Integrated Metabolomics and Transcriptomics Analyses Reveal the Critical Role of Caffeic Acid in Potato (Solanum tuberosum L.) Cold Tolerance

Owing to the high altitude and short frost-free period of the Tibetan Plateau, potato plants are frequently exposed to cold stress (CS), which severely restricts their growth and productivity. Thus, understanding the mechanisms underlying cold tolerance in potato varieties is crucial for breeding improvement. This study aims to investigate the role of caffeic acid in potato cold tolerance and to elucidate the molecular mechanisms underlying the CS response. To achieve this, we conducted comprehensive metabolomic and transcriptomic analyses of KY130 (cold-tolerant) and KY140 (cold-sensitive) potato cultivars under CS at the seedling stage. ELISA results showed that caffeic acid levels were higher in KY130 than in KY140, while CS-KY130 exhibited higher levels than those of CS-KY140. Across all treatments, KY130 showed significantly higher activities of antioxidant enzymes (CAT and SOD) and higher contents of osmolytes (proline, soluble protein, and soluble sugar) than those of KY140. Caffeic acid and naringenin* were identified as candidate metabolites potentially involved in the direct and indirect cold resistance of potatoes. <i>StPAL</i>(<i>Soltu.Atl.03_2G004060</i>, <i>Soltu.Atl.03_2G004070</i>, <i>Soltu.Atl.03_2G008130</i>) and <i>StCSE</i>(<i>Soltu.Atl.04_1G006370</i> and <i>Soltu.Atl.04_3G005440</i>), identified as upstream regulators of caffeic acid, were associated with the direct and indirect cold resistance of potatoes. KEGG pathway analysis of differentially accumulated metabolites and differentially expressed genes revealed several key metabolic pathways, including "flavonoid-related metabolism," "lipid metabolism," and "amino acid metabolism." This research enhances our understanding of caffeic acid and the molecular mechanisms involved in the response of potatoes to CS, and supports future efforts in potato screening and breeding programs.