Genome wide association analysis for saline-alkaline stress tolerance during the soybean germination stage

Soybean (Glycine max) is a globally important staple oilseed crop, yet its yield is severely limited by saline-alkaline stress. Developing soybean cultivars with enhanced saline-alkaline tolerance is therefore crucial for sustainable agriculture. To identify candidate genes associated with saline-alkaline stress tolerance in soybean, this study evaluated the saline-alkaline tolerance of a core panel of 198 soybean accessions at the germination stage, focusing on four key germination-related traits: germination energy (GE), germination rate (GR), radicle length (RL), and hypocotyl length (HL). Phenotypic analysis revealed significant variation in stress tolerance among the 198 accessions, with a subset exhibiting robust saline-alkaline tolerance and others showing significant sensitivity. This finding confirms substantial genetic diversity in saline-alkaline stress adaptability within the panel. Subsequently, whole-genome resequencing was performed on the panel, generating 385, 087 high-quality single nucleotide polymorphisms (SNPs). A genome-wide association study (GWAS) was conducted by integrating these SNP data with phenotypic traits under saline-alkaline stress, resulting in the identification of 428 candidate genes potentially associated with saline-alkaline tolerance. Notably, two previously reported salinity tolerance-related genes, GmLecRlk (Glyma.07G005700) and GmERF34 (Glyma.07G074200), were successfully validated in this study. Additionally, the superior haplotypes of Glyma.07G004400 and Glyma.15G022000—which showed significant associations with improved saline-alkaline tolerance—were characterized. Collectively, through phenotypic evaluation of 198 soybean accessions under saline-alkaline stress and genome-wide genetic dissection, this study provides a theoretical foundation and technical support for elucidating the molecular regulatory network of saline-alkaline tolerance in soybean and accelerating the breeding of saline-alkaline tolerant soybean cultivars.