Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx

BACKGROUND: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitor...

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Autores: Kleinman Ruiz, Daniel, Martínez Cruz, Begoña, Soriano, Laura, Lucena Pérez, María, Cruz, Fernando, Villanueva, Beatriz, Fernández, Jesús María, Godoy, José A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/34684
Acceso en línea:http://hdl.handle.net/10230/34684
http://dx.doi.org/10.1186/s12864-017-3946-5
Access Level:acceso abierto
Palabra clave:Genetic management
Genome-wide
SNPs
STRs
Non-invasive
Monitoring
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spelling Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynxKleinman Ruiz, DanielMartínez Cruz, BegoñaSoriano, LauraLucena Pérez, MaríaCruz, FernandoVillanueva, BeatrizFernández, Jesús MaríaGodoy, José A.Genetic managementGenome-wideSNPsSTRsNon-invasiveMonitoringBACKGROUND: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1.6 million SNPs, of which 1536 were selected and genotyped in an extended Iberian lynx sample. METHODS: We validated 1492 SNPs and analysed their heterozygosity, Hardy-Weinberg equilibrium, and linkage disequilibrium. We then selected a panel of 343 minimally linked autosomal SNPs from which we extracted subsets optimized for four different typical tasks in conservation applications: individual identification, parentage assignment, relatedness estimation, and admixture classification, and compared their power to currently used STR panels. RESULTS: We ascribed 21 SNPs to chromosome X based on their segregation patterns, and identified one additional marker that showed significant differentiation between sexes. For all applications considered, panels of autosomal SNPs showed higher power than the currently used STR set with only a very modest increase in the number of markers. CONCLUSIONS: These novel panels of highly informative genome-wide SNPs provide more powerful, efficient, and flexible tools for the genetic management and non-invasive monitoring of Iberian lynx populations. This example highlights an important outcome of whole-genome studies in genetically threatened species.Funding for this project was provided by the Spanish Dirección General de Investigación Científica y Técnica (CGL2013-47755-P), and Banco de Santander, CSIC and Fundación General CSIC through a “Proyectos Cero” grant. DKR and MLP were supported by PhD contracts from Programa Internacional de Becas “La Caixa-Severo Ochoa”. FC and BMC were hired under the EcoGenes project funded by the European FP7 programme (264125-FP7-REGPOT-2010-1). EBD-CSIC received support from the Spanish Ministry of Economy and Competitiveness under the 'Centro de Excelencia Severo Ochoa 2013-2017' program, grants SEV-2012-0262.BioMed Central201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/34684http://dx.doi.org/10.1186/s12864-017-3946-5reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBMC Genomics 2017 Dec; 18(1): 556info:eu-repo/grantAgreement/EC/FP7/264125info:eu-repo/grantAgreement/ES/1PE/CGL2013-47755-P© The Author(s). 2017 Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/346842026-06-12T07:21:37Z
dc.title.none.fl_str_mv Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
title Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
spellingShingle Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
Kleinman Ruiz, Daniel
Genetic management
Genome-wide
SNPs
STRs
Non-invasive
Monitoring
title_short Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
title_full Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
title_fullStr Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
title_full_unstemmed Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
title_sort Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx
dc.creator.none.fl_str_mv Kleinman Ruiz, Daniel
Martínez Cruz, Begoña
Soriano, Laura
Lucena Pérez, María
Cruz, Fernando
Villanueva, Beatriz
Fernández, Jesús María
Godoy, José A.
author Kleinman Ruiz, Daniel
author_facet Kleinman Ruiz, Daniel
Martínez Cruz, Begoña
Soriano, Laura
Lucena Pérez, María
Cruz, Fernando
Villanueva, Beatriz
Fernández, Jesús María
Godoy, José A.
author_role author
author2 Martínez Cruz, Begoña
Soriano, Laura
Lucena Pérez, María
Cruz, Fernando
Villanueva, Beatriz
Fernández, Jesús María
Godoy, José A.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genetic management
Genome-wide
SNPs
STRs
Non-invasive
Monitoring
topic Genetic management
Genome-wide
SNPs
STRs
Non-invasive
Monitoring
description BACKGROUND: The Iberian lynx (Lynx pardinus) has been acknowledged as the most endangered felid species in the world. An intense contraction and fragmentation during the twentieth century left less than 100 individuals split in two isolated and genetically eroded populations by 2002. Genetic monitoring and management so far have been based on 36 STRs, but their limited variability and the more complex situation of current populations demand more efficient molecular markers. The recent characterization of the Iberian lynx genome identified more than 1.6 million SNPs, of which 1536 were selected and genotyped in an extended Iberian lynx sample. METHODS: We validated 1492 SNPs and analysed their heterozygosity, Hardy-Weinberg equilibrium, and linkage disequilibrium. We then selected a panel of 343 minimally linked autosomal SNPs from which we extracted subsets optimized for four different typical tasks in conservation applications: individual identification, parentage assignment, relatedness estimation, and admixture classification, and compared their power to currently used STR panels. RESULTS: We ascribed 21 SNPs to chromosome X based on their segregation patterns, and identified one additional marker that showed significant differentiation between sexes. For all applications considered, panels of autosomal SNPs showed higher power than the currently used STR set with only a very modest increase in the number of markers. CONCLUSIONS: These novel panels of highly informative genome-wide SNPs provide more powerful, efficient, and flexible tools for the genetic management and non-invasive monitoring of Iberian lynx populations. This example highlights an important outcome of whole-genome studies in genetically threatened species.
publishDate 2017
dc.date.none.fl_str_mv 2017
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/34684
http://dx.doi.org/10.1186/s12864-017-3946-5
url http://hdl.handle.net/10230/34684
http://dx.doi.org/10.1186/s12864-017-3946-5
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv BMC Genomics 2017 Dec; 18(1): 556
info:eu-repo/grantAgreement/EC/FP7/264125
info:eu-repo/grantAgreement/ES/1PE/CGL2013-47755-P
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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