Integrated transcriptomic and metabolomic analysis of leaves from different Isodon rubescens populations identifies candidate genes related to diterpenoid biosynthesis

Background Isodon rubescens (Hemsl.) H. Hara is a medicinal plant mainly cultivated in Henan region of China. Diterpenoids represented by oridonin have good anti-tumor activity and significant clinical application value. However, the significant phenotypic variation and uneven quality among I. rubescens populations severely restrict its clinical application, making it urgent to breed elite varieties and promote standardized cultivation. Results We phenotyped nine populations and selected three with contrasting oridonin content-high (RrH), medium (RrM), and low (RrL, a space-mutagenized population)-for transcriptomic and terpenoid-targeted metabolomic analysis. A total of 776 terpenoid metabolites were detected, and the differential metabolites were significantly enriched in the diterpenoid biosynthesis pathway. Transcriptome sequencing generated 97,659 unigenes, revealing that key Mevalonate pathway (MVA)/Methylerythritol phosphate (MEP) pathway genes ( HMGR , DXS , DXR , GGPPS ) and multiple P450s were upregulated in RrH. Weighted Gene Co-expression Network Analysis (WGCNA) identified a green module strongly correlated with diterpenoid accumulation, containing 96 transcription factors from the ERF, WRKY, MYB, bHLH, NAC, and bZIP families. Gene-metabolite networks showed shared regulatory modules for oridonin, ponicidin, and rubescensin D, whereas rubescensin E appeared independently regulated. Conclusion This study provides a multi-omics resource and identifies candidate genes and transcription factors potentially involved in diterpenoid biosynthesis in I. rubescens . In addition, the RrH population was found to have both high oridonin content and high yield, making it a candidate population for elite varieties of I. rubescens to advance variety purification and standardized cultivation.