Integrated Transcriptomic and Metabolomic Analysis Elucidates Melatonin-Mediated Cold and Drought Tolerance during Grapevine Cane Overwintering

Cold-drought stress limits grapevine cane overwintering. Melatonin is known to enhance plant stress tolerance, but its regulatory mechanisms under natural overwintering remain unclear. We used the new grapevine line “140902” to investigate molecular responses to exogenous melatonin under combined cold-drought stress via integrated transcriptomic and metabolomic analyses. Melatonin increased endogenous hormones and antioxidant enzyme activities (e.g., SOD activity increased 23.6% under M3) and reduced MDA content by up to 31.9%, alleviating physiological damage. DEGs and DAMs were enriched in phenylpropanoid/flavonoid biosynthesis, hormone signaling, and starch/sucrose metabolism pathways. Melatonin upregulated JA/ABA signaling genes (GH3, JAZ, PYL), phenylpropanoid/flavonoid biosynthetic genes (C4H, 4CL, CAD, FLS), and carbon metabolism genes (β-glucosidase, cellulase), altering flavonoid (naringenin, eriodictyol) relative abundance. These coordinated changes may contribute to the melatonin-mediated alleviation of cold-drought injury in grapevines, offering insights into potential regulatory networks and a basis for nonburial cultivation in cold, arid northwestern China.