Study on the Accumulation of Flavonoids and Antioxidant Activity in ‘Fengtang’ Plum at Different Developmental Stages: Metabolomics and Transcriptomics Analysis

Harvest maturity critically determines the balance between eating quality (evaluated by soluble solids, sugars, acidity, and firmness) and nutritional bioactive compounds in fleshy fruits, yet the optimal window for ‘Fengtang’ plum—a high-sugar cultivar from Guizhou—remains unclear. This study systematically investigated the dynamic changes in fruit quality traits, flavonoid accumulation, antioxidant activity, and their underlying regulatory mechanisms across three on-tree maturity stages (PG, PB, and PY) using integrated metabolomic and transcriptomic approaches. As ripening progressed, soluble solids, soluble sugars, and reducing sugars increased significantly while firmness and titratable acidity declined, optimizing fresh-eating quality at the PY stage, whereas total flavonoid content and DPPH/ABTS antioxidant activities continuously decreased, peaking at the PG stage. Metabolomic analysis identified 35 differentially accumulated flavonoid-related metabolites, comprising 32 reliably annotated flavonoids and 3 tentatively annotated xanthones (MSI Level 3); the reliably annotated flavonoids, particularly flavan-3-ols and flavonols, exhibited persistent downregulation, whereas only a few, including dihydromyricetin-3-O-glucoside and apigenin-5-O-glucoside, showed PY-specific upregulation. Transcriptomic profiling revealed systemic reprogramming of the R2R3-MYB transcription factor family: the progressive downregulation of positive regulators, coupled with the PY-stage upregulation of repressive MYBs, was associated with the overall decline in flavonoid biosynthesis, while certain branch-specific MYBs positively correlated with the few upregulated flavonoid components, suggesting a possible association with localized activation of specific metabolic branches against a background of global downregulation. Collectively, these findings delineate a trade-off pattern between edible quality improvement and bioactive compound decline during ‘Fengtang’ plum ripening and establish a MYB-mediated regulatory network model, providing a theoretical basis for tailoring harvest timing according to industrial end-use and offering candidate gene resources for molecular breeding aimed at nutritional quality enhancement.