Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain

Autores
Mouresan, Elena Flavia; González Rodríguez, Aldemar; Cañas Álvarez, Jhon Jacobo; Munilla Leguizamon, Sebastian; Altarriba, Juan; Díaz, Clara; Baró, Jesús A.; Molina, Antonio; Lopez-Buesa, Pascual; Piedrafita, Jesús; Varona, Luis
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fil: Mouresan, Elena Flavia. Universidad de Zaragoza; España
Fil: González Rodríguez, Aldemar. Universidad de Zaragoza; España
Fil: Cañas Álvarez, Jhon Jacobo. Universitat Autònoma de Barcelona; España
Fil: Munilla Leguizamon, Sebastian. Universidad de Zaragoza; España. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; Argentina
Fil: Altarriba, Juan. Universidad de Zaragoza; España
Fil: Díaz, Clara. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria; España
Fil: Baró, Jesús A.. Instituto Agroalimentario de Aragón; España
Fil: Molina, Antonio. Universidad de Valladolid; España
Fil: Lopez-Buesa, Pascual. Universidad de Zaragoza; España
Fil: Piedrafita, Jesús. Universitat Autònoma de Barcelona; España
Fil: Varona, Luis. Universidad de Zaragoza; España
Materia
BEEF CATTLE
GENE ONTOLOGY
LINKAGE DISEQUILIBRIUM
MULTIPLE POPULATIONS
RECOMBINATION RATE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/128670
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/128670
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in SpainMouresan, Elena FlaviaGonzález Rodríguez, AldemarCañas Álvarez, Jhon JacoboMunilla Leguizamon, SebastianAltarriba, JuanDíaz, ClaraBaró, Jesús A.Molina, AntonioLopez-Buesa, PascualPiedrafita, JesúsVarona, LuisBEEF CATTLEGENE ONTOLOGYLINKAGE DISEQUILIBRIUMMULTIPLE POPULATIONSRECOMBINATION RATEhttps://purl.org/becyt/ford/4.2https://purl.org/becyt/ford/4In 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.Fil: Mouresan, Elena Flavia. Universidad de Zaragoza; EspañaFil: González Rodríguez, Aldemar. Universidad de Zaragoza; EspañaFil: Cañas Álvarez, Jhon Jacobo. Universitat Autònoma de Barcelona; EspañaFil: Munilla Leguizamon, Sebastian. Universidad de Zaragoza; España. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; ArgentinaFil: Altarriba, Juan. Universidad de Zaragoza; EspañaFil: Díaz, Clara. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria; EspañaFil: Baró, Jesús A.. Instituto Agroalimentario de Aragón; EspañaFil: Molina, Antonio. Universidad de Valladolid; EspañaFil: Lopez-Buesa, Pascual. Universidad de Zaragoza; EspañaFil: Piedrafita, Jesús. Universitat Autònoma de Barcelona; EspañaFil: Varona, Luis. Universidad de Zaragoza; EspañaFrontiers Media S.A.2019-11-20info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/128670Mouresan, Elena Flavia; González Rodríguez, Aldemar; Cañas Álvarez, Jhon Jacobo; Munilla Leguizamon, Sebastian; Altarriba, Juan; et al.; Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain; Frontiers Media S.A.; Frontiers in Genetics; 10; 1170; 20-11-2019; 1-121664-8021CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.3389/fgene.2019.01170info:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fgene.2019.01170/fullinfo:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880760/info:eu-repo/semantics/altIdentifier/url/https://pubmed.ncbi.nlm.nih.gov/31824571/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:37:27Zoai:ri.conicet.gov.ar:11336/128670instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:37:28.241CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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, Elena Flavia
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, Elena Flavia
González Rodríguez, Aldemar
Cañas Álvarez, Jhon Jacobo
Munilla Leguizamon, Sebastian
Altarriba, Juan
Díaz, Clara
Baró, Jesús A.
Molina, Antonio
Lopez-Buesa, Pascual
Piedrafita, Jesús
Varona, Luis
author Mouresan, Elena Flavia
author_facet Mouresan, Elena Flavia
González Rodríguez, Aldemar
Cañas Álvarez, Jhon Jacobo
Munilla Leguizamon, Sebastian
Altarriba, Juan
Díaz, Clara
Baró, Jesús A.
Molina, Antonio
Lopez-Buesa, Pascual
Piedrafita, Jesús
Varona, Luis
author_role author
author2 González Rodríguez, Aldemar
Cañas Álvarez, Jhon Jacobo
Munilla Leguizamon, Sebastian
Altarriba, Juan
Díaz, Clara
Baró, Jesús A.
Molina, Antonio
Lopez-Buesa, Pascual
Piedrafita, Jesús
Varona, Luis
author2_role author
author
author
author
author
author
author
author
author
author
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
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.2
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv 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.
Fil: Mouresan, Elena Flavia. Universidad de Zaragoza; España
Fil: González Rodríguez, Aldemar. Universidad de Zaragoza; España
Fil: Cañas Álvarez, Jhon Jacobo. Universitat Autònoma de Barcelona; España
Fil: Munilla Leguizamon, Sebastian. Universidad de Zaragoza; España. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario; Argentina
Fil: Altarriba, Juan. Universidad de Zaragoza; España
Fil: Díaz, Clara. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria; España
Fil: Baró, Jesús A.. Instituto Agroalimentario de Aragón; España
Fil: Molina, Antonio. Universidad de Valladolid; España
Fil: Lopez-Buesa, Pascual. Universidad de Zaragoza; España
Fil: Piedrafita, Jesús. Universitat Autònoma de Barcelona; España
Fil: Varona, Luis. Universidad de Zaragoza; España
description 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.
publishDate 2019
dc.date.none.fl_str_mv 2019-11-20
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/128670
Mouresan, Elena Flavia; González Rodríguez, Aldemar; Cañas Álvarez, Jhon Jacobo; Munilla Leguizamon, Sebastian; Altarriba, Juan; et al.; Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain; Frontiers Media S.A.; Frontiers in Genetics; 10; 1170; 20-11-2019; 1-12
1664-8021
CONICET Digital
CONICET
url http://hdl.handle.net/11336/128670
identifier_str_mv Mouresan, Elena Flavia; González Rodríguez, Aldemar; Cañas Álvarez, Jhon Jacobo; Munilla Leguizamon, Sebastian; Altarriba, Juan; et al.; Mapping recombination rate on the autosomal chromosomes based on the persistency of linkage disequilibrium phase among autochthonous beef cattle populations in Spain; Frontiers Media S.A.; Frontiers in Genetics; 10; 1170; 20-11-2019; 1-12
1664-8021
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.3389/fgene.2019.01170
info:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fgene.2019.01170/full
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6880760/
info:eu-repo/semantics/altIdentifier/url/https://pubmed.ncbi.nlm.nih.gov/31824571/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Frontiers Media S.A.
publisher.none.fl_str_mv Frontiers Media S.A.
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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