Genome-Wide DNA Methylation and Transcriptomic Analysis Under Salt Stress in ‘Shine Muscat’ Grapevine

Soil salinity severely restricts grapevine growth and development. Here, we integrated whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate DNA methylation changes and their relationship with gene expression under salt stress in Vitis vinifera L. ‘Shine Muscat’ grapevine. Salt stress altered genome-wide DNA methylation patterns, reducing methylation levels in CG, CHG, and CHH contexts following NaCl treatment. We identified 8606 differentially methylated regions (DMRs) and 3106 DMR-associated genes (DMGs) under salt stress. RNA-seq analysis revealed 2691 differentially expressed genes (DEGs), including multiple stress-related transcription factors (e.g., MYB, NAC, WRKY) and hormone-related genes strongly induced by salinity. Integrative analysis identified 171 genes that were both differentially methylated and differentially expressed, primarily enriched in metabolic pathways, fructose and mannose metabolism, and fatty acid biosynthesis. Notably, several key stress-responsive genes (e.g., VvNAC72, VvBAK1, VvMYBS3) showed coordinated changes between methylation status and transcript abundance. Collectively, this study provides a comprehensive integrative analysis of DNA methylation and transcriptome reprogramming in ‘Shine Muscat’ grapevine under salt stress, revealing potential epigenetic mechanisms involved in transcriptional regulation and salt adaptation. The identified candidate genes provide valuable targets for further functional validation and genetic improvement of grapevine salt tolerance.