Comparative Omics Analysis of Four Grape Varieties and Exploration of Their Anthocyanin Synthesis Mechanisms

Background: Vitis vinifera L. exhibits diverse varietal traits influencing fruit quality and stress tolerance. The summer black grape (Xiahei), known for its superior tolerance to abiotic stress and intense pigmentation, was hypothesized to possess distinct metabolic and genetic profiles, particularly in flavonoid and anthocyanin biosynthesis. This study aimed to elucidate the metabolic and molecular basis underlying these phenotypic traits by comparing carbohydrate composition and metabolomic and transcriptomic profiles of four grape varieties (summer black, flame seedless, black grape, and red milk). Methods: Grapes were consistently sampled five days after full maturity, and metabolites were analyzed using UPLC-MS/MS and GC-MS, while transcriptome analysis employed RNA sequencing followed by qRT-PCR validation. Results: The results demonstrated that carbohydrate content was similar among all grape varieties, whereas the summer black grape showed significantly higher levels of flavonoids, particularly anthocyanins such as delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, and pelargonidin-3-O-glucoside. Metabolomic analyses revealed substantial enrichment of metabolites involved in flavonoid biosynthesis pathways, in agreement with transcriptomic data showing significant upregulation of key regulatory genes (CHS, DFR, and ANS) specific to anthocyanin biosynthesis. These findings suggest that the pronounced anthocyanin accumulation in summer black grape contributes to its distinctive dark pigmentation and enhanced resistance to abiotic stresses compared to other varieties. Conclusion: This study provides novel insights into the molecular and metabolic mechanisms driving anthocyanin accumulation in summer black grapes, which could inform future breeding programs aimed at improving grape resilience.