Development and characterization of 30 microsatellite loci for Plagiorhegma dubium (Berberidaceae)

Abstract

Premise of the Study Plagiorhegma dubium (Berberidaceae) has been listed as an endangered species in Korea due to extensive collection and destruction of natural habitats. In this study, 30 microsatellite loci, including 25 polymorphic loci, were developed for P. dubium for use in population‐level genetic analyses.Methods and ResultsWe carried out transcriptome sequencing and isolated a total of 30 expressed sequence tag–simple sequence repeat markers from P. dubium using Illumina HiSeq high‐throughput sequencing. To test utility of the developed markers, we genotyped 60 individuals from three populations and estimated the number of alleles and levels of observed and expected heterozygosity. Expected heterozygosity levels ranged from 0.000 to 0.594, 0.000 to 1.000, and 0.000 to 0.744 in the three populations, respectively.ConclusionsThese transcriptome‐derived simple sequence repeat markers are highly polymorphic and can be widely used in characterization of the endangered P. dubium. Population genetic studies with these markers will provide valuable insights for conservation by unraveling evolutionary patterns of P. dubium.

Genetic diversity and genetic structure of Puya raimondii (Bromeliaceae) for its conservation in the Peruvian Andes

“…We also found that the total heterozygosity was 0.217, a value that could not be compared with other populations of P. raimondii, since no other study using the same type of marker is available for the species. Studies in the genus Corybas showed ranges of observed and expected heterozygosity of 0-1 and 0-0.859 respectively (Etten et al 2018) and for the species Psammosilene tunicoides, ranges of 0-1 were found for Ho and 0-0.615 for He (Zhang et al 2018); as well as for Plagiorhegma dubium, where the He ranged from 0-0.594, 0-1 and 0-0.744 for the three populations under study (Kim et al 2018).…”

Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations

“…Plagiorhegma dubium Maxim. (Figure ) is an herbaceous perennial that belongs to family Berberidaceae (Kim, Lee, Kim, & Kim, in press; Rhie et al., ). P .…”

“…Fourteen microsatellite loci were used to genotype the total of 198 individuals from 10 populations using primers developed and tested for Plagiorhegma dubium (Kim et al., in press; see Table for the sample information). We performed PCRs in a volume of 25 μl containing 1 ul of 10 ng template DNA, 2 μl dNTPs (20 mM), 2.5 μl 10 × PCR buffer containing MgCl 2 (Takara, Japan), fluorescently labeled (FAM, HEX, and NED) forward and reverse primers, 0.5 μl (10 pmol each).…”