QTL Mapping and Multiomics Identify Candidate Genes for Hundred-Seed Weight in Soybean (Glycine max L.)

Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Seed yield and quality are quantitative traits that are controlled by multiple genes. Although several genes associated with hundred-seed weight have been reported, the underlying molecular mechanisms remain poorly understood. In this study, quantitative trait locus (QTL) mapping was employed using six generations derived from a cross between Changjiang Chun 2 (high hundred-seed weight) and Jiyu166 (low hundred-seed weight). A total of 64 QTLs, including 24 QTLs for hundred-seed weight (HSW), 17 QTLs for seed length (SL), and 23 QTLs for seed width (SW), were identified. Among these, six QTLs shared common intervals in both linkage mapping and bulked segregant analysis (BSA)-seq. Ninety genes contained variations in the region of the coding sequence within these genomic regions. Furthermore, transcriptome analysis revealed 24 differentially expressed genes (DEGs) within the QTL regions. In conjunction with QTL mapping, BSA-seq, and RNA-seq, a total of 6 genes were identified as candidate genes controlling hundred-seed weight- in soybean. These results provide valuable genetic resources for both candidate gene exploration and marker-assisted breeding aimed at enhancing the soybean yield potential.