The coloration of vegetative organs in grapevine (Vitis vinifera L. ) is an important phenotypic trait associated with environmental responsiveness and stress adaptation; however, its genetic regulatory mechanisms remain poorly understood. To systematically elucidate the genetic basis of vegetative coloration, a genome-wide association study (GWAS) was performed using 151 grapevine accessions, integrating high-depth whole-genome resequencing data with phenotypic evaluations of eight coloration traits across two consecutive years (2023–2024). Using a mixed linear model (MLM), 13 stable and significant SNP loci were identified on chromosomes 3, 5, 6, 13, 14, 15, 16, and 18, explaining 13. 28–19. 35% of the phenotypic variation. Within ±15 kb of these loci, 16 candidate genes were identified. qRT-PCR analysis of key candidates revealed that VIT₀6s0004g03620 (mitogen-activated protein kinase), VIT₁6s0039g01900 (MYB-like domain-containing protein), and VIT₁4s0083g01050 (MADS-box protein 2) showed significant positive correlations between expression levels and coloration intensity, with distinct expression patterns among accessions exhibiting different coloration grades. These genes are likely involved in the regulation of anthocyanin accumulation. Collectively, this study elucidates the genomic architecture underlying vegetative organ coloration in grapevine and provides valuable candidate genes and SNP markers for functional validation and molecular-assisted breeding.
Yang et al. (Sun,) studied this question.