Common metabolite and antioxidant activity analyses of soybeans reveal biochemical variation and associated genomic regions across seed and cotyledon colors

Abstract

Understanding variation in biochemical traits and their genetic basis across seed-related traits in soybeans is critical for functional food development and breeding programs. This study analyzed targeted metabolites, total metabolite contents, antioxidant activity, and associated genes in soybeans with different seed and cotyledon colors. The coefficient of variation ranged from 2.02% for total unsaturated fatty acids to 146.69% for cyanidin-3-O-glycoside, indicating substantial biochemical diversity. Black soybeans exhibited significantly higher phenolic and anthocyanin contents, stronger antioxidant capacity, and more favorable fatty acid profiles than brown, green, and yellow soybeans (p < 0.05), demonstrating superior functional potential. In contrast, cotyledon color had limited effects on most biochemical traits. Major metabolites, including 6 ''-O-malonylgenistin, cyanidin-3-O-glucoside, and linoleic acid, predominated within their respective classes regardless of color. Multivariate analyses revealed distinct metabolite association patterns among seed colors. Genome-wide association analysis identified significant genomic regions associated with phenolic content, isoflavones, fatty acids, and antioxidant activities. Within LD-defined intervals, several putative candidate genes, including Glyma.15G122200, Glyma.11G107600, Glyma.13G154400, Glyma.13G194500, Glyma.19G119100, and Glyma.09G207700, were prioritized based on marker proximity, functional annotation, biological relevance, and GO enrichment analysis. These genes provide testable hypotheses for further fine-mapping, expression analysis, and functional validation. They also support the use of seed coat color as a practical indicator of functional metabolite richness and highlight genomic regions and putative candidate genes for further validation and potential future use in soybean quality breeding with enhanced nutritional quality and health-promoting properties.