Regulation of gene expression by 5mC DNA methylation during the bolting process of cabbage (Brassica oleracea L. var. capitata L.)

DNA methylation is an essential epigenetic modification. However, the dynamics of DNA methylation during cabbage bolting remain poorly understood. To investigate changes in DNA methylation during cabbage bolting, we performed whole-genome bisulfite sequencing (WGBS) on both vegetative leaves of non-bolting plants and reproductive leaves of bolting plants in two cabbage accessions. Across the whole genome, the DNA methylation levels on each chromosome showed a negative correlation with gene density, and the methylation levels in reproductive leaves after bolting were higher than those in vegetative leaves before bolting. We identified a total of 10,159 differentially methylated regions (DMRs). GO enrichment analysis revealed that differentially methylated genes were significantly enriched in pathways related to reproductive process and floral organ development. At the subgenome level, MF2 exhibited a higher DNA methylation advantage, and the dominance of all three subgenomes was greater in reproductive leaves than in vegetative leaves. Integrating the transcriptomic data, we found that genes with DNA methylation modifications showed markedly lower expression levels than those without methylation. Two meristem-development-related genes, STM and WUS, displayed reduced DNA methylation and significantly elevated expression during bolting, suggesting that their expression was regulated by methylation. In summary, our study revealed a comprehensive DNA methylation profile of cabbage bolting and highlighted the critical role of DNA methylation in this process. These results provide a theoretical foundation for further molecular studies on bolting in Brassicaceae plants.