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

Abstract

Simple Summary Soil salinization is an expanding threat to soybean production worldwide. Resolving the genetic basis of salt tolerance at early growth stages supports the development of resilient cultivars. In this study, we evaluated 256 soybean accessions for salt tolerance at emergence and seedling stages and conducted genome-wide association analysis (GWAS) using a high-density single nucleotide polymorphism (SNP) array. We identified 19 genomic regions (quantitative trait loci, QTLs) associated with salt tolerance, including 16 at the emergence stage and 3 at the seedling stage, along with four putative candidate genes with predicted functions in stress responses. Salt tolerance at the two developmental stages was weakly correlated, indicating that tolerance is stage-specific and that at each stage requires separate selection. These findings provide genetic targets for breeding salt-tolerant soybean varieties.