Mechanism Underlying the Color Differences in Apples Based on Metabolomic and Transcriptomic Analyses

Apple peel color is a key determinant of fruit quality and consumer preference. To elucidate the molecular basis underlying the peel color difference between 'Jinhong' (JH) apples and 'Hongjinhong' apples (HJH, a deep red bud sport of JH apples), we integrated physiological assays, widely targeted metabolomics, transcriptomics, and quantitative real-time PCR (qRT-PCR) to analyze peel pigment contents, metabolite profiles, and gene expression dynamics during fruit development. The deep red phenotype of HJH peel was primarily attributed to enhanced anthocyanin accumulation rather than alterations in chlorophyll content. Metabolomics identified 418 differentially accumulated metabolites. Among these, three cyanidin-type anthocyanins--cyanidin-3-O-(6″-O-malonyl) glucoside, cyanidin-3-O-(2″-O-xylosyl) galactoside, and cyanidin-3-O-glucoside--were significantly upregulated in HJH peel, serving as the key pigments responsible for its deep red coloration. Transcriptomics revealed 533 differentially expressed genes. Combined with qRT-PCR validation, the anthocyanin biosynthetic gene MdDFR (dihydroflavonol reductase) exhibited consistently high expression during critical developmental stages of HJH fruit, closely mirroring the anthocyanin accumulation pattern. Collectively, the upregulation of MdDFR drives the specific accumulation of cyanidin-type anthocyanins, representing the core molecular event underlying the deep red peel color of HJH apples. This study provides novel insights into the regulatory network of apple coloration and offers candidate genes for the genetic improvement of fruit quality.