Integrated transcriptomic and metabolomic analyses reveal mechanisms of thermotolerance in peach (Prunus persica)

Large-scale peach production is increasingly threatened by heat stress associated with global climate change. To investigate the molecular basis of heat tolerance in peach, we conducted integrated physiological, transcriptomic, and metabolomic analyses to compare a heat-tolerant cultivar (‘Zhe Zhen’) with a heat-sensitive cultivar (‘Kang Zhen’). Physiological measurements showed that Zhe Zhen exhibited lower electrolyte leakage, reduced accumulation of H₂O₂ and malondialdehyde, and higher antioxidant enzyme activities (CAT, POD, and SOD) under heat stress, indicating improved cellular stability. Transcriptomic analysis revealed that Zhe Zhen displayed broader transcriptional reprogramming, including higher expression of genes involved in photosystem repair (PsbY), electron transport (FD3), and ATP synthesis (ATPC1). Metabolomic profiling identified 5177 metabolites, with Zhe Zhen showing stronger metabolic adjustments and greater enrichment of pathways related to starch and sucrose metabolism, flavonoid biosynthesis, and secondary metabolism. Integrated multi-omics analysis further indicated that Zhe Zhen preferentially accumulated protective sugars, including sucrose, raffinose, and d -mannose, and showed enhanced activation of ABA- and JA-related signaling pathways. In addition, several flavonoids, including apigenin 7-O-glucoside, luteolin derivatives, and quercetin 3-gentiobioside, were significantly enriched and co-expressed with a network of stress-responsive genes, including HSPs, GSTs , and transcription factors from the MYB, bZIP , and HSF families . Together, these results indicate that coordinated regulation of antioxidant defense, hormone signaling, sugar metabolism, and flavonoid biosynthesis underlies the superior heat tolerance of Zhe Zhen. Our findings provide new insights into thermotolerance mechanisms in peach and offer potential targets for breeding heat-resilient cultivars.