Cargando…
Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing
Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detect...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924560/ https://www.ncbi.nlm.nih.gov/pubmed/29673217 http://dx.doi.org/10.3390/genes9040218 |
_version_ | 1783318575506784256 |
---|---|
author | Hou, Lu Cui, Yanhong Li, Xiang Chen, Wu Zhang, Zhiyong Pang, Xiaoming Li, Yingyue |
author_facet | Hou, Lu Cui, Yanhong Li, Xiang Chen, Wu Zhang, Zhiyong Pang, Xiaoming Li, Yingyue |
author_sort | Hou, Lu |
collection | PubMed |
description | Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean N(A) = 5.481, H(E) = 0.548) and moderate population differentiation (pairwise F(st) = 0.048–0.078, N(m) = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. |
format | Online Article Text |
id | pubmed-5924560 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-59245602018-05-03 Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing Hou, Lu Cui, Yanhong Li, Xiang Chen, Wu Zhang, Zhiyong Pang, Xiaoming Li, Yingyue Genes (Basel) Article Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean N(A) = 5.481, H(E) = 0.548) and moderate population differentiation (pairwise F(st) = 0.048–0.078, N(m) = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. MDPI 2018-04-17 /pmc/articles/PMC5924560/ /pubmed/29673217 http://dx.doi.org/10.3390/genes9040218 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Hou, Lu Cui, Yanhong Li, Xiang Chen, Wu Zhang, Zhiyong Pang, Xiaoming Li, Yingyue Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title | Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title_full | Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title_fullStr | Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title_full_unstemmed | Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title_short | Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing |
title_sort | genetic evaluation of natural populations of the endangered conifer thuja koraiensis using microsatellite markers by restriction-associated dna sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924560/ https://www.ncbi.nlm.nih.gov/pubmed/29673217 http://dx.doi.org/10.3390/genes9040218 |
work_keys_str_mv | AT houlu geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT cuiyanhong geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT lixiang geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT chenwu geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT zhangzhiyong geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT pangxiaoming geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing AT liyingyue geneticevaluationofnaturalpopulationsoftheendangeredconiferthujakoraiensisusingmicrosatellitemarkersbyrestrictionassociateddnasequencing |