker
density; generally, cross-pollinated species should have a
substantially higher marker density than self-pollinated spe-
cies. Traits with high heritability requires less dense markers
set as compared to those with low heritability (Sahoo et al.
2022d).
Gene effects and GEI
Genotype Environment Interactions (GEI) pose a signifi-
cant challenge to the practical use of GS in agricultural
crops, because most economically important traits have
complex natures and are significantly influenced by environ-
mental variables due to cross-over interactions (Boer et al.
2007; Cooper 1999). With the use of the equation ∆G =
ihσa/L, it is possible to see how GEI influences genetic gain
by dragging heritability downward. As a result, environmen-
tal trait prediction accuracy would be impacted, especially
during the multi-environment trial (MET) test. In addition
to GEI, non-additive genetic effects that may include domi-
nance (intra-locus) or epistasis (inter-locus) might also be
problematic for the use of GS in plant breeding. Breeding
populations can have various allele substitution effects at
the relevant QTL when non-additive effects are present. To
measure the QTL allele substitution effects for their con-
sistency across populations, TPs and BPs should both be
examined.
Heritability
Trait heritability can also have an impact on prediction accu-
racy, particularly when it is smaller (h2 = 0.4) (Hayes et al.
2009). In general, it is believed that target traits with high
heritability have accurate predictions, and vice versa. The
majority of agricultural traits, notably in plants, have low
to moderate heritability, which makes genomic selection
research difficult. To achieve the same prediction accuracy
as for characters with moderate to high heritability, low
heritable traits would need a bigger training population.
However, if data are available on numerous traits, the prob-
lem of low heritability could be addressed. By applying the
13
Molecular Genetics and Genomics (2023) 298:813–821
right MTGS (multi trait genomic selection) – based model,
few characters with low heritability and a strong associa-
tion with other characters which shows high heritability can
draw information from those traits. By using this, eventu-
ally scientists can more precisely and accurately predict the
GEBV in such cases by employing the MTGS model (Sahoo
et al. 2022d).
Linkage disequilibrium (LD)
Target marker densities for GS can be calculated using LD
estimations because at equilibrium, recombination counter-
acts drift by causing LD to decrease; therefore adjacent loci
should have greater LD values than far-off loci. Before exe-
cuting GS, it is important to fully comprehend how LD will
affect how operable GS will be. The non-random connec-
tion of alleles at various loci is referred to as LD. Average
neighboring marker r2 of 0.15 for high heritability traits has
been found to be sufficient, although r2 of 0.2 for low herit-
ability traits improves the accuracy of GEBV predictions
(Calus et al. 2007; Sahoo et al. 2023). However, some appli-
cations of GS in plant breeding are illustrated in Table 1.
GS as a prominent and promising strategy will become an
increasingly widespread application in plant breeding, as
in livestock, with the evolution of key GS components and
associated platforms. Breeding programs are often designed
to have fewer replications in the early generations viz; F2
and subsequent generations and more replications during
the advanced generations, along with larger plot sizes and
multi-location testing (Bernardo 2010; Sahoo et al. 2023).
By removing one or two selfing cycles, Genomic Selec-
tion in the early generation causes a significant drop in the
breeding cycle (Hickey et al. 2014). The length of the repro-
ductive cycle is shortened by re-introducing a few individu-
als with high GEBVs as parents. To balance the phenotypic
and genomic selection, either one or up to two cycles of
GS succeeded by one cycle of PS are advised with regard
to the costs and genetic advantages associated with the
breeding program (Rutkoski et al. 2015; Sahoo et al. 2023).
Applications of HTP are actively being pursued in wheat
genomics, but remain in their infancy for integration in GS
studies (Sweeny et al. 2019). The development of HTP for
routine use in crop breeding programs is lagging behind the
genotyping technologies. Therefore, more efforts are needed
to develop cost-effective and high-performance platforms
(Shakoor et al 2017). A recent concept of ‘envirotyping’
could benefit from recent advances in HTP to capture and
account for the source of variation in agronomic traits that
are related to quantifiable environmental variables (Cooper
2014). Envirotyping involves the collection and utilization
of information on environmental factors such as soil, geo-
graphic, climatic conditions by multi-location empirical
evaluations for phenotypic prediction (Chenu et al 2011; Xu
Molecular Genetics and Genomics (2023) 298:813–821 819

