Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight

Detalhes bibliográficos
Autor(a) principal: Toro Ospina, Alejandra M. [UNESP]
Data de Publicação: 2019
Outros Autores: Maiorano, Amanda Marchi [UNESP], Curi, Rogerio A. [UNESP], Pereira, Guilherme L. [UNESP], Zerlotti-Mercadante, Maria Eugenia, Santos Goncalves Cyrillo, Joslaine Noely dos, Aspilcueta-Borquis, Rusbel R., Silva, Josineudson A. de V. [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1111/rda.13559
http://hdl.handle.net/11449/194895
Resumo: Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (N-e) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25-50 kb, 50-100 kb, 100-500 kb and 0.5-1 Mb. The N-e was estimated based on 5 past generations. The r(2) values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r(2) = .29). The N-e was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low N-e, which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.
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spelling Linkage disequilibrium and effective population size in Gir cattle selected for yearling weightBos indicusgenetic variabilitylinkage disequilibriumLinkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (N-e) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25-50 kb, 50-100 kb, 100-500 kb and 0.5-1 Mb. The N-e was estimated based on 5 past generations. The r(2) values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r(2) = .29). The N-e was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low N-e, which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Agence Universitaire de la Francophonie (PRISA)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Sao Paulo State Univ, Fac Agr & Vet Sci, Genet Anim Breeding, Jaboticabal, SP, BrazilSao Paulo State Univ, Fac Vet Med & Anim Sci, Dept Breeding & Anim Nutr, Botucatu, SP, BrazilInst Anim Sci, Ctr Beef Cattle, Sertaozinho, BrazilFed Univ Grande Dourados, Fac Agr Sci, Dourados, BrazilSao Paulo State Univ, Fac Agr & Vet Sci, Genet Anim Breeding, Jaboticabal, SP, BrazilSao Paulo State Univ, Fac Vet Med & Anim Sci, Dept Breeding & Anim Nutr, Botucatu, SP, BrazilFAPESP: 2015/06686-7Agence Universitaire de la Francophonie (PRISA): 1140/2018CNPq: 304047/2017-1Wiley-BlackwellUniversidade Estadual Paulista (Unesp)Inst Anim SciFed Univ Grande DouradosToro Ospina, Alejandra M. [UNESP]Maiorano, Amanda Marchi [UNESP]Curi, Rogerio A. [UNESP]Pereira, Guilherme L. [UNESP]Zerlotti-Mercadante, Maria EugeniaSantos Goncalves Cyrillo, Joslaine Noely dosAspilcueta-Borquis, Rusbel R.Silva, Josineudson A. de V. [UNESP]2020-12-10T16:57:59Z2020-12-10T16:57:59Z2019-10-13info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8http://dx.doi.org/10.1111/rda.13559Reproduction In Domestic Animals. Hoboken: Wiley, 8 p., 2019.0936-6768http://hdl.handle.net/11449/19489510.1111/rda.13559WOS:000489825200001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengReproduction In Domestic Animalsinfo:eu-repo/semantics/openAccess2021-10-23T00:00:20Zoai:repositorio.unesp.br:11449/194895Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-23T00:00:20Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
title Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
spellingShingle Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
Toro Ospina, Alejandra M. [UNESP]
Bos indicus
genetic variability
linkage disequilibrium
title_short Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
title_full Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
title_fullStr Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
title_full_unstemmed Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
title_sort Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight
author Toro Ospina, Alejandra M. [UNESP]
author_facet Toro Ospina, Alejandra M. [UNESP]
Maiorano, Amanda Marchi [UNESP]
Curi, Rogerio A. [UNESP]
Pereira, Guilherme L. [UNESP]
Zerlotti-Mercadante, Maria Eugenia
Santos Goncalves Cyrillo, Joslaine Noely dos
Aspilcueta-Borquis, Rusbel R.
Silva, Josineudson A. de V. [UNESP]
author_role author
author2 Maiorano, Amanda Marchi [UNESP]
Curi, Rogerio A. [UNESP]
Pereira, Guilherme L. [UNESP]
Zerlotti-Mercadante, Maria Eugenia
Santos Goncalves Cyrillo, Joslaine Noely dos
Aspilcueta-Borquis, Rusbel R.
Silva, Josineudson A. de V. [UNESP]
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Inst Anim Sci
Fed Univ Grande Dourados
dc.contributor.author.fl_str_mv Toro Ospina, Alejandra M. [UNESP]
Maiorano, Amanda Marchi [UNESP]
Curi, Rogerio A. [UNESP]
Pereira, Guilherme L. [UNESP]
Zerlotti-Mercadante, Maria Eugenia
Santos Goncalves Cyrillo, Joslaine Noely dos
Aspilcueta-Borquis, Rusbel R.
Silva, Josineudson A. de V. [UNESP]
dc.subject.por.fl_str_mv Bos indicus
genetic variability
linkage disequilibrium
topic Bos indicus
genetic variability
linkage disequilibrium
description Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (N-e) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25-50 kb, 50-100 kb, 100-500 kb and 0.5-1 Mb. The N-e was estimated based on 5 past generations. The r(2) values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r(2) = .29). The N-e was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low N-e, which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.
publishDate 2019
dc.date.none.fl_str_mv 2019-10-13
2020-12-10T16:57:59Z
2020-12-10T16:57:59Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1111/rda.13559
Reproduction In Domestic Animals. Hoboken: Wiley, 8 p., 2019.
0936-6768
http://hdl.handle.net/11449/194895
10.1111/rda.13559
WOS:000489825200001
url http://dx.doi.org/10.1111/rda.13559
http://hdl.handle.net/11449/194895
identifier_str_mv Reproduction In Domestic Animals. Hoboken: Wiley, 8 p., 2019.
0936-6768
10.1111/rda.13559
WOS:000489825200001
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Reproduction In Domestic Animals
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 8
dc.publisher.none.fl_str_mv Wiley-Blackwell
publisher.none.fl_str_mv Wiley-Blackwell
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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