Annual transcriptomic trajectory of grapevine buds reveals the coordinated regulation of thiamine and stilbenoid biosynthesis during winter dormancy.

Bud dormancy is a critical survival strategy for perennial plants in temperate climates to endure winter, involving complex transcriptional reprogramming. While previous studies have investigated gene expression during discrete phases of the grapevine bud annual cycle, a holistic understanding requires an integrated, season-wide analysis. We conducted a meta-analysis by combining and reexamining the transcriptomic data from two seminal studies on grapevine bud development. Using Self-Organizing Maps, we parsed the combined gene expression data into three major clusters corresponding to distinct seasonal activities, which we termed "summer-upregulated," "winter-upregulated," and "intermediate." Our analysis revealed that genes whose expression was predominantly upregulated during the winter months were significantly enriched in Gene Ontology terms related to stilbenoid biosynthesis and thiamine biosynthesis. This finding prompted a deeper investigation into these two pathways. We observed profound and coordinated upregulation of key genes in both pathways during the coldest winter months, suggesting that these genes are integral components of the bud's strategy for surviving low temperatures and maintaining viability. These results confirm the role of stilbenoids as stress-responsive compounds and reveal a novel role for thiamine biosynthesis in the molecular mechanisms of grapevine bud dormancy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08190-w.