Development and characterization of EST‐SSR markers for Begonia luzhaiensis (Begoniaceae)

Abstract

Premise of the study:Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure.Methods and Results:Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa.Conclusions:The expressed sequence tag–simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure

“…To overcome difficulty of extracting quality DNA of Begonia species, a modified CTAB protocol optimized by Kopperud and Einset (1995) was followed (e.g., Chung et al 2014). Samples from 15 populations were genotyped by 16 EST-SSR markers using primer pairs developed for B. luzhaiensis (Tseng et al 2017). Amplification and genotyping conditions followed the protocol described in Tseng et al (2017).…”

“…Samples from 15 populations were genotyped by 16 EST-SSR markers using primer pairs developed for B. luzhaiensis (Tseng et al 2017). Amplification and genotyping conditions followed the protocol described in Tseng et al (2017). Based on our preliminary tests for marker variability as well as efficiency of PCR amplification, the trn C- ycf 6 intergenic spacer of the chloroplast genome was chosen for phylogeographic analysis.…”

“…The scenario predicted by Chung et al (2014) has been supported by analyses of the Primulina eburnea (Hance) Yin Z.Wang species complex that is distributed in limestone karsts of southern China (Gao et al 2015). To further test these hypotheses, expressed sequence tag-simple sequence repeat (EST-SSR) markers (Tseng et al 2017) and cpDNA sequences of trn C- ycf 6 intergenic spacer were collected for Begonia luzhaiensis T.C.Ku (Fig. 1e–h).…”

Insights Into the Evolution of the Chloroplast Genome and the Phylogeny of Begonia

“…Simple sequence repeats are frequently observed in plastomes, which are of particular interest in studies of evolution, population genetics and genome polymorphism (Ebert & Peakall, 2009;Qi et al, 2016). Several nuclear SSRs in Begonia have been identified in previous studies (Hughes et al, 2003;Twyford et al, 2013a;Chan et al, 2014;2015;Tseng et al, 2017); however, the results of only one study based on plastid-derived microsatellite markers have been published so far (Twyford et al, 2013b). In our study, we successfully detected approximately 150 (range, 115-171) plastome-derived SSRs per species, which could be useful for further population genetic and biogeographical analyses of Begoniaceae.…”

A Hybrid Capture Bait Set for Begonia

“…Begonia L. is one of the largest plant genera (Frodin, 2004;Moonlight et al, 2018) and presents a number of phylogenetic problems requiring increased resolution at both deep (sectional divisions) and shallow (recent radiations) levels. Additionally, there is a need to better understand the influence of past hybridisation events on present Begonia species diversity, given the evidence of multiple ancient and recent hybridisations (Goodall-Copestake et al, 2010;Thomas et al, 2012;Moonlight et al, 2015;Tseng et al, 2017;Liu et al, 2019a). Hybrid capture provides a wealth of genetic data that can help resolve these issues and provide data for further studies of diversity and evolution across the genus.…”