Multiomics Reveal Low Temperatures Play Positive Roles in Flavonoids and Phenolic Accumulation in Meconopsis punicea

Meconopsis punicea, a Himalayan alpine medicinal herb, faces low-temperature constraints due to shifting thermal niches at high altitudes. Low temperature constrains plant growth and development but aids the accumulation of active compounds. However, the response mechanisms of plant seedlings to low temperatures remain unclear. In this study, metabolomic and transcriptomic analyses were performed to investigate the dynamic changes and molecular regulatory mechanisms of flavonoids and phenolic compounds. The results revealed that under low-temperature stress, the expression levels of related genes and the content of flavonoid and phenolic compounds increased significantly with treatment duration, indicating that these compounds actively participate in the low-temperature response. Specifically, in the comparison between 0 and 5 days low-temperature treatment (M0 vs. M5), 7905 differentially expressed genes (DEGs) were significantly upregulated and 21,823 DEGs were downregulated. In the comparison between 0 and 10 days low-temperature treatments (M0 vs. M10), 6253 genes were significantly upregulated and 8754 were downregulated. These DEGs were primarily enriched in metabolic processes and phenylpropanoid biosynthesis. Additionally, through correlation analysis and weighted gene co-expression network analysis (WGCNA), we identified the low-temperature-responsive transcription factor GASA11. With prolonged treatment, most metabolites show an increased level. In conclusion, this study elucidates the specific response mechanisms of flavonoids and phenolic compounds in Meconopsis punicea under low temperatures. These findings enrich the current understanding of plant metabolic responses to low temperatures and provide an important reference for subsequent in-depth studies on the roles of GASA11 and other key genes involved in flavonoid biosynthesis in the low-temperature adaptive responses of Meconopsis punicea.