Comparative transcriptome and metabolome analysis revealed key cold-tolerant metabolic pathways under cold stress in Prunus salicina × armeniaca

• The cold-tolerant cultivar ‘Weiwang’ (WW) exhibited superior osmotic regulation and reactive oxygen species (ROS) detoxification capacity under freezing stress. • Joint transcriptome-metabolome profiling revealed the pivotal role of the raffinose family oligosaccharides (RFOs) biosynthesis pathway in conferring cold tolerance of WW. • Transcription factors belonging to the bHLH, ERF, and NAC families showed marked differential expression under cold stress. • Candidate transcription factors co-expression with RFOs-related genes in weighted gene co-expression network analysis (WGCNA) modules further substantiates their central regulatory roles in cold adaptation. Low-temperature stress poses a significant threat to the growth and development of Prunus salicina × armeniaca . As a relatively novel hybrid fruit species, its underlying cold tolerance mechanisms remain largely uncharacterized. This study employed one-year-old branches of the cold-tolerant cultivar ‘Weiwang’ (WW) and the cold-sensitive cultivar ‘Weidi’ (WD) to elucidate the cold tolerance mechanisms through integrated physiological, transcriptomic and metabolomic analyses. Result demonstrated that WW exhibited superior osmotic regulation and reactive oxygen species (ROS) detoxification capacity under freezing stress, conferring enhanced cold tolerance. Joint transcriptome-metabolome profiling revealed elevated accumulation of RFO precursors (e.g., galactinol, raffinose) and significant upregulation of key biosynthetic genes (e.g., GOLS, RAFS ) in WW, highlighting the pivotal role of the raffinose family oligosaccharides (RFOs) biosynthesis pathway in conferring cold resilience. Additionally, differentially expressed genes (DEGs) and metabolites (DAMs) between WW and WD were significantly enriched in pathways related to ‘sucrose and starch metabolism’, ‘plant hormone signal transduction’, ‘ABC transporters’, ‘amino acid biosynthesis’, and ‘phenylpropanoid biosynthesis’. Notably, transcription factors belonging to the bHLH, ERF, and NAC families showed marked differential expression under cold stress. Their co-expression with RFOs-related genes in weighted gene co-expression network analysis (WGCNA) modules further substantiates their central regulatory roles in cold adaptation. These findings advance the molecular understanding of cold tolerance in Prunus salicina × armeniaca during dormancy and offer candidate genes for targeted breeding of cold-hardy cultivars.