Field-based insights into global grapevine methylation under conditions of recurring water constraint

Abstract

Water limitation is a major environmental constraint affecting grapevine productivity and fruit quality worldwide. While DNA methylation has been widely implicated in drought responses in herbaceous species, its role in woody perennials such as grapevine remains underexplored under field conditions. Using a long-term, field-based model vineyard established to investigate grapevine adaptation and resilience under water limitation, an initial comparative global DNA methylation analysis was performed using an ELISA-based assay to provide a first description of potential epigenetic changes. The vineyard comprises 90 sampling points, representing five biological replicates of three scion cultivars—Cabernet Sauvignon (CAB), Pinotage (PIN), and Shiraz (SHI)—each grafted onto two rootstocks, Richter 110 (110R) and US87, and exposed to three irrigation regimes (well-watered, reduced irrigation, and dryland) since establishment. Leaf samples were collected during the 2021/2022 season across contrasting within-season conditions and again in the 2023/2024 season across six key developmental stages to capture seasonal methylation dynamics. DNA methylation data were contextualized using soil moisture and plant physiological metadata generated within the broader multidisciplinary study. Global DNA methylation varied across sampling periods and genetic backgrounds. A~10% decrease occurred between the first sampling under non-limiting soil moisture and the second sampling following differential irrigation. Pronounced genotype effects were observed: Shiraz grafted onto 110R showed ~30% higher methylation than Cabernet Sauvignon on 110R, and ~30% higher than Shiraz on US87. Developmental stage further contributed to variability, with fluctuations of up to ~15%. Methylation showed strong associations with physiological and soil parameters in specific scion–rootstock–irrigation combinations, most notably with stomatal conductance (r = -0.93) and total soil moisture (r = 0.99). Together, these findings provide one of the first field-based global methylation profiles of grapevine under long-term water limitation and demonstrate that epigenetic responses are shaped by environmental, developmental, and genetic factors. Building on this foundation, a subset of samples will be analyzed using whole-genome bisulfite sequencing (WGBS) to characterize DNA methylation at single-base resolution and identify differentially methylated regions associated with irrigation regime, developmental stage, and scion–rootstock combination.