Transcriptomic and Metabolomic Profiling Reveals the Mechanisms of Color Development in Rosa roxburghii Fruits

Rosa roxburghii fruits are highly favored by Chinese consumers due to their substantial nutritional value, particularly the richness in vitamin C and flavonoids, contributing to the fruits' high economic significance. However, the specific composition and biosynthetic mechanisms of key pigments, including flavonoids, phenylpropanoids, and anthocyanins during the fruit's color development, remain unclear. In this study, we conducted an integrated phenotypic, metabolomic, and transcriptomic analysis across three ripening stages: green-yellow (GY), light-yellow (LY), and orange-yellow (OY). KEGG enrichment analysis of differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) underscored the phenylpropanoid, flavonoid, and anthocyanin biosynthesis pathways as central to the color transition. The results demonstrated that the phenylpropanoid pathway supplied essential precursors, while the transcriptional regulation of core structural genes within the flavonoid pathway directly influenced the color phenotype. Specifically, the transition from GY to LY was driven by the activation of the phenylpropanoid pathway and the coordinated action of chalcone synthase and flavonol synthase (CHS-FLS), leading to increased flavonol accumulation. Subsequently, the shift from LY to OY was characterized by the upregulation of dihydroflavonol 4-reductase (DFR), which redirected metabolic flux toward anthocyanin biosynthesis, supported by a complementary antioxidant system. This study elucidates the stage-specific transcriptional and metabolic programs governing color evolution in R. roxburghii and provides a molecular framework for future fruit quality improvement.