SSR development and utilization with Rehmannia glutinosa transcriptome.

Mingjie Li; Yanhui Yang; Fajie Feng; Xinyu Li; Li Gu; Yunhe Tian; Jianming Wang; Jiankai Wang; Zhenfang Li; Aiguo Chen; Xinjian Chen; Zhongyi Zhang

Rehmannia glutinosa Libosch is a well-known medicinal plant in China. Despite its common use, very few molecular markers are available for this species, severely impeding any improvement of key agronomic traits. In this study, gene-based SSR (simple sequence repeat) markers were mined from the R. glutinosa transcriptome, assembled from leaf and root libraries, to obtain polymorphic information content (PIC). A total of 1,812 SSR (≥18 bp) loci were identified from 1,747 transcripts, in which 1,018 transcripts had significant homology to known proteins, and 35 transcripts were identified as non-coding RNA. Of all SSR loci, AG/GT was the most frequent SSRs repeat type, and bias of base composition presented SSRs loci from noncoding RNA. A set of 279 SSR primers (≥20 bp) were synthesized, of which 204 were successfully amplified in the Wen85-5 genome and 91 had a polymorphic information content between 0.33 and 0.90. Seven pairs of polymorphic SSR primers were selected to evaluate the genetic diversity of 36 R. glutinosa germplasms, and results demonstrated that cultivars are differ considerably from wild strains and that distinct genetic relationships exist among wild strains. The SSRs identified in this study provide critical information for future R. glutinosa breeding.