Development of microsatellites from Rehmannia glutinosa transcriptome and evaluation of genetic diversity among Rehmannia species

• Fifteen primers of SSR markers were designed from Transcriptome sequences of Rehmannia glutinosa tuberous root.
• Rehmannia species showed the relatively low level of genetic diversity.
• Genetic relationships among Rehmannia species were investigated by both clustering and principal coordinates analysis.

Rehmannia glutinosa is a famous traditional Chinese medicinal plant with important medicinal value. However, the genetic background of Rehmannia glutinosa and related species remains largely unknown partially due to the lack of the molecular genetic markers. In this study, we developed 15 polymorphic microsatellite markers from Rehmannia glutinosa transcriptome databases and determined the genetic diversity among Rehmannia species. A total of 11,048 contigs containing perfect SSR loci were isolated from 374,444 Rehmannia glutinosa transcriptome reads. Among them, tetranucleotide repeat unit is the main type of SSR, accounting for 27% of all repeat types, followed by pentanucleotide, trinucleotide, dinucleotide and hexanucleotide motifs. Genetic diversity analysis showed that the number of alleles per locus ranged from 3 to 16, with the mean value of 9 and the average polymorphic information content of 0.71. The range of mean observed heterozygosity (Ho) and mean expected heterozygosity (HE) were 0.21–0.54 and 0.24–0.34, respectively, indicating the relatively low level of genetic diversity in Rehmannia. Both clustering and principal coordinates analysis (PCoA) supported that populations from the same Rehmannia species formed one distinct lineage, Rehmannia glutinosa, Rehmannia solanifolia and Rehmannia henryi are closely related while Rehmannia piasezkii are separated from other species. Our work offered a rapid and simple method to develop microsatellites and these novel set of SSR markers provided an effective tool for population genetics study of Rehmannia.