4.8
Genomics Assisted Breeding
Marker-assisted selection (MAS) is the indirect selection method where the linked
molecular marker is used to transfer important agronomical traits from one genotype
to another genotype. Marker-assisted backcrossing is an important approach in
soybean for transferring trait of interest (Lee et al. 2006). The high-throughput
genotyping technologies eased the process of marker identification and QTL
mapping for different traits in soybean. The molecular breeding approaches such
as marker-assisted backcrossing (MABC) and marker-assisted recurrent selection
(MARS) aided in the introgression of the trait of interest in soybean. The soybean
cyst nematode-resistant line, LDX01-1-65(PI636464) was developed using MABC
(Chaudhary et al. 2019). Gene pyramiding involves combining favorable alleles
controlling the same attribute from more than two parental lines (Melchinger 1990).
Marker-assisted gene pyramiding was successfully carried out to develop durable
resistance to several pathogens causing diseases in soybean (Walker et al. 2010).
Although drought tolerance is accompanied by many traits which governed by
mainly polygenes/QTLs, introgression of minor QTLs from donor to recipient
cultivar is not an easy task. In QTL mapping in five biparental populations, a total
of ten genomic regions or QTLs (Table 4.3) were mapped to be associated with
canopy wilting under drought, with varied phenotypic contributions, and the majority of these QTLs (9/10) have donor alleles for slow wilting phenotypes from PI
416937, Jackson, or both (Charlson et al. 2009; Abdel-Haleem et al. 2012; Hwang
et al. 2015). Molecular markers associated with these QTLs (identified in Meta-QTL
studies) can be used to perform MAS to introgress the slow canopy wilting
phenotypes from the donor in elite backgrounds. However, transferring these
QTLs is a challenging job for breeders due to complex, quantitative nature and
sensitivity to environmental factors of canopy-wilting trait under drought. Most of
the mapped minor QTLs were found to be unstable across independent environments
and populations. For instance, even major QTLs on chromosome 12 (R2 ¼ 0.27)
were identified in all five environments from Benning  PI 416937 (Abdel-Haleem
et al. 2012) but were not detected in any populations or site-years, including the
Benning  PI 416937 cross reported by Hwang et al. (2015). For this reason, QTL
confirmation in more advanced generations should be performed to validate each
individual QTL. This also indicates that stacking all confirmed QTLs in the same
elite background by MAS is necessary to build the drought tolerance shown in the
donor (Valliyodan et al. 2016).
Marker-assisted breeding for simple Mendelian traits is effective, but it can be
challenging for complex traits such as drought stresses that are generally polygenic.
Even major QTLs linked to drought tolerance traits can explain only a small fraction
of phenotypic variation and may show unexpected trait expression in new genetic
backgrounds because of epistatic interactions or GE interaction. These limitations
can be effectively overcome by the use of strategy called “Genomic-selection” (GS).
GS is a relatively simple and more powerful approach since it uses all marker
information simultaneously to develop a prediction model avoiding biased marker
effects (Heffner et al. 2009). In soybean, some efforts have been made to evaluate
106
G. K. Satpute et al.
Genomics Assisted Breeding
Marker-assisted selection (MAS) is the indirect selection method where the linked
molecular marker is used to transfer important agronomical traits from one genotype
to another genotype. Marker-assisted backcrossing is an important approach in
soybean for transferring trait of interest (Lee et al. 2006). The high-throughput
genotyping technologies eased the process of marker identification and QTL
mapping for different traits in soybean. The molecular breeding approaches such
as marker-assisted backcrossing (MABC) and marker-assisted recurrent selection
(MARS) aided in the introgression of the trait of interest in soybean. The soybean
cyst nematode-resistant line, LDX01-1-65(PI636464) was developed using MABC
(Chaudhary et al. 2019). Gene pyramiding involves combining favorable alleles
controlling the same attribute from more than two parental lines (Melchinger 1990).
Marker-assisted gene pyramiding was successfully carried out to develop durable
resistance to several pathogens causing diseases in soybean (Walker et al. 2010).
Although drought tolerance is accompanied by many traits which governed by
mainly polygenes/QTLs, introgression of minor QTLs from donor to recipient
cultivar is not an easy task. In QTL mapping in five biparental populations, a total
of ten genomic regions or QTLs (Table 4.3) were mapped to be associated with
canopy wilting under drought, with varied phenotypic contributions, and the majority of these QTLs (9/10) have donor alleles for slow wilting phenotypes from PI
416937, Jackson, or both (Charlson et al. 2009; Abdel-Haleem et al. 2012; Hwang
et al. 2015). Molecular markers associated with these QTLs (identified in Meta-QTL
studies) can be used to perform MAS to introgress the slow canopy wilting
phenotypes from the donor in elite backgrounds. However, transferring these
QTLs is a challenging job for breeders due to complex, quantitative nature and
sensitivity to environmental factors of canopy-wilting trait under drought. Most of
the mapped minor QTLs were found to be unstable across independent environments
and populations. For instance, even major QTLs on chromosome 12 (R2 ¼ 0.27)
were identified in all five environments from Benning  PI 416937 (Abdel-Haleem
et al. 2012) but were not detected in any populations or site-years, including the
Benning  PI 416937 cross reported by Hwang et al. (2015). For this reason, QTL
confirmation in more advanced generations should be performed to validate each
individual QTL. This also indicates that stacking all confirmed QTLs in the same
elite background by MAS is necessary to build the drought tolerance shown in the
donor (Valliyodan et al. 2016).
Marker-assisted breeding for simple Mendelian traits is effective, but it can be
challenging for complex traits such as drought stresses that are generally polygenic.
Even major QTLs linked to drought tolerance traits can explain only a small fraction
of phenotypic variation and may show unexpected trait expression in new genetic
backgrounds because of epistatic interactions or GE interaction. These limitations
can be effectively overcome by the use of strategy called “Genomic-selection” (GS).
GS is a relatively simple and more powerful approach since it uses all marker
information simultaneously to develop a prediction model avoiding biased marker
effects (Heffner et al. 2009). In soybean, some efforts have been made to evaluate
106
G. K. Satpute et al.