Metabolomic and Transcriptomic Analyses of Nutritional Quality Differences and Underlying Molecular Mechanisms in Soybeans with Different Coat Colors

Soybean is a globally valuable crop, and the development of high-quality cultivars is essential. This study assessed quality differences and their underlying mechanisms in four types of soybeans with different coat colors: black (BL), brown (BR), green (GR), and yellow (YE). Nutritional analyses revealed that BR exhibited elevated total oil and linoleic acid, whereas GR demonstrated elevated total protein and BL showed elevated polyphenol and flavonoids. Metabolomic and transcriptomic analyses indicated that differential metabolites (DMs) and genes (DEGs) were mainly enriched in flavonoid and isoflavone biosynthesis. Combined analysis of DMs and DEGs revealed that all six comparison groups except BR vs GR were enriched in the isoflavone biosynthesis pathway. Moreover, formononetin 7-O-glucoside-6-O-malonate, biochanin A 7-6-malonylglucoside, and medicarpin were identified as candidate DMs, and CYP93A, IF7GT, and IF7MAT were identified as candidate DEGs. These results provide a foundation for breeding high-quality soybean cultivars.