Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain

12 Pág.

Detalles Bibliográficos
Autores: Mouresan, E. F., González-Rodríguez, A., Cañas-Álvarez, J. J., Munilla, S., Altarriba, Juan, Díaz, Clara, Baró, J. A., Molina, Antonio, López-Buesa, P., Piedrafita, J., Varona, Luis
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/370696
Acceso en línea:http://hdl.handle.net/10261/370696
https://api.elsevier.com/content/abstract/scopus_id/85076692565
Access Level:acceso abierto
Palabra clave:Beef cattle
Gene ontology
Linkage disequilibrium
Multiple populations
Recombination rate
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spelling Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in SpainMouresan, E. F.González-Rodríguez, A.Cañas-Álvarez, J. J.Munilla, S.Altarriba, JuanDíaz, ClaraBaró, J. A.Molina, AntonioLópez-Buesa, P.Piedrafita, J.Varona, LuisBeef cattleGene ontologyLinkage disequilibriumMultiple populationsRecombination rate12 Pág.In organisms with sexual reproduction, genetic diversity, and genome evolution are governed by meiotic recombination caused by crossing-over, which is known to vary within the genome. In this study, we propose a simple method to estimate the recombination rate that makes use of the persistency of linkage disequilibrium (LD) phase among closely related populations. The biological material comprised 171 triplets (sire/dam/offspring) from seven populations of autochthonous beef cattle in Spain (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta, and Rubia Gallega), which were genotyped for 777,962 SNPs with the BovineHD BeadChip. After standard quality filtering, we reconstructed the haplotype phases in the parental individuals and calculated the LD by the correlation -r- between each pair of markers that had a genetic distance < 1 Mb. Subsequently, these correlations were used to calculate the persistency of LD phase between each pair of populations along the autosomal genome. Therefore, the distribution of the recombination rate along the genome can be inferred since the effect of the number of generations of divergence should be equivalent throughout the genome. In our study, the recombination rate was highest in the largest chromosomes and at the distal portion of the chromosomes. In addition, the persistency of LD phase was highly heterogeneous throughout the genome, with a ratio of 25.4 times between the estimates of the recombination rates from the genomic regions that had the highest (BTA18-7.1 Mb) and the lowest (BTA12-42.4 Mb) estimates. Finally, an overrepresentation enrichment analysis (ORA) showed differences in the enriched gene ontology (GO) terms between the genes located in the genomic regions with estimates of the recombination rate over (or below) the 95th (or 5th) percentile throughout the autosomal genome.We thank the AGL 2010-15903 grant from the Spanish government and the KBBE.2011.1.3-06 project from the European Union’s Seventh Framework. We also thank the Breed Societies for their collaboration in collecting samples. The support of FEAGAS is acknowledged. JC-Á acknowledges the COLCIENCIAS support by the Francisco José De Caldas Fellowship 497/2009, and AG-R acknowledges the financial support provided by the BES-2011-045434 fellowship.Peer reviewedFrontiers MediaMinisterio de Ciencia e Innovación (España)European CommissionMouresan, E. F. [0000-0002-1335-7610]González-Rodríguez, A. [0000-0001-9869-524X]Cañas-Álvarez, J. J. [0000-0002-8101-8602]Munilla, S. [0000-0003-2666-2566]Altarriba, Juan [0000-0002-3042-2250]Baró, J. A. [0000-0002-3255-2585]López-Buesa, P. [0000-0001-5992-2913]Piedrafita, J. [0000-0003-1127-6988]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242019info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/370696https://api.elsevier.com/content/abstract/scopus_id/85076692565reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MICINN//AGL2010-15903Departamento de ​Mejora Genética Animalhttps://doi.org/10.3389/fgene.2019.01170Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3706962026-05-22T06:33:51Z
dc.title.none.fl_str_mv Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
title Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
spellingShingle Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
Mouresan, E. F.
Beef cattle
Gene ontology
Linkage disequilibrium
Multiple populations
Recombination rate
title_short Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
title_full Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
title_fullStr Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
title_full_unstemmed Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
title_sort Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain
dc.creator.none.fl_str_mv Mouresan, E. F.
González-Rodríguez, A.
Cañas-Álvarez, J. J.
Munilla, S.
Altarriba, Juan
Díaz, Clara
Baró, J. A.
Molina, Antonio
López-Buesa, P.
Piedrafita, J.
Varona, Luis
author Mouresan, E. F.
author_facet Mouresan, E. F.
González-Rodríguez, A.
Cañas-Álvarez, J. J.
Munilla, S.
Altarriba, Juan
Díaz, Clara
Baró, J. A.
Molina, Antonio
López-Buesa, P.
Piedrafita, J.
Varona, Luis
author_role author
author2 González-Rodríguez, A.
Cañas-Álvarez, J. J.
Munilla, S.
Altarriba, Juan
Díaz, Clara
Baró, J. A.
Molina, Antonio
López-Buesa, P.
Piedrafita, J.
Varona, Luis
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
European Commission
Mouresan, E. F. [0000-0002-1335-7610]
González-Rodríguez, A. [0000-0001-9869-524X]
Cañas-Álvarez, J. J. [0000-0002-8101-8602]
Munilla, S. [0000-0003-2666-2566]
Altarriba, Juan [0000-0002-3042-2250]
Baró, J. A. [0000-0002-3255-2585]
López-Buesa, P. [0000-0001-5992-2913]
Piedrafita, J. [0000-0003-1127-6988]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Beef cattle
Gene ontology
Linkage disequilibrium
Multiple populations
Recombination rate
topic Beef cattle
Gene ontology
Linkage disequilibrium
Multiple populations
Recombination rate
description 12 Pág.
publishDate 2019
dc.date.none.fl_str_mv 2019
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/370696
https://api.elsevier.com/content/abstract/scopus_id/85076692565
url http://hdl.handle.net/10261/370696
https://api.elsevier.com/content/abstract/scopus_id/85076692565
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MICINN//AGL2010-15903
Departamento de ​Mejora Genética Animal
https://doi.org/10.3389/fgene.2019.01170
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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