Metabolomics insights into the shared and cultivar-related mechanisms controlling postharvest cold tolerance in Cucurbita pepo L

• Metabolomic markers of chilling injury were identified across zucchini cultivars. • Polyphenol accumulation contributed to improved fruit quality during cold storage. • Amino acids, nucleotides and phytohormones supported postharvest cold tolerance. • Tocopherol and pyridoxal enhanced antioxidant protection during cold storage. • The tolerant inbred line 4.7 accumulated cucurbitacins B and I under cold conditions. Zucchini (Cucurbita pepo L.) is highly sensitive to chilling injury during cold storage, which leads to surface damage, quality loss, and reduced nutraceutical value. Fruits were stored at 4 °C, and samples were collected at harvest (T0), 3 days (T3), and 14 days (T14) of cold storage. To elucidate the biochemical determinants of cold tolerance, we selected five cold-tolerant and five cold-sensitive cultivars from a previous screening of 126 accessions based on differences in chilling injury index (CI), weight loss (WL), and physiological indicators of oxidative stress. Metabolomic profiling was performed on fruit exocarp tissue using an untargeted LC–MS approach. Despite genotypic variability, all cultivars displayed a shared metabolic response to cold storage characterized by the accumulation of N6,N6,N6-trimethyl-L-lysine and 6-hydroxymethyl-7,8-dihydropterin, intermediates in carnitine and folate biosynthesis. Notably, tolerant cultivars maintained higher levels of these metabolites throughout storage, suggesting the presence of a metabolic signature associated with improved cold tolerance. Beyond this shared response, tolerant cultivars exhibited distinct metabolic adjustments involving nucleotides, phenolic compounds, amino acids, phytohormones, vitamins, and cucurbitacins. Overall, these results provide new insights into metabolic responses associated with postharvest cold tolerance in zucchini and highlight candidate metabolic markers that may be useful for breeding programs aimed at improving postharvest performance and shelf life.