Multi-omics reveals terpenoid biosynthesis and antioxidant activity at maturity stage in Zanthoxylum armatum DC. fruits

Sichuan Green pepper (Zanthoxylum armatum DC.) is a medicinal and culinary plant rich in bioactive compounds, particularly terpenoids, which contribute to its flavor and antioxidant activities. This study employed multi-omics (transcriptomics, proteomics, and metabolomics) to investigate antioxidant mechanisms during fruit maturation (S1: immature green; S2: semi-mature; S3: near-mature; S4: fully mature). Metabolomics revealed a total of 8 terpenoid metabolites (including geranylgeraniol, 20-deoxyingenol, and catalpol), with the highest terpenoid expression level observed at the S4 stage, which was consistent with the trend of enhanced antioxidant activity. Transcriptomics revealed 72 differentially expressed genes (e.g., Zardc23197 in bHLH family, Zardc54476 in STAT family) and proteomics identified 22 differentially expressed proteins (e.g., Zardc23656.t1 in IspS family) involved in terpenoid biosynthesis. Mantel tests showed correlations between six volatile terpenoids (e.g., α-pinene, β-myrcene) and transcriptome, while β-elemene and humulene correlated with metabolome. Partial least squares path modeling (GOF = 0.56) indicated transcriptome and proteome regulate antioxidant activity via terpenoid pathways. Our findings on the stage-specific molecular networks of Z. armatum support its use as a source of natural antioxidants for food preservation.