Table 1  Applications of GS in plant breeding

Crop Population size
Training population Breeding population Number of GEBV ­accuracya GS ­Modelb References
markers

Maize 95 119 1339 0.40–0.50 BLUP Lorenzana and Bernardo

28,35,70 349 160 0.59–0.72 BLUP (2009)
Arabi- 50-133 415 69 0.90–0.93 BLUP
dopsis
thaliana
Barley 54,96,120 150 223 0.64–0.83 BLUP
Maize 208 208 136 1.00 Severalc Piepho (2009)
Wheat 60 599 1279 0.48–0.61 PM-RKHSc Crossa et al. (2010)
Maize 270 300 1148 0.42–0.79 LASSO
Wheat 24, 48, 96 209 399 0.32–0.84 RRBLUP Heffner et al. (2010)
Wheat 24, 48, 96 174 574 0.41–0.73 RR- BLUP
Maize 25–157 for each population 25 population of 126–196 1,106 0.26–0.57 RRBLUP Guo et al. (2012)

2016). Parameters associated with envirotyping could also
be included in the linear mixed models for genomic predic-
tion to enhance heritability and thereby the prediction accu-
racies for different traits (van Eeuwijk 2018). However, some
contributions of GS to some traits are elaborated in Table 2.
Conclusion
To fulfill the rising demand for food on a global scale,
genetic gain must accelerate. To accomplish quick genetic
gain, modern breeding techniques are necessary. One such
tried-and-true technology in plant breeding initiatives is
Genomic Selection (GS). In general, for characters con-
trolled by genes with minor genes with cumulative effects,
GS may be a potential method to increase genetic gain for
a given time period and cost. The creation of affordable
genotyping platforms and high-efficiency breeding tech-
niques will aid in the extension of GS-assisted breeding
from livestock to plants and from narrow applications in a
few crops for specific traits to broad applications in all main
crop plants for all relevant traits. Methodological advance-
ments will surely help GS in plant as well as animal breeding
programs to become successful (such as the implementa-
tion of G × E interaction, imputation of missing genotypic
value, haplotypes, knowledge of epigenetic regulation, as
well as multiple traits information into prediction models).
It is highly desired to update the training dataset for GS
consistently by integrating the new markers in every genera-
tion. How well the prediction models perform is extremely
affected by the assessment of the TP, thus it should be done
under regulated, well-managed circumstances. To provide
successful outcomes, a structured program in the area of GS
is required, encompassing trait phenotyping, human resource
development, and advanced data recording technologies.
Acknowledgements Not applicable.

Table 2  Contributions of GS to some traits of interest

GS for Contribution

Quality traits and Yield

Complex polygenic characters governed by many genes with small effect that is affected by interactions between
genes and environment.
Prediction accuracies have been improved by include GxE effects in models
Disease resistance Aids in overcoming quantitative disease resistance, which is controlled by a large number of genes with small effects
and is difficult for pathogens to overcome. Most commonly are fusarium head blight, Wheat rust, and rice blast
resistance.
Germplasm enhancement With GS, it is possible to achieve high genome-enabled prediction accuracy, which could aid breeding program to
incorporate beneficial genetic variants.
This is in favor of utilizing GS to incorporate primitive cultivars into superior germplasm and produce gene pools and
populations ideal for genetic enhancement.
Hybrid breeding Improve the performance of crosses based on genotyped parent performance.
Used to aid in hybrid selection and predict hybrid performance.

13
820
Author contributions Rabiya: drafting of manuscript, final referencing
and editing; Swapnil: collection of supporting papers and written a part
of manuscript; DZ: written a part of manuscript and helped in editing
manuscript ; Mankesh: editing the manuscript; Monika: collection of
papers; JP: Coordinates the process. All authors read and approve the
final version of the manuscript.
Funding Not applicable.
Data availability All data generated or analyzed during this study are
included in this article.
Declarations
Conflicts of interest The authors declare no conflict of interest.
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