Transcriptome analysis-based inference of magnolin metabolic pathways in Magnolia: Enhancing Xinyi production and quality management

• We investigate the underlying biosynthetic mechanisms of magnolin of developing flower buds from distinct Magnolia species. • Substantial variations in magnolin levels were observed among distinct Magnolia species. • The phenylpropane biosynthesis pathway is primarily responsible for magnolin level differences. • The identification of 25 upregulated transcripts involved in magnolin biosynthesis. • A preliminary metabolic pathway of magnolin in Magnolia was constructed. Xinyi, the dried flower buds of specific Magnolia species used in traditional Chinese medicine, relies on magnolin as a key quality marker. Yet its biosynthetic pathway remains largely unknown. This study aimed to elucidate the molecular mechanisms underlying species-specific and developmental variation in magnolin accumulation in Magnolia flower buds. We quantified magnolin content via HPLC and performed transcriptome analysis on flower buds of Magnolia biondii, M. denudata and M. liliiflora during key developmental stages (October and November). M. biondii exhibited significantly higher magnolin content than M. denudata and M. liliiflora . Transcriptomics identified the phenylpropanoid biosynthesis pathway as central to magnolin variation. Crucially, 25 differentially expressed genes (DEGs) encoding key pathway enzymes were upregulated in high-magnolin accessions and during October compared to November. Quantitative reverse transcriptase PCR validation further revealed that expression of downstream biosynthetic genes peaked in August-September, preceding peak magnolin accumulation in October. Taken together these findings elucidate the core magnolin biosynthetic pathway and identified key regulatory genes, providing a molecular basis for selecting elite M. biondii germplasm and optimizing harvest timing to enhance the yield and therapeutical quality of Xinyi.