Integrative transcriptome and metabolome analysis identifies flavonoid biosynthesis as well as ascorbate and aldarate metabolism driving natural cold tolerance variation in dormant peach (Prunus persica)

Winter cold stress severely restricts the growth, overwintering survival, and geographical distribution of peaches ( Prunus persica ). Elucidating the key regulatory pathways and hub genes underlying genotypic divergence in cold tolerance is essential for the improvement of peach production. In this study, four cold-tolerant (T group) and four cold-sensitive (S group) cultivars were selected from 73 peach cultivars via field freeze-injury investigation and laboratory lethal temperature of 50% (LT₅₀) assays. Transcriptomic analyses were performed on dormant one-year-old branches of the T and S groups under 4°C control and − 25°C cold-stress treatments, and corresponding widely targeted metabolomic analyses were conducted under − 25°C cold-stress treatment. The results indicated that the MAPK signaling and plant hormone signal transduction pathway was universally activated by cold stress in both cold-tolerant and cold-sensitive peach groups. KEGG enrichment analysis revealed significant differences in gene expression associated with flavonoid biosynthesis and ascorbate aldarate metabolism between the T and S groups. Under control conditions, flavonoid biosynthesis-related DEGs exhibited distinct basal expression patterns between the two groups. Two L-ascorbate oxidase (AO) genes and one AO-like gene enriched in the ascorbate and aldarate metabolism pathway were markedly downregulated in the T group, while their associated metabolite, L-ascorbic acid-2-glucoside, was upregulated in the T group. Collectively, conserved cold-induced signaling pathways such as the MAPK cascade and plant hormone signal respond uniformly to cold stress in peaches, whereas constitutive differences in flavonoid biosynthesis and ascorbate and aldarate metabolism pathways constitute the key factors driving genotypic divergence in cold tolerance during dormancy. This study provides novel mechanistic insights into natural variation in peach cold tolerance and supplies valuable candidate genes and metabolites for the molecular breeding of cold-tolerant peach cultivars.