Integrated Physiological, Transcriptomic, and Methylation Analyses Reveal Near-Freezing Temperature-Mediated Multi-Gene Expression Regulation to Preserve Postharvest Yellow Peach Quality and Antioxidant Capacity

• NFT storage alleviated chilling injury (CI) and reduced softening in yellow peach. • NFT enhanced the antioxidant capacity by activating the AsA-GSH cycle. • NFT activates the PpLOX1/3 -mediated oxidation pathway to enhance flavor quality. • The methylation and transcription of PpNAC2 jointly regulate CI and flavor. Near-freezing temperature (NFT) storage is an effective strategy for alleviating chilling injury (CI) in peach fruit; however, the metabolic dynamics and regulatory mechanisms underlying this protective process have remained poorly understood. In this study, integrated transcriptomic and DNA methylation analyses were performed to evaluate CI symptoms, antioxidant activity, and flavor quality of yellow peach fruit following NFT storage. Compared with storage at 5 °C and 0 °C, NFT storage significantly delayed CI onset, suppressed firmness loss, and reduced the accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS). Furthermore, NFT storage enhanced the activities of glutathione reductase (GR), dehydroascorbate reductase (DHAR), and monodehydroascorbate reductase (MDHAR), while also promoting the biosynthesis of glutathione and ascorbic acid—collectively indicating an elevated antioxidant capacity. Concurrently, NFT storage up-regulated PpLOX1 and PpLOX3 , thereby sustaining higher levels of key aroma-active compounds including 1-hexanol, (E)-2-hexen-1-ol, and linalool, and ultimately contributing to aroma quality preservation. Integrated transcriptomic and weighted gene co‑expression network analysis (WGCNA) further indicated that NFT storage activated the MAPK signaling pathway and the plant–pathogen interaction pathway, accompanied by significant enrichment of several transcription factors, including five PpNACs, two PpMADSs, six PpERFs, and three PpWRKYs, which may cooperatively contribute to chilling tolerance and the maintenance of aroma quality. At the epigenetic level, NFT storage attenuated the increase in total DNA methylation. Importantly, the promoter regions of PpNAC2, PpERF71 , and PpWRKY33 exhibited reduced methylation levels—a modification that may enhance the binding capacity of PpWRKY33 to its downstream targets (such as PpLOX1 and PpLOX3 ). The coordinated transcriptional and epigenetic regulation mediated by NFT storage serves as a key mechanistic basis for improved aroma, enhanced cold tolerance, delayed ripening, and ultimately mitigated CI in peach fruit.