Quantitative lipidomics reveals differences in oil metabolism and nutritional profiles of soybeans with various seed coat colors

Soybean seeds are rich in high-quality lipids. However, the oil content, differential metabolic pathways, and nutritional characteristics of soybeans with different seed coat colors remain unclear. In this study, the oil content of 169 soybean accessions, including yellow, green, brown, and black soybeans, was determined using the Soxhlet extraction. The results revealed a negative association between oil content and seed coat pigmentation, with yellow seeds exhibiting the highest oil content and black seeds the lowest. Metabolomic analysis of two representative accessions from each seed coat color group showed that lipid subclasses were consistently involved in the significantly altered metabolic pathways across soybean color groups. Subsequent quantitative lipidomic profiling of the 8 accessions identified 650 lipid species belonging to 5 major classes and 26 subclasses. HPLC quantification further showed that total lipid content decreased progressively with increasing seed coat pigmentation, mainly due to changes in triglycerides (TGs), phosphatidylethanolamines (PEs), phosphatidylcholines (PCs), and phosphatidylinositols (PIs). In addition, 38 differentially accumulated lipids were identified between common yellow and black soybeans, and these lipids were significantly enriched in the sphingolipid metabolism pathway. Overall, this study elucidates the relationship between soybean seed coat color and oil composition, providing a potential scientific basis for the functional utilization and dietary application of different color soybeans.