Elicitor-induced stilbene production and lignin reduction in peanut hairy roots: Insights from transcriptomic and metabolomic analysis

• Elicitor treatment enhanced stilbenes and phenolics in peanut hairy roots. • Phenolics increased, lignin decreased, indicating metabolic adjustments. • Upregulated phenylpropanoid genes correlated with metabolite accumulation. • Transcriptomics and tissue staining confirmed lignin reduction during elicitation. • Lignin biosynthesis genes downregulated, boosting defense-related metabolites. Secondary metabolites are crucial for plant defense. This study investigates the time-dependent transcriptomic and metabolomic responses of peanut hairy root cultures to a combined elicitor treatment of chitosan (CHT), methyl jasmonate (MeJA), and cyclodextrin (CD). Differentially accumulated metabolites (DAMs), particularly stilbenes and phenolic/flavonoid compounds, increased significantly compared to the baseline group. Phenolic, flavonoid, and stilbene levels rose, while lignin content decreased over time. Transcriptomic analysis revealed upregulation of key genes in the phenylpropanoid pathway, including PAL, C4H, and 4CL , which correlated with elevated levels of hydroxybenzoic acid and related compounds. Genes involved in stilbene biosynthesis, such as STS, ROMT, R4DT-1 , and R3’DT-4 , as well as flavonoid biosynthesis genes, including CHS, CHI, F3H, CHR, FLS , and UGT72E , were also upregulated, corresponding to the accumulation of their respective metabolites. In contrast, lignin biosynthesis genes, such as HCT, CSE, CCoAOMT, CCR, CAD, and POD , were downregulated, while lignin-degrading genes were upregulated. This was further supported by tissue staining results and the reduction of lignin content during the elicitation period. The shift from lignin synthesis to degradation underscores a redirection of metabolic flux toward the production of defense-related secondary metabolites, particularly stilbenes, phenolics, and flavonoids.