DNA methylation, transcriptomic, and metabolomic analyses provide new mechanistic insights into cold shock-induced chilling tolerance in cucumber

Cucumber is cold-sensitive; improper storage induces chilling injury. To investigate how 3 h 0 °C cold shock (CS) alleviates chilling injury in 'Baijinyu' cucumbers at 4 °C, we performed integrated DNA methylation, transcriptomic, and metabolomic analyses. CS alleviated chilling injury, delayed quality decline (soluble solids, firmness, color), and altered accumulation of lipids, keto acids/esters, amino acids, and organic acids. CS increased methylation of peroxidase, caffeic acid 3‑O‑methyltransferase, and cinnamyl‑alcohol dehydrogenase, upregulating peroxidase but downregulating the latter two, accompanied by accumulation of (E)-ferulic acid, L‑tyrosine, and trans‑5‑O‑(p‑coumaroyl)shikimate. CS induced hypomethylation of CG‑type distal intergenic region of NCED and CHH‑type promoter region of abscisic acid receptor PYL, leading to downregulation of NCED and upregulation of PYL, thereby suppressing ABA biosynthesis and modulating ABA signaling. Moreover, CS maintained membrane lipid stability. Overall, CS enhances chilling tolerance by DNA methylation-mediated regulation of transcriptional and metabolic networks, supporting its potential as a green postharvest treatment.