This study aimed to elucidate the physiological, biochemical, and transcriptional regulatory responses of potato plants to iron deficiency stress. Two potato varieties were selected for analysis: 05P (high tuber iron content) and CI5 (low tuber iron content). Tissue culture seedlings of both varieties were subjected to iron deficiency, and the effects on stem length, root length, fresh weight, soluble sugar and protein contents, as well as the activities of superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA), and leaf chlorophyll content (SPAD) values were evaluated. Additionally, the impact of iron deficiency on zinc (Zn), magnesium (Mg), calcium (Ca), manganese (Mn), and copper (Cu) concentrations in different tissues were analyzed. Transcriptomic sequencing and quantitative real-time PCR (qRT-PCR) were performed on various seedling tissues. The results showed that iron deficiency significantly inhibited seedling growth and development, resulting in reduced plant height and fresh weight, increased root length, decreased leaf SPAD content, and elevated soluble sugar and protein concentration. SOD, POD, and MDA activities were also significantly increased. Elemental analysis revealed that iron deficiency enhanced the uptake and accumulation of Zn, Mg, Ca, Mn, and Cu across different tissues. Transcriptomic analysis identified differentially expressed genes (DEGs) significantly enriched in pathways related to photosynthesis, carbon metabolism, and ribosome function in roots, stems, and leaves. Iron deficiency induced the upregulation of H⁺-ATPase genes in roots (PGSC0003DMG400004101, PGSC0003DMG400033034), acidifying the rhizosphere to increase active iron availability. Subsequently, this was followed by the upregulation of FRO genes (PGSC0003DMG400000184, PGSC0003DMG400010125, PGSC0003DMG401009494, PGSC0003DMG401018223), which reduce Fe³⁺ to Fe²⁺, and activation of IRT genes, facilitating Fe²⁺ transport to various tissues. Iron deficiency also reduced SPAD content in leaves, negatively impacting photosynthesis and overall plant growth. In response, the osmotic regulation and antioxidant defense systems were activated, enabling the plant to mitigate iron deficiency stress. Additionally, the absorption and accumulation of other metal ions were enhanced, likely as a compensatory mechanism for iron scarcity. At the transcriptional level, iron deficiency induced the expression of genes involved in metal absorption and transport, as well as those related to photosynthesis, carbon metabolism, and ribosomal function, thereby supporting iron homeostasis and maintaining metabolic balance under stress conditions.

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. StPAL(Soltu.Atl.03_2G004060, Soltu.Atl.03_2G004070, Soltu.Atl.03_2G008130) and StCSE(Soltu.Atl.04_1G006370 and Soltu.Atl.04_3G005440), 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.