Variety-Specific Metabolomic Configurations Underlie Differences in Seed Color, Nutritional Quality, and Antioxidant Activity of Faba Bean (Vicia faba L.).

Faba bean (Vicia faba L.) is a legume crop with diverse nutritional and bioactive properties, yet the metabolic basis underlying inter-varietal quality differences remains poorly understood. This study investigated four faba bean varieties (JD, GB, DB, and XJ) to test the hypothesis that variety-specific metabolomic configurations systematically govern phenotypic variations in seed color, nutritional composition, and antioxidant activity. Seed color parameters, proximate components (protein, soluble sugar, starch, and total dietary fiber), and antioxidant activities (DPPH and FRAP) were evaluated. Untargeted UPLC-MS/MS-based metabolomics was employed to characterize global metabolic profiles, screen differential metabolites, and perform KEGG pathway enrichment analysis, followed by TCMSP-based identification of bioactive compounds. JD exhibited the darkest seed color and the strongest antioxidant activity, whereas XJ showed the highest crude protein and total dietary fiber contents. Metabolomic profiling revealed that phenolic acids and flavonoids were predominantly up-regulated in JD, with coordinated down-regulation of multiple lipid species. KEGG enrichment indicated that JD's antioxidant superiority was associated with activation of the flavonoid biosynthesis pathway and suppression of carotenoid biosynthesis. Ten JD-specific bioactive compounds were identified through TCMSP screening, among which gallic acid and licochalcone B exhibited strong DPPH radical scavenging and lipid peroxidation inhibitory activities, providing a material basis for the superior antioxidant capacity of JD. These findings demonstrate that variety-specific metabolomic configurations serve as the intrinsic basis for quality differentiation in faba bean and provide metabolite-level markers for breeding programs targeting enhanced antioxidant capacity and functional quality.