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Abstract

In this study, the genomic variation characteristics of Vidal grape (Vitis vinifera cv. Vidal) and its bud sports based on the VvAADC gene were systematically analyzed using whole-genome resequencing technology. Through integrated analysis of whole-genome resequencing and metabolomic data, this study explicitly identified two core genes directly regulating 2-phenylethanol synthesis (VvAADC: aromatic amino acid decarboxylase; VvPDC: phenylalanine decarboxylase). These two genes form a physically linked "metabolic gene cluster" in the 23.5-24.1 Mb interval of chromosome 5, synergistically regulating the conversion of phenylalanine to 2-phenylethanol. In addition, 58 variant genes were screened in the phenylalanine metabolism pathway (vvi00940) (FDR=1.2×10⁻⁵); these genes are mainly involved in key downstream steps of the pathway, such as "aromatic amino acid decarboxylation" and "aldehyde reduction", indirectly affecting the synthesis efficiency of 2-phenylethanol. Furthermore, their molecular associations with 2-phenylethanol synthesis were explored by integrating metabolomic data with genomic data. The results revealed 5,147,177 and 5,118,467 single-nucleotide polymorphism (SNP) loci in the wild-type and bud sport materials, respectively, with unique SNPs accounting for 4.06% and 3.52%. Non-synonymous mutations in coding sequence regions reached 51.48%, significantly affecting gene function. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed genes were predominantly enriched in phenylalanine metabolism (vvi00940), vacuolar membrane transport (GO:0005774), and heat shock protein binding (GO:0031072). Notably, a C>T mutation (rs102345) in the VvAADC gene (Chr5:23.5–24.1 Mb) enhanced phenylalanine decarboxylase activity by 3.2-fold (p<0.01), leading to a marked increase in 2-phenylethanol content. This study elucidates the molecular regulatory mechanisms underlying aroma metabolism in bud sports and provides a genetic basis for improving grape flavor quality

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