Genome-Wide Association Study and Candidate Gene Mining for Plant Height and Main Stem Node Number in Soybean from Northwest China

The Northwest soybean production region (covering Shanxi, Shaanxi, Gansu, Ningxia, Xinjiang, central and western Inner Mongolia and northern parts of Hebei) possesses vast cultivated land resources and advantageous light–temperature conditions, endowing soybean with substantial yield potential. In this study, two natural soybean populations originating from this region were used to systematically investigate the phenotypic variation in two important agronomic traits, plant height (PH) and main stem node number (NN). The results showed abundant genetic variation for both traits. Through genome-wide association analysis (GWAS) and employing a joint detection across multi-environments (control false positives), 5 SNPs significantly associated with PH and 18 SNPs significantly associated with NN were identified, among which four SNPs were detected associated with both traits. Candidate genes were further screened within the ±100 kb intervals flanking lead SNPs at association peaks. By integrating gene expression levels of different soybean tissues and their correlations with the phenotypes, two candidate genes associated with both PH and NN were determined. These findings provide a theoretical basis for the identification and utilization of soybean germplasm resources in Northwest China, and lay a solid foundation for breeding high-yield and high-quality soybean varieties through molecular breeding.