Persistent Epigenetic Reprogramming Is Associated With Contrasting Drought-Response Strategies in Citrus Scion-Rootstock Systems.

Recurrent drought limits the productivity of perennial crops such as citrus, whose tolerance to water deficit largely depends on scion-rootstock interactions. Although physiological responses to recurrent drought are well documented, the epigenetic states associated with these responses remain poorly understood, limiting the use of epigenetic variation to improve drought resilience. Here, we investigated whole-genome DNA methylation profiles and transcriptional responses in "Pera-D6" sweet orange (LP) grafted onto two rootstocks with contrasting physiological strategies for coping with water deficit: "Rangpur" lime (RL), associated with dehydration avoidance through enhanced water acquisition, and "Sunki Maravilha" mandarin (SM), associated with tighter regulation of transpiration and physiological adjustments under stress. Grafted plants were exposed to three cycles of water deficit followed by rehydration. In the scion, we detected rootstock-dependent methylation dynamics, with LP/RL exhibiting broader patterns of methylation change and LP/SM showing a more targeted response. In the LP/SM combination, drought-associated differentially methylated regions were linked to genes involved in photosynthesis, stomatal regulation, and transcriptional processes. For several stress-responsive genes, promoter methylation changes coincided with qualitative trends in gene expression; however, no significant methylation-expression correlations were detected after multiple-testing correction. These findings indicate that recurrent drought is associated with rootstock-dependent persistent DNA methylation patterns with potential functional relevance. Overall, the results highlight the importance of considering epigenetic variation in studies of drought response and suggest that rootstock selection may play a role in shaping regulatory responses to water deficit in citrus.