Integrated transcriptomics and metabolomics reveal dynamic quinolizidine alkaloid accumulation and key genes involved in their biosynthesis during root development of Sophora flavescens

Sophora flavescens , a traditional Chinese medicinal herb, is rich in quinolizidine alkaloids (QAs) in its roots, which are the core substances responsible for its anti-inflammatory and anti-tumor pharmacological activities. Therefore, understanding the biosynthetic regulation of these components during root development is crucial for improving the medicinal quality of S. flavescens . In this study, field-grown S . flavescens roots were used to investigate alkaloid biosynthesis and accumulation during development by integrating transcriptomics and widely-targeted metabolomics. In total, 140 alkaloids were identified, among which 39 were QAs. QAs showed a significant phased accumulation pattern, with a small amount accumulated during the Root1-Root2 period and a large amount accumulated during the Root7-Root8 period. Transcriptomics identified 23,224 differentially expressed genes (DEGs) among 7 comparisons, which were significantly enriched in pathways including lysine biosynthesis, alkaloid biosynthesis, and plant hormone signal transduction. Based on the correlation analysis of metabolites and genes, eight potential core transcription factors (TFs) regulating QA biosynthesis were screened out. WGCNA identified 17 co-expression modules, among which five were significantly correlated with QAs (| r | > 0.75, p < 0.05). The purple module was significantly enriched in the biosynthesis of various alkaloids pathway. Correlation analysis linked the expression of 10 hub genes to differential alkaloids contents, identifying six core genes: SfERF073 , SfERF035 , SfCuAO06 , SfENO , SfACO3M , and SfPHSH . Our results can reveal a dynamic alkaloid accumulation pattern during S. flavescens root development, indicate potential regulatory relationships between key genes and TFs, and provide candidates for molecular breeding.