A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis

Abstract

Mapping quantitative trait loci through the use of linkage disequilibrium (LD) in populations of unrelated individuals provides a valuable approach for dissecting the genetic basis of complex traits in soybean (Glycine max). The haplotype-based genome-wide association study (GWAS) has now been proposed as a complementary approach to intensify benefits from LD, which enable to assess the genetic determinants of agronomic traits. In this study a GWAS was undertaken to identify genomic regions that control 100-seed weight (SW), plant height (PH) and seed yield (SY) in a soybean association mapping panel using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean cultivars (N = 169) were field-evaluated across four locations of southern Brazil. The genome-wide haplotype association analysis (941 haplotypes) identified eleven, seventeen and fifty-nine SNP-based haplotypes significantly associated with SY, SW and PH, respectively. Although most marker-trait associations were environment and trait specific, stable haplotype associations were identified for SY and SW across environments (i.e., haplotypes Gm12_Hap12). The haplotype block 42 on Chr19 (Gm19_Hap42) was confirmed to be associated with PH in two environments. These findings enable us to refine the breeding strategy for tropical soybean, which confirm that haplotype-based GWAS can provide new insights on the genetic determinants that are not captured by the single-marker approach.

Adapting legume crops to climate change using genomic approaches

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SSR-based genetic analysis of sweet corn inbred lines using artificial neural networks

“…Consequently, several breeding programs have been undertaken to achieve genetic gains in several traits of interest (e.g., Kulka et al 2018). Studies of diversity and genetic structure allow plant breeders to investigate the population variability and thus provide basic information at the molecular level (Ballesta et al 2015, Contreras-Soto et al 2017); a key aspect in maize breeding programs (Saavedra et al 2013, Amaral et al 2016.…”

Genetic components of root architecture and anatomy adjustments to water‐deficit stress in spring barley

“…Genome‐wide association study (GWAS) based on linkage disequilibrium (LD) has been applied in crops to dissect the genetic and molecular basis of several highly complex quantitative traits (Jighly et al, ; Contreras‐Soto et al, ; Fang et al, ; Oyiga et al, , ; Ogbonnaya et al, ; Thoen et al, ). Decades of research have led to the uncovering of genes involved in root growth and development, such as Deeper Rooting 1 (Uga et al, ; Arai‐Sanoh et al, ), Retarded Root Growth (Zhou et al, ), Roothairless5 (Nestler et al, ), Root Systems Architecture 1 (Rosas et al, ), and Crown Rootless1 (Coudert et al, ).…”