Integrative GWAS and Transcriptome Analysis Reveal Genetic Architecture and Candidate Genes for Drought Tolerance During Soybean Germination

Drought stress severely limits soybean production, and understanding the genetic basis of drought tolerance at the germination stage is important for breeding tolerant varieties. In this study, a panel of 270 soybean accessions was used for phenotypic evaluation and a genome-wide association study (GWAS) of five drought tolerance indices under control and PEG-simulated drought conditions. Using single-locus and multi-locus GWAS models, we detected 109, 115, 121, 86, and 46 significant SNPs, and 14, 7, 9, 10, and 3 QTNs for the five indices, respectively. Combining the results from both models, 97 important QTNs consisting of those controlling multiple traits under the single-locus model and those detected by both models were identified. These QTNs were distributed across 14 genomic intervals, with qDT-4-2 and qDT-9-1 which were associated with all five indices, being the key loci. Transcriptome analysis revealed 2109 genes that were commonly differentially expressed in three tolerant accessions under PEG treatment compared with control conditions. GO and KEGG enrichment analyses showed significant enrichment of pathways related to cell wall metabolism, osmotic adjustment, and antioxidant defense, including amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, galactose metabolism, and ascorbate and aldarate metabolism. Integration of GWAS and transcriptome data predicted 12 candidate genes within these loci, which may function in drought stress responses through regulating cell wall-modifying enzyme activity, accumulating osmoprotectants, and scavenging reactive oxygen species. Our findings provide useful information for understanding the genetic regulatory network of drought tolerance during soybean germination and offer candidate gene resources for marker-assisted breeding and functional gene discovery.