Multi-omics dissection of flavor metabolism in Allium fistulosum identifies AfMYB11 as a core regulator of γ-glutamyl-S-methylcysteine and alliin accumulation.

Allium fistulosum is a globally significant vegetable prized for its distinctive organosulfur profile, yet the transcriptional regulatory mechanisms underlying the biosynthesis of flavor-associated metabolites remain largely elusive. Here, we performed an integrated metabolomic and transcriptomic comparison between a reference green onion accession (CK) and a Tibetan accession (CD) exhibiting an enhanced accumulation of organosulfur compounds. CD accumulated higher levels of key flavor precursors, predominantly γ-glutamyl-S-methylcysteine, alliin, and related sulfides, underpinned by the coordinated upregulation of core biosynthetic genes including AfGGT and AfAlliinase20. Through weighted gene co-expression network analysis and regulatory network construction, AfMYB11 was identified as a crucial hub transcription factor. Yeast one-hybrid and luciferase assays demonstrated that AfMYB11 directly binds to and activates the promoters of both AfGGT and AfAlliinase20. Transient overexpression of AfMYB11 in green onion tissues significantly elevated the transcript levels of these target genes and concomitantly increased the contents of γ-glutamyl-S-methylcysteine and alliin. These results establish an AfMYB11-AfGGT/AfAlliinase20 regulatory module that governs the accumulation of characteristic flavor precursors in A. fistulosum. Our findings not only elucidate a previously uncharacterized transcriptional mechanism modulating the accumulation of Allium flavor-associated metabolites but also provide actionable molecular targets for the genetic breeding of green onion metabolic traits.