Development of Novel Low-Copy Nuclear Gene Primers by Transcriptomes in an Endemic Genus Orinus Hitchc. (Poaceae) from the Qinghai-Tibet Plateau

Abstract

In the present study, a total of eleven low-copy nuclear gene markers were developed using transcriptomes for the plant genus Orinus Hitchc. (Poaceae), which comprises three species of grasses widely distributed in the Qinghai-Tibet Plateau. These developed markers were successfully amplified and sequenced for 90 individuals from nine populations of three Orinus species. The DNA sequences for the eleven loci ranged from 606 to 1152 aligned based pairs. Compared with four candidate DNA barcoding markers in our previous studies, the newly developed markers had a relatively higher number of parsimony informative sites than three cpDNA spacers (7–20 vs. 1–8), but slightly lower than those of the internal transcribed spacers (ITS). Hence, these novel low-copy nuclear gene primer pairs were validly useful for the study of phylogeography, phylogenetic analysis and population genetics. Moreover, they could be used in phylogeny reconstruction and speciation for a broad range of Orinus and even the entire subtribe Tridentinae.