Dynamic flavor profiles in sweet cherry during cold storage: integrated multi‑omics and volatile profiling reveals regulatory networks underlying flavor deterioration

Cold storage induces flavor deterioration in sweet cherry, while cultivar-specific regulatory mechanisms are poorly understood. In this study, two mainstream commercial cultivars, ‘Rainier’ and ‘Tieton’, were stored at 4 °C for 21 days. We comprehensively integrated physiological phenotyping, transcriptomics, metabolomics, and volatile compound profiling to explore their flavor deterioration patterns. Physiological results demonstrated that fruit softening and sugar-acid imbalance were typical deterioration symptoms, and ‘Tieton’ reached a 100% decay rate at the end of storage, far higher than 51.55% of ‘Rainier’. Metabolomic analysis identified 1876 metabolites, and the two cultivars showed asynchronous metabolic reprogramming. ‘Tieton’ underwent dramatic metabolic changes at the early storage stage, while obvious metabolic shifts occurred in ‘Rainier’ at the mid stage. “Starch and sucrose metabolism” and “phenylpropanoid biosynthesis” were confirmed as two universally core pathways associated with flavor variation. We also detected 45 differential volatile compounds linked to fruit aroma. Furthermore, a flavor regulatory network was constructed, verifying that PavMYB3/13 as candidate positive regulators and PavC2H2 is a candidate negative regulator of flavor maintenance. This work elaborates on the genotype-specific patterns of cold-induced flavor decay and provides a theoretical foundation for developing variety-targeted postharvest preservation technologies for sweet cherries.