Multi-Omics Analysis of High-, Medium-, and Low-Ascorbic-Acid Jujube Cultivars Identifies Potential Key Regulatory Genes in Ascorbic Acid Metabolism

Ascorbic acid (vitamin C) is a critical antioxidant influencing the nutritional quality of fruits. This study integrates metabolomic and transcriptomic analyses to investigate high-ascorbic-acid (HAA), medium-ascorbic-acid (MAA), and low-ascorbic-acid (LAA) jujube cultivars. Metabolomic profiling revealed significant enrichment of ascorbic acid and its precursors in HAA cultivars, whereas MAA and LAA cultivars showed lower levels. Transcriptomic analysis identified 107 differentially expressed genes (DEGs) across the three groups. Compared with LAA, 139 differentially accumulated metabolites (DAMs) were identified in HAA, with more down-accumulated (77) than up-accumulated (62); compared with MAA, 235 DAMs were found in HAA, with significantly more up-accumulated (180) than down-accumulated (55); 250 DAMs with different accumulation patterns between LAA and MAA included 199 up-accumulated and 51 down-accumulated; and 16 DAMs were common in all three comparison combinations. Potential key regulatory genes such as GDP-mannose-3′,5′-epimerase (GME) and L-galactose-1-phosphate phosphatase (GPP) were highlighted. Weighted Gene Co-expression Network Analysis (WGCNA) detected possible core genes participating in ascorbic acid biosynthesis pathways. This study provides novel insights into the genetic and metabolic basis of ascorbic acid accumulation, potentially providing valuable targets for molecular breeding.