Background: Flavor quality in grape berries is shaped by complex metabolic and regulatory networks during development. Methods: In this study, we integrated transcriptomic and LC–MS-based metabolomic analyses to investigate three cultivars (‘Mei Xiangbao’, ‘Adena Rose’, and ‘Kyoho’) at two ripening stages. Results: A total of 491 differentially accumulated metabolites (DAMs) were identified, mainly lipids, organic acids, and heterocyclic compounds. Among them, 33 core metabolites, including LysoPCs, malic acid, and linalool derivatives, were closely linked to aroma, membrane remodeling, and polyphenol biosynthesis. Transcriptome integration revealed 29 transcription factors (TFs) such as AP2/ERF, MYB, and bHLH, which showed strong associations with key metabolites, suggesting their involvement in lipid remodeling and phenylpropanoid-related pathways. Conclusions: These results provide new insights into the molecular regulation of grape flavor metabolism and highlight candidate genes and metabolites for improving berry sensory quality.

The aroma metabolites in grape berries have received attention in recent years, but a global analysis of gene-regulated metabolites is still lacking. In this study, three grape cultivars, “Kyoho”, “Adenauer Rose”, and “Mei Xiangbao”, were used to determine the differential accumulation of metabolites and identify candidate genes related to grape berry aroma. A total of 27,228 genes were detected from the transcriptome, and 128 differentially accumulated metabolites (DAMs) were identified. Terpenoids and ester were the major substances in these three cultivars. KEGG enrichment showed that 12, 8, and 5 compounds were significantly enriched during the maturation process of these three grape cultivars, with most being terpenoids. A combined transcriptome and metabolome analysis found that the associated genes and metabolites were enriched in the following pathways: “Glycine, serine, and threonine metabolism”, “Cysteine and methionine metabolism”, “Tyrosine metabolism”, “Phenylalanine metabolism”, and “Phenylalanine, tyrosine, and tryptophan biosynthesis”. Seven structural genes (VvOMR1, VvGLYK, VvLPD2, VvAK2, VvSHM7, VvASP3, and VvASP1) and four transcription factors (VvERF053, VvERF4, VvMYB46, and VvMYB340) related to grape berry aroma accumulation were discovered. Our findings provide new insights into grape aroma formation and regulatory mechanism research, and the results will be beneficial for grape aroma breeding in the future.

Background: Fruit skin color is a key determinant of grape quality and market value, primarily governed by anthocyanin biosynthesis. Methods: In this study, we explored the molecular basis of skin color variation in the grape cultivar Zaoheibao and its bud mutant, which displays a striking shift from purple-black to yellow-green. Integrated metabolomic and transcriptomic analyses revealed extensive reprogramming of the flavonoid pathway in the mutant. Results: Metabolite profiling identified 233 differentially accumulated metabolites (DAMs), with a drastic reduction in anthocyanins, particularly cyanidin- and peonidin-derivatives, together with altered levels of flavonols and flavonoid glycosides. Transcriptome analysis detected 4036 differentially expressed genes (DEGs), with key anthocyanin biosynthetic genes (DFR, ANS, UFGT, GST) and MYB significantly downregulated. Multi-omics integration confirmed consistent enrichment of flavonoid-related pathways, while correlation network analysis highlighted strong associations between MYB regulators, structural genes, and anthocyanin-type metabolites. Conclusions: Collectively, these findings demonstrate that suppression of a MYB-centered regulatory module underlies the loss of pigmentation in the bud mutant, providing new insights into the molecular regulation of grape skin coloration and a theoretical basis for grape breeding and quality improvement.