Integrative multi-omics reveals differential salt tolerance traits and candidate genes in domestic and foreign soybeans

In crops, exposure to salt stress triggers pronounced water shortage, disruption of nutrient balance, and metabolic dysfunction, which collectively curtail biomass accumulation and cause substantial yield losses. Thus, identifying the genetic basis and underlying mechanisms that confer salt tolerance is therefore critical for crop improvement. However, functional validation of loci associated with salinity resilience remains limited to a small subset of genes in soybean. In this study, we comparatively evaluated plant height, root length, and fresh weight under salt stress using soybean germplasms from China, the United States, and Uruguay, and analyzed the differential salt tolerance among varieties from these regions. Subsequent genome-wide association study (GWAS) of the relative values for these three growth parameters revealed two statistically significant single-nucleotide polymorphisms (SNPs). Scanning a 200-kb linkage disequilibrium region flanking these SNPs yielded 67 candidate genes. Through integration of GWAS and transcriptomic analyses, two salt-tolerance-associated genes, RRL7 and RPH2, were identified. The phenylpropanoid biosynthesis pathway, to which RRL7 belongs, was co-enriched in both transcriptomic and metabolomic datasets. Further transcriptomic and metabolomic analysis revealed that RRL7 is associated with increased accumulation of sinapaldehyde and 1-O-sinapoyl-β-D-glucose under salt stress. Taken together, this work advances current understanding of the genomic factors underlying soybean salt responses and identifies promising candidate genes for further functional characterization and breeding applications in soybean.