Genome-Wide Association Identifies Candidate Genes for Salt Tolerance in Soybean at Emergence and Seedling Stages

Salt stress is an abiotic constraint on crop production, impairing growth while reducing yield and quality. As a source of edible oil and protein, soybean is particularly vulnerable to salt stress during emergence and seedling establishment, so the genetic basis of salt tolerance bears directly on productive cultivation. Here, a natural population of 256 soybean accessions was phenotyped for salt tolerance at emergence and seedling stages and genotyped using the Zhongdouxin No.1 (ZDX1) single nucleotide polymorphism (SNP) array. Genome-wide association analysis identified 60 salt tolerance-associated SNPs consolidated into 19 quantitative trait loci (QTL), 16 associated with emergence-stage and 3 with seedling-stage salt tolerance. Five QTLs mapped to chromosomal regions harboring previously reported stress-tolerance genes, including GmSALT3, approximately 192 kb from qSTG-SSB-03. Four putative candidate genes were prioritized: Glyma.10G040000, encoding a glutathione S-transferase (GST), was identified at the emergence stage, while Glyma.10G148700, Glyma.10G149200, and Glyma.10G149600, encoding a calmodulin-binding protein (CaM), drought-induced protein 19 (Di19), and a protein phosphatase 2C (PP2C), respectively, were identified at the seedling stage, all with reported roles in salt-stress responses.