Linkage and association mapping of wild soybean (Glycine soja) seeds germinating under salt stress

Salinity threatens soybean germination, growth and production. The germination stage is a key period in the life of soybean. Wild soybean contains many genes related to stress resistance that are valuable resources for the genetic improvement of soybean. To identify the genetic loci of wild soybean that are active during seed germination under salt stress, two populations, a soybean interspecific hybrid population comprising 142 lines and a natural population comprising 121 wild soybean accessions, were screened for three germination-related traits in this study. By using single-nucleotide polymorphism (SNP) markers with three salt tolerance indices, 25 quantitative trait loci (QTLs), 21 significant SNPs [−Log10(P)≥4.0] and 24 potential SNPs [3.5<−Log10(P)<4.0] were detected by linkage mapping and a genome-wide association study (GWAS) in two environments. The key genetic region was identified based on these SNPs and QTLs. According to the gene functional annotations of the W05 genome and salt-induced gene expression qRT-PCR analysis, GsAKR1 was selected as a candidate gene that responded to salt stress at the germination stage in the wild soybean. These results could contribute to determining the genetic networks of salt tolerance in wild soybean and will be helpful for molecular marker-assisted selection in the breeding of salt-tolerant soybean.