Integrated multi-omics elucidates StAN1 as a key regulator reprogramming flavonoid partitioning and co-regulatory...

The R2R3-MYB transcription factor StAN1, a crucial regulator of anthocyanin biosynthesis in potato tubers, exerts previously unexplored global control over flavonoid diversification. Integrated transcriptomics (RNA-seq) and flavonoid metabolomics (UPLC-MS/MS) of StAN1-overexpressing tubers revealed its dual role in metabolic reprogramming: among 186 identified flavonoids, 122 exhibited tissue-specific accumulation shifts, with anthocyanins (e.g., pelargonidin/cyanidin), flavanones, and flavanonols upregulated in red flesh while flavonols (kaempferol/quercetin derivatives) were suppressed. Transcriptomic analyses identified 4783 flesh-specific and 2935 skin-specific differentially expressed genes (DEGs), pinpointing key biosynthetic genes and novel co-regulators (ERF, WRKY, bHLH TFs). Mechanistically, DAP-seq demonstrated StAN1 binding to promoters of flavonoid genes (e.g., StDFR), and dual-luciferase assays confirmed its direct activation of StDFR expression. Regulatory network expansion was evidenced by co-upregulation of RLKs (e.g., LRK10-like kinases), implicating kinase signaling in flavonoid partitioning. This study elucidates StAN1's multifaceted role beyond anthocyanin activation-orchestrating metabolic flux, engaging novel TF/kinase networks, and directly targeting structural genes-providing a foundation for engineering potatoes with enhanced nutraceutical properties via targeted manipulation of the StAN1 regulatory network.