Abstract

Cucumber fruit exhibited progressive increases in chilling injury (CI) index, relative electrolyte leakage and chlorophyll fluorescence parameter Y(NO), while Fv/fm values progressively decreased during cold storage. To unravel the mechanisms underlying CI, we performed an integrated transcriptomic and metabolomics analysis. Transcriptomic analysis revealed that differentially expressed genes (DEGs) upregulated during cold storage were significantly enriched in lipid metabolism pathways, whereas the downregulated DEGs were predominantly enriched in flavonoid biosynthesis pathways. These shifts were corroborated by metabolomics data, which showed a decrease in the abundance of 17 flavonoids as CI worsened, contrasted by an increase in 21 lipids, notably including 4 lipid peroxides, with extended cold durations. The decline in flavonoids likely compromises the fruit's ability to scavenge reactive oxygen species, thereby promoting lipid peroxidation, especially membrane lipids. The observed imbalance between flavonoids and lipid metabolism may represent a key mechanism underlying CI development in cold-stored cucumber fruit