depends on meiotic events (crossing-over) (Kover et al. 2009). In contrast, the
genome-wide association study (GWAS) approach provides opportunities to explore
the tremendous allelic diversity existing in natural soybean accessions. Mapping
resolution of GWAS is also higher since millions of crossing events have been
accumulated in the germplasm during evolution. The recent advances in highthroughput genotyping have played important role in the genome-wide association
studies in soybean. The large data sets generated from NGS and high-density
genotyping require sound computational algorithms for detection of minor QTLs
as well as rare alleles with major effect phenotype. GWAS is routinely being used in
many plant species, but only a few studies have been reported in soybean in regard to
drought tolerance. GWAS for quantitative traits like drought tolerance is predictable
to be affected by a confounding population. Different models have been developed
for population stratification and spurious allelic associations like MLM and CMLM
which takes into account the population structure and kinship (Deshmukh et al.
2014). Development in statistical tools, genotyping approaches, and studies involving larger set will definitely improve GWAS power. Recently, a large number of
QTLs associated with shoot ureide were mapped in both biparental populations and
genome-wide association studies (GWAS) in diverse lines (Hwang et al. 2013; Ray
et al. 2015), which indicated the complexity of N-fixation under drought and
suggested that genomic selection should be better suited to improve such complex
trait. Dhanapal et al. (2015) analyzed a population of 373 genotypes with 12,347
single nucleotide polymorphisms (SNPs) in four environments for carbon isotope
ratio (δ13C), an important physiological trait acting as surrogate for water use
efficiency (WUE) and found association of 39 SNPs, which are likely tagged to
21 different loci with this drought-tolerant trait (Table 4.4).
Likewise Kaler et al. (2017) also reported 54 environment-specific SNPs
associated with δ
13 C and 47 SNPs associated with δ
18
O, which are tagged with
46 putative loci and 21 putative loci for δ
13 C and δ
18 O, respectively. There are many
loci reported for several drought related traits, viz. chlorophyll fluorescence (Hao
et al. 2012; Herritt et al. 2018), canopy temperature (Kaler et al. 2018), delayed
canopy wilting (Steketee et al. 2020; Ye et al. 2020), and drought susceptibility
index (Chen et al. 2020) (Table 4.4). Latest updates on GWAS in soybean for
drought tolerance were reported in germplasm association panel containing 259 soybean released Chinese cultivars for drought related traits based on germinating
soybean seeds. The enquiry was based on a total of 4616 SNPs, and 15 SNP trait
associations were identified by GWAS, among which three SNPs were suggestively
linked with two of the drought-tolerance indices (Liu et al. 2020a).
4.6
Transcriptomic Approaches
Transcriptome analysis provides gene function information under various
conditions, which differs in dissimilar environments, cell types, developmental
stages, and cell states. There has been a tremendous progress in the application of
transcriptome analysis for the abiotic stress tolerance. During abiotic stresses, a wide
100
G. K. Satpute et al.
genome-wide association study (GWAS) approach provides opportunities to explore
the tremendous allelic diversity existing in natural soybean accessions. Mapping
resolution of GWAS is also higher since millions of crossing events have been
accumulated in the germplasm during evolution. The recent advances in highthroughput genotyping have played important role in the genome-wide association
studies in soybean. The large data sets generated from NGS and high-density
genotyping require sound computational algorithms for detection of minor QTLs
as well as rare alleles with major effect phenotype. GWAS is routinely being used in
many plant species, but only a few studies have been reported in soybean in regard to
drought tolerance. GWAS for quantitative traits like drought tolerance is predictable
to be affected by a confounding population. Different models have been developed
for population stratification and spurious allelic associations like MLM and CMLM
which takes into account the population structure and kinship (Deshmukh et al.
2014). Development in statistical tools, genotyping approaches, and studies involving larger set will definitely improve GWAS power. Recently, a large number of
QTLs associated with shoot ureide were mapped in both biparental populations and
genome-wide association studies (GWAS) in diverse lines (Hwang et al. 2013; Ray
et al. 2015), which indicated the complexity of N-fixation under drought and
suggested that genomic selection should be better suited to improve such complex
trait. Dhanapal et al. (2015) analyzed a population of 373 genotypes with 12,347
single nucleotide polymorphisms (SNPs) in four environments for carbon isotope
ratio (δ13C), an important physiological trait acting as surrogate for water use
efficiency (WUE) and found association of 39 SNPs, which are likely tagged to
21 different loci with this drought-tolerant trait (Table 4.4).
Likewise Kaler et al. (2017) also reported 54 environment-specific SNPs
associated with δ
13 C and 47 SNPs associated with δ
18
O, which are tagged with
46 putative loci and 21 putative loci for δ
13 C and δ
18 O, respectively. There are many
loci reported for several drought related traits, viz. chlorophyll fluorescence (Hao
et al. 2012; Herritt et al. 2018), canopy temperature (Kaler et al. 2018), delayed
canopy wilting (Steketee et al. 2020; Ye et al. 2020), and drought susceptibility
index (Chen et al. 2020) (Table 4.4). Latest updates on GWAS in soybean for
drought tolerance were reported in germplasm association panel containing 259 soybean released Chinese cultivars for drought related traits based on germinating
soybean seeds. The enquiry was based on a total of 4616 SNPs, and 15 SNP trait
associations were identified by GWAS, among which three SNPs were suggestively
linked with two of the drought-tolerance indices (Liu et al. 2020a).
4.6
Transcriptomic Approaches
Transcriptome analysis provides gene function information under various
conditions, which differs in dissimilar environments, cell types, developmental
stages, and cell states. There has been a tremendous progress in the application of
transcriptome analysis for the abiotic stress tolerance. During abiotic stresses, a wide
100
G. K. Satpute et al.