Differences in powdery mildew resistance and associated miRNA expression in cucumber grafted onto contrasting rootstocks

Grafting markedly influences scion resistance to powdery mildew; however, the divergence in resistance induced by different rootstocks and the underlying regulatory mechanisms remain poorly understood. In this study, the cucumber cultivar Xintaimici was used as the scion and grafted onto pumpkin rootstocks nd8 (resistant) and nd4 (susceptible), generating resistant (C/R) and susceptible (C/S) graft combinations, with self-grafted plants (C/C) serving as the control. Following powdery mildew inoculation, disease resistance, physiological responses, and miRNA expression profiles were systematically analyzed. Compared with C/C, the disease index of C/R was reduced by 63.17%, whereas C/S showed only a modest reduction (9.65%), indicating pronounced rootstock-dependent differences in scion resistance. Consistently, C/R plants exhibited significantly enhanced activities of antioxidant enzymes (SOD, POD, and CAT) and key enzymes involved in phenylpropanoid metabolism, along with effective suppression of membrane lipid peroxidation. In contrast, C/S plants displayed limited activation of defense-related enzymes and suffered from increased oxidative damage. At 48 h post-inoculation, a total of 209 miRNAs were identified. Differentially expressed miRNAs were mainly distributed among C/R-specific miRNAs (28%), miRNAs shared among all graft combinations (14%), and miRNAs shared between C/R and C/S (3.5%), suggesting the coexistence of rootstock-specific and shared miRNA regulatory patterns during scion responses to powdery mildew. Target gene analysis revealed that these miRNAs predominantly regulate hormone-related transcription factors, signal transduction components, defense metabolism-related genes, and genes associated with membrane homeostasis. Furthermore, qRT-PCR validation demonstrated that the miR156SPL13B, miR169BAK1, and miR172RAP2-7/SCD1 modules exhibited regulatory patterns in C/R opposite to those in C/S, identifying them as key regulatory modules underlying rootstock-induced divergence in scion resistance to powdery mildew.