# Multi-Omics Insights into Altered Flavonoid Metabolism Underlying Skin Color Variation in a Bud Mutant of Vitis vinifera Zaoheibao

## TL;DR

This study investigates how a grape bud mutant changes color from purple-black to yellow-green by analyzing flavonoid metabolism and gene expression.

## Contribution

The study reveals a MYB-centered regulatory module suppression as the cause of pigmentation loss in a grape bud mutant.

## Key findings

- Metabolite profiling identified 233 differentially accumulated metabolites with reduced anthocyanins in the mutant.
- Transcriptome analysis found 4036 differentially expressed genes, with key anthocyanin biosynthesis genes significantly downregulated.
- Multi-omics integration showed strong associations between MYB regulators, structural genes, and anthocyanin metabolites.

## Abstract

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.