Multi-omics analyses reveal the effect of DNA methylation on iridoid glycosides biosynthesis in Rehmannia glutinosa

Rehmannia glutinosa roots produce a group of lipophilic bioactive components known as iridoid glycosides. However, the molecular mechanisms by which DNA methylation regulates the biosynthesis of iridoid glycosides in R. glutinosa remain unknown. Herein, the development of R. glutinosa roots and the content of iridoid glycosides in the Wenxian region were significantly higher than those in Xinxiang. Low methylation level contributed to the accumulation of iridoid glycosides and the expression of related enzyme genes. Demethylation promoted both roots growth and development, as well as the accumulation of iridoid glycosides. Up-regulated RgALDH13, RgHDR1, RgG10H4, RgDXR1, RgG10H3, and RgUPD1, along with transcription factors (TFs), form the regulatory network for the biosynthesis of iridoid glycosides. Furthermore, the primary active region of the RgG10H4 promoter is located in the -164 bp region, where the RgMYB2 protein specifically binds to the TAACCA motif in the RgG10H4 promoter. Collectively, low levels of DNA methylation enhance the expression of core genes, followed by inducing the accumulation of iridoid glycosides, which suggests that RgMYB2-RgG10H4 plays a positive role in this process. These findings will contribute to a deeper understanding of the role of DNA methylation in the accumulation of iridoid glycosides. HighlightLow levels of DNA methylation contribute to the accumulation of iridoid glycosides and the expression of key enzyme genes in R. glutinosa.