(Akond et al. 2013), and the Axiom Soya SNP array for approximately 180,000
SNPs (Lee et al. 2015), which are being used for the genotyping of soybean lines
(Chaudhary et al. 2019). GBS is becoming one of the popular sequencing-based
genotyping approaches which has significantly reduced labor and time and improved
precision in the identification of key genes as compared to the conventional
PCR-based genotyping methods and being utilized in several crop species and
soybean (Poland and Rife 2012; Sonah et al. 2013). Additionally, GBS also allows
the detection of new variants in the population of interest, which can be utilized in
future breeding programs (Chaudhary et al. 2019).
4.4
Quantitative Trait Loci for Drought Tolerance Related
Traits
Different type of molecular markers has been used to map genomic location of major
genes and quantitative trait loci (QTLs) for many traits in soybean. More than
thousand QTLs representing more than 100 agronomically important traits have
been mapped in soybean (Grant et al. 2010). Current information on all mapped
QTLs in soybean is available on the USDA-ARS soybean genetic database SoyBase
(http://soybase.org). Although a number of QTLs were mapped in the soybean but
introgression and pyramiding of genes or QTLs affecting the same trait is a great
challenge to breeding programs. Due to increasing necessity to develop droughttolerant soybean with enhanced yield, breeding strategies with molecular tools have
progressed at a massive rate in the past decade. Since molecular markers identified
genetic variants for different drought related traits more precisely, markers are
important in developing genetic linkage maps, genetic resource evaluation, and
selection of desired alleles and mapping of genes/QTLs. Since microsatellites
(SSRs) are less abundant in the genome, SNP markers became more popular and
facilitated QTL analysis for nearly every agronomic trait in soybean (https://soybase.
org, http://soykb.org). Gene/QTLs mapping in soybean has become more standard
with the availability of whole-genome sequence (WGS) (Schmutz et al. 2010). This
ground-breaking change in genome sequencing made available of the development
of thousands of SSRs and millions of SNP markers. QTL analysis plays a significant
role in identifying genomic regions which control over phenotypic variation and it
requires a large segregating population (biparental mapping population) such as an
F 2 population or recombinant inbred lines (RILs). In general, QTL mapping uses a
large number of RILs, which are established for at least several generations of
Selfing (typically up to F 6 or F 7 ) (Takuno et al. 2012). However, RILs are helpful
for the QTL detection, but it estimates the influence of single QTL depending on
population size. Moreover, the results are highly population specific for multigenic
traits like drought tolerance traits (Deshmukh et al. 2014). On the other hand, plants
that are homozygous for the unfavorable allele are eliminated in an F 2 population
and frequencies of favorable alleles increase during inbred development (Bernardo
2010). There are a number of important QTL studies (Table 4.3) for traits related to
drought tolerance reported in the past three decades. Although QTL mapping has
4 Breeding and Molecular Approaches for Evolving Drought-Tolerant Soybeans
95
SNPs (Lee et al. 2015), which are being used for the genotyping of soybean lines
(Chaudhary et al. 2019). GBS is becoming one of the popular sequencing-based
genotyping approaches which has significantly reduced labor and time and improved
precision in the identification of key genes as compared to the conventional
PCR-based genotyping methods and being utilized in several crop species and
soybean (Poland and Rife 2012; Sonah et al. 2013). Additionally, GBS also allows
the detection of new variants in the population of interest, which can be utilized in
future breeding programs (Chaudhary et al. 2019).
4.4
Quantitative Trait Loci for Drought Tolerance Related
Traits
Different type of molecular markers has been used to map genomic location of major
genes and quantitative trait loci (QTLs) for many traits in soybean. More than
thousand QTLs representing more than 100 agronomically important traits have
been mapped in soybean (Grant et al. 2010). Current information on all mapped
QTLs in soybean is available on the USDA-ARS soybean genetic database SoyBase
(http://soybase.org). Although a number of QTLs were mapped in the soybean but
introgression and pyramiding of genes or QTLs affecting the same trait is a great
challenge to breeding programs. Due to increasing necessity to develop droughttolerant soybean with enhanced yield, breeding strategies with molecular tools have
progressed at a massive rate in the past decade. Since molecular markers identified
genetic variants for different drought related traits more precisely, markers are
important in developing genetic linkage maps, genetic resource evaluation, and
selection of desired alleles and mapping of genes/QTLs. Since microsatellites
(SSRs) are less abundant in the genome, SNP markers became more popular and
facilitated QTL analysis for nearly every agronomic trait in soybean (https://soybase.
org, http://soykb.org). Gene/QTLs mapping in soybean has become more standard
with the availability of whole-genome sequence (WGS) (Schmutz et al. 2010). This
ground-breaking change in genome sequencing made available of the development
of thousands of SSRs and millions of SNP markers. QTL analysis plays a significant
role in identifying genomic regions which control over phenotypic variation and it
requires a large segregating population (biparental mapping population) such as an
F 2 population or recombinant inbred lines (RILs). In general, QTL mapping uses a
large number of RILs, which are established for at least several generations of
Selfing (typically up to F 6 or F 7 ) (Takuno et al. 2012). However, RILs are helpful
for the QTL detection, but it estimates the influence of single QTL depending on
population size. Moreover, the results are highly population specific for multigenic
traits like drought tolerance traits (Deshmukh et al. 2014). On the other hand, plants
that are homozygous for the unfavorable allele are eliminated in an F 2 population
and frequencies of favorable alleles increase during inbred development (Bernardo
2010). There are a number of important QTL studies (Table 4.3) for traits related to
drought tolerance reported in the past three decades. Although QTL mapping has
4 Breeding and Molecular Approaches for Evolving Drought-Tolerant Soybeans
95