Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep

Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)

Detalles Bibliográficos
Autores: García Gámez, Elsa, Sahana, Goutam, Gutiérrez Gil, Beatriz, Arranz Santos, Juan José
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2012
País:España
Institución:Universidad de León
Repositorio:BULERIA. Repositorio Institucional de la Universidad de León
OAI Identifier:oai:buleria.unileon.es:10612/24707
Acceso en línea:https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-13-43#rightslink
https://hdl.handle.net/10612/24707
Access Level:acceso abierto
Palabra clave:Producción animal
Veterinaria
Linkage disequilibrium
Inbreeding
Spanish Churra sheep
3109 Ciencias Veterinarias
3104 Producción Animal
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spelling Linkage disequilibrium and inbreeding estimation in Spanish Churra sheepGarcía Gámez, ElsaSahana, GoutamGutiérrez Gil, BeatrizArranz Santos, Juan JoséProducción animalVeterinariaLinkage disequilibriumInbreedingSpanish Churra sheep3109 Ciencias Veterinarias3104 Producción AnimalCreative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)[EN] Background: Genomic technologies, such as high-throughput genotyping based on SNP arrays, have great potential to decipher the genetic architecture of complex traits and provide background information concerning genome structure in domestic animals, including the extent of linkage disequilibrium (LD) and haplotype blocks. The objective of this study was to estimate LD, the population evolution (past effective population size) and the level of inbreeding in Spanish Churra sheep.Results: A total of 43,784 SNPs distributed in the ovine autosomal genome was analyzed in 1,681 Churra ewes. LD was assessed by measuring r2 between all pairs of loci. For SNPs up to 10 kb apart, the average r2 was 0.329; for SNPs separated by 200-500 kb the average r2 was 0.061. When SNPs are separated by more than 50 Mbp, the average r2 is the same as between non-syntenic SNP pairs (0.003). The effective population size has decreased through time, faster from 1,000 to 100 years ago and slower since the selection scheme started (15-25 generations ago). In the last generation, four years ago, the effective population size was estimated to be 128 animals. Inbreeding coefficients, although differed depending on the estimation approaches, were generally low and showed the same trend, which indicates that since 2003, inbreeding has been slightly increasing in the studied resource population.Conclusions: The extent of LD in Churra sheep persists over much more limited distances than reported in dairy cattle and seems to be similar to other ovine populations. Churra sheep show a wide genetic base, with a long-term viable effective population size that has been slightly decreasing since selection scheme began in 1986. The genomic dataset analyzed provided useful information for identifying low-level inbreeding in the sample, whereas based on the parameters reported here, a higher marker density than that analyzed here will be needed to successfully conduct accurate mapping of genes underlying production traits and genomic selection prediction in this sheep breed. Although the Ovine Assembly development is still in a draft stage and future refinements will provide a more accurate physical map that will improve LD estimations, this work is a first step towards the understanding of the genetic architecture in sheepSIThis work was supported by the Spanish Ministry of Science (Project AGL2009-07000) and by the European Commission by 3SR Project (Sustainable Solutions for Small Ruminants; http://www.3srbreeding.eu). Elsa García-Gámez is funded by an FPU contract from the Spanish Ministry of Education. on. The support and availability to the computing facilities of the Foundation of Supercomputing Center of Castile and León (FCSCL) (http:// www.fcsc.es) is greatly acknowledgedBiomed CentralProducción AnimalFacultad de Veterinaria2012info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-13-43#rightslinkhttps://hdl.handle.net/10612/24707reponame:BULERIA. Repositorio Institucional de la Universidad de Leóninstname:Universidad de LeónInglésinfo:eu-repo/grantAgreement/MICINN/Programa Nacional de Investigación Fundamental/AGL2009-07000http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:buleria.unileon.es:10612/247072026-06-24T12:43:27Z
dc.title.none.fl_str_mv Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
title Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
spellingShingle Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
García Gámez, Elsa
Producción animal
Veterinaria
Linkage disequilibrium
Inbreeding
Spanish Churra sheep
3109 Ciencias Veterinarias
3104 Producción Animal
title_short Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
title_full Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
title_fullStr Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
title_full_unstemmed Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
title_sort Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep
dc.creator.none.fl_str_mv García Gámez, Elsa
Sahana, Goutam
Gutiérrez Gil, Beatriz
Arranz Santos, Juan José
author García Gámez, Elsa
author_facet García Gámez, Elsa
Sahana, Goutam
Gutiérrez Gil, Beatriz
Arranz Santos, Juan José
author_role author
author2 Sahana, Goutam
Gutiérrez Gil, Beatriz
Arranz Santos, Juan José
author2_role author
author
author
dc.contributor.none.fl_str_mv Producción Animal
Facultad de Veterinaria
dc.subject.none.fl_str_mv Producción animal
Veterinaria
Linkage disequilibrium
Inbreeding
Spanish Churra sheep
3109 Ciencias Veterinarias
3104 Producción Animal
topic Producción animal
Veterinaria
Linkage disequilibrium
Inbreeding
Spanish Churra sheep
3109 Ciencias Veterinarias
3104 Producción Animal
description Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
publishDate 2012
dc.date.none.fl_str_mv 2012
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 https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-13-43#rightslink
https://hdl.handle.net/10612/24707
url https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-13-43#rightslink
https://hdl.handle.net/10612/24707
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/MICINN/Programa Nacional de Investigación Fundamental/AGL2009-07000
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.publisher.none.fl_str_mv Biomed Central
publisher.none.fl_str_mv Biomed Central
dc.source.none.fl_str_mv reponame:BULERIA. Repositorio Institucional de la Universidad de León
instname:Universidad de León
instname_str Universidad de León
reponame_str BULERIA. Repositorio Institucional de la Universidad de León
collection BULERIA. Repositorio Institucional de la Universidad de León
repository.name.fl_str_mv
repository.mail.fl_str_mv
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