Mycorrhiza, water stress, and rootstock–scion combinations shape plant physiological traits and gene expression in grapevine

• Mycorrhiza and irrigation regime shaped some plant physiological traits • 1103P rootstock sustained biomass better under water stress • SO4 rootstock improved growth in well-watered conditions • Mycorrhiza improved P uptake, chlorophyll, and osmoprotectants • Transcriptomic shifts were stronger with SO4 under drought, esp. with mycorrhiza Rootstock–scion combination and arbuscular mycorrhizal fungi (AMF) are key determinants of grapevine performance under water deficit, but their combined influence on stress responses remains insufficiently understood. Four grafted grapevine combinations (Pinot Noir and Chardonnay grafted onto SO4 or 1103P) were grown under well-watered (WW) or water stress (WS) conditions, with (+Myc) or without (-Myc) inoculation by Rhizophagus irregularis . Physiological traits (biomass, nutrient concentrations, chlorophyll, carbohydrates, proline) and root transcriptomes of both grapevine and AMF (intraradical) were analyzed by RNA sequencing. Physiological traits were mainly influenced by AMF inoculation and irrigation, whereas transcriptomic variation was driven by rootstock genotype and water regime. Mycorrhizal plants showed higher chlorophyll content and osmoprotectant accumulation, consistent with improved water-use efficiency. Correlation analyses revealed strong associations between gene expression and physiological parameters, indicating coordinated regulation of carbon allocation and photosynthetic balance under mycorrhization and water stress. Under WS, 1103P maintained root biomass, while SO4 promoted higher shoot growth under WW. Transcriptomic responses were genotype dependent: intraradical R. irregularis showed greater intraradical transcriptional activity in SO4 combinations, while grapevine roots displayed stronger reprogramming in SO4 than in 1103P. These results demonstrate that mycorrhization enhances physiological stability and transcriptional coordination under drought, while genotype-specific traits modulate the magnitude and nature of these responses. The integration of physiological, transcriptional, and correlation data underscores the importance of rootstock–scion genetic background and symbiotic potential in shaping adaptive strategies to water stress, providing insights for optimizing grapevine resilience under climate change.