Identifying candidate genes for trichome traits in grapevine through a genome-wide association study

As the primary organ for photosynthesis in plants, the leaf surface trichomes play crucial roles in modulating light energy absorption and defending against biotic and abiotic stresses. The characteristic distribution of trichomes on grape leaves serves as an important diagnostic trait for cultivar identification, yet their genetic regulatory mechanisms remain poorly understood. In this study, we performed the first genome-wide association study (GWAS) on seven leaf trichome-related traits in grapevine. Utilizing resequencing data from 153 grape accessions combined with two-year phenotypic observations, we identified 201 significant single nucleotide polymorphisms (SNPs) consistently detected across both years, and further screened 314 candidate genes. These SNPs were distributed across 16 chromosomes, with chromosome 16 harboring the highest number of associated loci. Functional enrichment analysis revealed that the candidate genes were primarily involved in transcriptional regulation, ubiquitination modification, signal transduction, and cell wall metabolism. RT-qPCR validation confirmed that several candidate genes were highly expressed in young leaves, with significantly higher transcript levels in densely trichomatous cultivars compared to sparse-trichome varieties. Notably, the expression levels of VIT_18s0001g14070, VIT_05s0077g01370, VIT_05s0020g01710, and VIT_15s0046g01010 showed significant positive correlations with trichome density. This study provides new insights into the genetic basis of leaf trichome formation in grapevine and offers valuable references for breeding stress-resistant grape cultivars. Importantly, we highlight a grapevine-specific signal: a significant association interval enriched with multiple stilbene synthase genes (e.g., the VIT_16s0100g00770 cluster), suggesting a potential mechanistic link between trichome architecture and stilbenoid-mediated chemical defense. Collectively, the stable SNPs and candidate genes reported here provide immediate resources for developing breeder-friendly markers and accelerating marker-assisted selection to improve grapevine resilience to biotic stresses.