Transcriptomic and epigenetic dynamics during dormancy release in grapevine

In perennial species such as grapevine the annual phenological development, including the transition from dormancy to budbreak, is strongly affected by changes and fluctuations in environmental stimuli such as temperature. Higher winter temperatures resulting from climate change cause premature bud deacclimation and budbreak: this increases the risk derived from the exposure of vulnerable tissues to spring frost events, which in turn affects bud survival and impairs shoot production. Grapevine cultivars show a high degree of variability in their budbrek timing and are therefore differentially susceptible to frost damage. Understanding the molecular regulation of dormancy and budbreak, as well as the determinants shaping cultivar variability, is therefore essential to support the selection of varieties better suited to the changing climate. To this end, complementary approaches were used to identify and characterise phenology-related molecular determinants, which included the analysis of gene expression at the organ and cell level and the analysis of DNA methylation. DNA methylation dynamics were explored in Cabernet Sauvignon buds collected during cold acclimation, chilling treatment and deacclimation. Although no genome-wide changes in DNA methylation were detected, more directional changes were observed at the single-locus level. Cold acclimation and dormancy were associated with minimal hypomethylation of promoters and coding regions, while more frequent and extensive methylation and demethylation events were detected during deacclimation, consistent with the more extensive reactivation of growth and metabolism. Moreover, several genes involved in the acquisition of cold tolerance, maintenance of meristem activity, cell cycle regulation, and organ differentiation were identified as putatively regulated through DNA methylation. A comparative transcriptomic analysis was conducted to explore transcriptome dynamics in buds from Chardonnay and Cabernet Sauvignon, two cultivars with early and a late budbreak timing respectively. To this end, an experimental setup based on the monitoring of the dormancy-to-budbreak transition using single-bud cuttings was implemented, which allowed the replication under controlled condition of the expected phenotypical difference. The time course used was suitable to capture key stages exhibiting clear transcriptomic differences between the two cultivars. During dormancy Chardonnay showed a transcriptomic profile compatible with the priming for growth resumption prior to deacclimation, while Cabernet Sauvignon remained in a deep dormancy state. Upon budbreak induction an extensive transcriptomic reprogramming was detected: notably, several genes involved in key biological processes showed a delayed regulation in Cabernet Sauvignon compared to Chardonnay, consistent with its delayed phenotypic progression. Moreover, several genes with roles in dormancy release and budbreak showed distinct expression trends between cultivars. Gene expression in dormant and deacclimating Cabernet Sauvignon buds was also analysed at a single-nucleus level, providing the first evidence of a cell-type resolved transcriptional map of grapevine buds. In dormant buds the presence of cell-resolved physiological states associated with dormancy maintenance and response to abiotic stimuli was detected. Deacclimating buds were characterised by populations with clear cell identity and physiological role arising from organ differentiation, although cell states associated with dormancy were also detected, consistent with the delayed and slower reactivation of Cabernet Sauvignon buds. The integration of transcriptomic and epigenetic profiling, both at the whole organ and single cell level, provided a comprehensive picture of the regulation of the dormancy-to-budbreak transition in grapevine buds, establishing a solid framework for further studies in grapevine and other perennial species.