Low temperature stress negatively impacts plant growth and development, reducing crop yields by disrupting metabolite production and accumulation. Cassia obtusifolia L., a widely cultivated medicinal plant in subtropical regions, is particularly vulnerable to such stress. Methyl jasmonate (MeJA) regulates plant growth, defense mechanisms, and secondary metabolite production. This study investigated how C. obtusifolia responds to low temperature stress under MeJA treatment using transcriptomic and metabolomic approaches. MeJA treatment upregulated several transcription factor families, including APE/ERF-ERF, WRKY, NAC, and MYB-related, which modulated the plant's response to cold stress. These transcription factors influenced the expression of genes involved in glycolysis, sugar metabolism, and amino acid pathways, contributing to the plant's adaptive responses. Differentially expressed genes were associated with key metabolic processes such as flavonoid biosynthesis, ribosome function, glycolysis/gluconeogenesis, and sugar metabolism. Using H-NMR and LC-MS techniques, we observed that MeJA induced the accumulation of sugars and amino acids in the leaves of C. obtusifolia seedlings under cold stress, while levels of three flavonoid compounds Isoliquiritigenin, Kaempferol-7-O-glucoside, and Phloretin significantly decreased. Enrichment analysis indicated that MeJA modulates the biosynthetic pathways of these compounds in a dose-dependent manner. Integrating metabolomic and transcriptomic data further elucidated alterations in the flavonoid biosynthetic network and other metabolic pathways under low temperature stress. These findings offer insights into the molecular mechanisms underlying flavonoid synthesis and other metabolic adjustments in C. obtusifolia under MeJA treatment.
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