Genome-Wide Identification of Candidate Loci Associated with the Regulation of the Protein, Oil, and Carbohydrate Content in Soybean

Soybean (Glycine max (L.) Merr.) is a globally important legume valued for the high protein, oil, and carbohydrate content of its seeds. However, it is difficult to simultaneously optimize the content of these three macronutrients due to their negatively correlated metabolic pathways and complex quantitative inheritance patterns. In this study, a genome-wide association study (GWAS) was conducted to elucidate the genetic architecture underlying the seed protein, oil, and carbohydrate content in 328 soybean accessions evaluated over two years using near-infrared spectroscopy. Significant negative correlations (r = −0.323 to −0.656, p < 0.001) were observed between the three traits, confirming the trade-off in carbon partitioning during seed development. The GWAS identified nine significant loci distributed across chromosomes 4, 6, 8, 9, 10, 16, and 18 as stable quantitative trait loci (QTLs) regulating the three traits. Of these, three pleiotropic loci (qProOil.4, qProOil.16, and qOilCarb.6) were found to be associated with multiple seed compositional traits. Haplotype analysis revealed seven haplotype blocks with distinct phenotypic variation, indicating that they have the potential for use as trait-specific markers in marker-assisted selection. Functional annotation of the stable QTL regions identified 22 putative genes, among which five candidate genes, Glyma.06g201700, Glyma.08g281900, Glyma.09g164900, Glyma.13g155600, and Glyma.16g209800 were likely to be involved in carbon allocation, protein biosynthesis, lipid metabolism, and carbohydrate modification pathways based on their relative expression levels. Overall, this study enhances the understanding of the genetic and molecular mechanism controlling the composition of soybean seed and identifies promising genomic targets for precision breeding programs aimed at improving nutritional quality.