Metabolome and transcriptome landscapes reveal potential genes and metabolites involved in formation of leaf color in red-leafed apple mutants

Abstract Leaf color mutations in plants serve as valuable resources for investigating metabolic pathways related to biosynthesis of chlorophyll, flavonoid, and carotenoid. In this study, a comprehensive analysis of the physiological characteristics, transcriptomes, and metabolomic profiles of a mutant of Malus hupehensis var. pingyiensis with red leaves (RM) and normal plant (CK) with green leaves was performed. A total of 283 differentially abundant metabolites (DAMs) and 9,822 differentially expressed genes (DEGs) were identified between RM and CK. Compared with the CK, RM presented a reduced chlorophyll content and elevated levels of carotenoids, flavonoids, and anthocyanins. KEGG pathway enrichment analysis revealed that the DAMs and DEGs were associated mainly with the metabolism of chlorophyll, carotenoids, and flavonoids, with the anthocyanidin biosynthesis pathway showing the greatest enrichment. Several key anthocyanin biosynthetic genes, including chalcone isomerase ( CHI ), dihydroflavonol 4-reductase ( DFR ), UDP-Glucose:Flavonoid 3-O-Glucosyltransferase ( UFGT ), and UDP-glycosyltransferases ( UGT ), were upregulated in the red leaves, in line with a significant increase in cyanidin 3-O-glucoside (C3G) and pelargonidin 3-O-glucoside (pg3G). Furthermore, RNA sequencing (RNA-seq) analysis revealed upregulation of MdMYB10 and MdUFGT . Yeast one-hybrid (Y1H), chromatin immunoprecipitation (ChIP), and dual-luciferase reporter (LUC) assays demonstrated that MdMYB10 bound to the MdUFGT promoter fragment and subsequently upregulated its expression, leading to the accumulation of C3G and pg3G in RM. Our findings provide new insights into the regulatory mechanisms of leaf coloration and offer a foundation for the development of new cultivars with alteration of leaf color.