Scion-Rootstock interactions shape early transcriptional responses to controlled water deficit in newly selected table grape genotypes

Water limitation represents a major constraint in viticulture, affecting both physiological and molecular responses in grapevines. This study evaluated the physiological responses and scion transcriptomic profiles of two newly selected table grape genotypes, Genusia and Maula, grafted onto two contrasting rootstocks, 1103P (V. berlandieri × V. rupestris) and SO4 (V. berlandieri × V. riparia), under controlled water deficit conditions. Physiological measurements, including stomatal conductance and stem water potential, were integrated with RNA sequencing analyses to evaluate differential gene expression in actively growing shoots. Results revealed that rootstock identity significantly modulated scion responses to water limitation. SO4-grafted plants displayed a higher number of differentially expressed genes and a broader transcriptional reprogramming compared to 1103P, indicating a stronger molecular response to reduced water availability. Functional enrichment analyses indicated that SO4 combinations preferentially activated stress-related and defense-associated pathways, whereas 1103P combinations maintained a more stable expression of photosynthetic and primary metabolic processes. Overall, these findings highlight the central role of rootstock-scion interaction in shaping early physiological and transcriptional adjustments to water deficit and provide valuable insights for optimizing grafting combinations in table grape breeding programs to cope with water deficit.