Multi‐omics analysis reveals the potential role of MbDDC in tissue‐specific alkaloid biosynthesis and distribution in Meconopsis betonicifolia

SUMMARY Plants of the Meconopsis ( Meconopsis spp.), endemic to the Qinghai‐Tibet Plateau, are prized in traditional Tibetan medicinal herbs for their bioactive alkaloids, particularly their antispasmodic and analgesic properties. To elucidate the mechanisms underlying tissue‐specific alkaloid accumulation in Meconopsis betonicifolia , we integrated metabolomic and transcriptomic analyses across four organs (roots, stems, leaves, and flowers) and functionally characterized the rate‐limiting enzyme MbDDC‐3. Our results demonstrate that roots are the primary site of alkaloid accumulation, with codeinone and salutaridine identified as key intermediates in the isoquinoline pathway. Eleven differentially expressed genes (DEGs) were strongly correlated with these metabolites. Heterologous overexpression of MbDDC‐3 in tobacco ( Nicotiana tabacum ) significantly increased total alkaloid by 274% in roots ( P < 0.05), with (S)‐cis‐ N ‐methylstylopine and its precursors (tyramine/dopamine) significantly enriched. Notably, MbDDC‐3 protein contains a non‐classical nuclear localization signal (NLS)—RLKPAAIFNRKLG—located near its C‐terminal region and exhibits key residue substitutions compared to lowland species, suggesting adaptive evolution under high‐altitude stress. Collectively, this study reveals how M. betonicifolia optimizes alkaloid distribution for ecological fitness, while offering a genetic tool for metabolic engineering of medicinal alkaloids.