Transcriptomic analysis reveals a coordinated stress response and metabolic reprogramming in ‘Muscat Hamburg’ grape berries subjected to partial root-zone irrigation

Water management in viticulture significantly influences grape berry development and wine quality, making it crucial to understand molecular responses to different irrigation strategies. This study investigated the physiological and transcriptomic responses of ‘Muscat Hamburg’ grape berries to partial root-zone irrigation (PRI), conventional irrigation (CI), and regulated deficit irrigation (RDI). Physiologically, irrigation treatments induced significant metabolic shifts without altering berry weight. The PRI treatment maximized sugar accumulation, while both PRI and RDI significantly elevated anthocyanin content and reduced titratable acidity compared to CI, promoting fruit ripening and quality. RNA-sequencing analysis of berries collected at 8 and 12 days post-veraison yielded high-quality transcriptomic profiles with distinct molecular signatures for each treatment. The most pronounced responses occurred in the CI vs. PRI12 comparison (3,205 differentially expressed genes). GO and KEGG analyses consistently highlighted the activation of stress response pathways, particularly heat response, reactive oxygen species, and protein processing in the endoplasmic reticulum. PRI induced comprehensive metabolic reprogramming characterized by the unfolded protein response, systematic downregulation of mitochondrial oxidative phosphorylation, and strategic reallocation of carbon and lipid metabolism. Key adjustments included enhanced trehalose biosynthesis, coordinated suppression of flavonoid biosynthesis genes despite the observed anthocyanin accumulation, and selective upregulation of antioxidant xanthophyll synthesis. Furthermore, cell wall metabolism was extensively modified alongside divergent regulation of the phenylpropanoid pathway. These findings demonstrate that PRI triggers a sophisticated cellular response involving protein quality control and resource conservation, offering molecular insights for optimizing sustainable irrigation while maintaining fruit quality.