Time-series transcriptomics of grapevine deacclimation reveals chilling-dependent genetic responses to temperature increase during dormancy

During winter, grapevine (Vitis vinifera) bud dormancy and cold hardiness are regulated by complex interactions between chilling accumulation and temperature cues. However, the molecular mechanisms underlying physiological transitions during winter remain poorly understood. In this study, we performed time-series RNA-seq on Cabernet Sauvignon dormant buds with varying chilling accumulation, followed by warm temperature exposure. Using weighted gene co-expression network analysis, empirical modeling, and a novel calculation of molecular temperature response rate, we identified gene expression patterns responsive to temperature alone, chilling alone, and their interaction. Temperature-responsive genes showed rapid, chilling-independent activation and were primarily associated with metabolism, environmental sensing, and auxin signaling. Chilling-responsive genes were enriched for functions of chromatin remodeling and heat shock protein pathways, suggesting progressive cellular reprogramming under field conditions. Interaction-responsive genes, including those involved in ABA/auxin metabolism and cell wall modification, seem to function in both dormancy progression and deacclimation. These findings provide a mechanistic framework for how chilling and temperature synergistically regulate dormancy transitions in grapevine, which enhances the understanding of temperature sensing and response and the chilling-mediate dormancy progression underlying grapevine dormant season physiology.