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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...

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Autores principales: Hou, Lu, Cui, Yanhong, Li, Xiang, Chen, Wu, Zhang, Zhiyong, Pang, Xiaoming, Li, Yingyue
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
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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.
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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
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