Integrated transcriptomic and metabolomic profiling reveals a JAZ-transcription factor network governing MeJA-induced...

Methyl jasmonate (MeJA) is a potent elicitor of secondary metabolism in plants, but its regulatory role in flavonoid biosynthesis in Scutellaria barbata remains unclear.

Here, we performed an integrated transcriptomic and metabolomic analysis of S. barbata seedlings following exogenous MeJA treatment, combining differential expression and correlation network approaches to identify candidate genes, metabolites, and transcription factors (TFs) associated with flavonoid accumulation.

MeJA treatment significantly promoted the accumulation of multiple flavonoids and upregulated key biosynthetic genes, including Sbar2C282T9_CHS2, Sbar5A47T51_CHI, and Sbar9A209T130_C4H. A total of 2,453 differentially expressed genes (DEGs) were identified, which were significantly enriched in flavonoid biosynthesis and plant hormone signal transduction pathways. Among these, 180 differentially expressed TFs were detected, with the ERF, MYB, bHLH, NAC, and bZIP families being markedly enriched. Integrative correlation analysis revealed 40 TFs whose expression patterns were strongly correlated with 19 flavonoids. TF binding site prediction further identified seven candidate TFs predicted to target flavonoid structural genes, including Sbar2C282T9_CHS2 and Sbar9A209T130_C4H. Protein‑protein interaction prediction suggested that several of these TFs, particularly bHLH members, may interact with JAZ repressors and form intra‑family interaction clusters.

Collectively, these findings suggest a potential JA-responsive transcriptional regulatory network and point to a conserved JAZ-TF module that may modulate flavonoid biosynthesis in S. barbata. This study provides valuable insights into the regulatory mechanisms of secondary metabolism in medicinal plants and offers candidate gene resources for metabolic engineering and molecular breeding of high‑flavonoid varieties.