Multi-omics profiling reveals an extensive regulation network shift in the domestication process of the traditional Chinese medicinal herb Rehmannia glutinosa Liboschitz (Orobanchaceae)

Plant domestication plays a vital role in human evolution and society development. Contrasted to the major crops, the domesticated procedure of medicinal herbs remains largely unknown. Here we analyzed the epigenomic, transcriptomic, and metabolomic profiling of three wild and nine cultivated samples of Dihuang (Rehmannia glutinosa Liboschitz), a well-known traditional Chinese medicinal herb, to elucidate the genetic differentiation and regulation mechanism during domestication. The results unraveled that tremendous differentiation existed among wild and cultivated types from genomes to metabolites. The cultivars presented significantly more methylated sites than the wild type and conjoint analyses indicated that hypermethylation of key genes was generally related to their down-regulated expressions and up-regulated metabolites in the pathways of monoterpenoid biosynthesis and carbohydrate metabolism involved in main components production and tuberous root enlargement. We also identified the key gene related to plant circadian rhythms and potential adaptation in the domestication of Dihuang. This work unveiled the systematic transformation from wild to cultivated Dihuang and provides new insights into the regulatory networks of genetic architectures, benefiting germplasm collection, cultivation, and utilization in the future. [Display omitted] •Wild and cultivated samples showed significant differences.•Genetic regulatory networks were hypothesized.•Key genes linked to domestication and quality were screened.