Metabolome transcriptome and antioxidant capacity in Ferula fukanensis roots

Ferula fukanensis is a valuable medicinal and edible plant whose root gum resin is widely used in traditional medicine, but the optimal harvest time remains unclear. Here, we analyzed metabolomes, transcriptomes, and in vitro antioxidant activity of roots at three maturity stages (S1: April, pre-bolting; S2: May, rapid growth; S3: June, aboveground wilting). Using GC-MS, UPLC-MS/MS, and antioxidant assays, we found that S3 roots showed the highest antioxidant activity and the greatest accumulation of volatile organic compounds (VOCs), including volatile sulfur compounds (VSCs) such as (E)-sec-butyl propenyl disulfide, and non-volatile metabolites like amino acids and derivatives. Antioxidant activity was positively correlated with root sulfur compound content, while phenolic acids also contributed and exhibited dynamic changes during development. Transcriptomic analysis identified key pathways for flavor and antioxidant formation, highlighting cysteine synthase and serine O-acetyltransferase in VSC regulation, and acetyl-CoA C-acetyltransferase and hydroxymethylglutaryl-CoA reductase in sesquiterpene biosynthesis. Additionally, 4-coumarate–CoA ligase and caffeic acid 3-O-methyltransferase played central roles in phenolic acid biosynthesis. Overall, F. fukanensis roots at the S3 stage possess high antioxidant activity and distinctive flavor components, supporting their use as functional food ingredients.