Genome-Wide Association Mapping for Seed Composition Provides Insights into Soybean Nutrient Improvement and the Impacts of Domestication and Breeding.

Soybean (Glycine max) has the world largest oilseed production and the largest protein meal consumption as well. However, the complex genetic architecture of quality traits has hindered efforts to modify seed nutrients in soybean. To better understand the genetic architecture of the traits, genome-wide association studies (GWAS) using 313 diverse soybean germplasm accessions genotyped with the SoySNP50K array was conducted for the concentration of seed protein, oil, fatty acids and amino acids. Both single-locus mixed linear model (MLM) and multi-locus MLM were applied for association analyses. A total of 87 chromosomal regions were identified to be associated with seed composition, explaining 8-89% of genetic variances. The candidate genes GmSAT1, AK-HSDH, SACPD-C and FAD3A of known function, and putative MtN21 nodulin, FATB and steroid-5-α-reductase involved in N₂ fixation, amino acid biosynthesis and fatty acid metabolism were found at the major-effect loci. Further analysis indicated that these loci had been subjected to soybean domestication or modern breeding selection. This study also revealed that amino acid concentrations related to seed weight and to total protein have different genetic bases, suggesting a possibility of manipulating amino acid profile without affecting protein. The candidate genes and markers identified in this study are valuable for soybean nutrient improvement both in quantitatively and qualitatively. This study helps uncover the in-depth genetic mechanism of the intricate relationships among the seed compounds and provides insights into the alteration of soybean quality during domestication and breeding.