Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2015.00005 http://hdl.handle.net/11449/131308 |
Resumo: | The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation. |
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Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypesBos indicusCattleDisease resistanceFertilityRuns of homozygositySelectionThe use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation.Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia.Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria.Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.Bioinformatics and Animal Genomics Laboratory, Embrapa Dairy Cattle Juiz de Fora, Minas Gerais, Brazil.Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil.Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.GenSys Consultores Associados Porto Alegre, Rio Grande do Sul, Brazil ; Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil.Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista Jaboticabal, São Paulo, Brazil ; Laboratório de Bioquímica e Biologia Molecular Animal, Departamento de Apoio, Produção e Saúde Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Araçatuba, São Paulo, Brazil.Frontiers In GeneticsUniversidade Estadual Paulista (Unesp)Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia.Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria.Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Zavarez, Ludmilla B. [UNESP]Utsunomiya, Yuri T. [UNESP]Carmo, Adriana S. [UNESP]Neves, Haroldo H. R. [UNESP]Carvalheiro, Roberto [UNESP]Ferenčaković, MajaPérez O'Brien, Ana M.Curik, InoCole, John B.Van Tassell, Curtis P.Silva, Marcos V. G. B. daSonstegard, Tad S.Sölkner, JohannGarcia, José F. [UNESP]2015-12-07T15:33:42Z2015-12-07T15:33:42Z2015info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article5application/pdfhttp://dx.doi.org/10.3389/fgene.2015.00005Frontiers In Genetics, v. 6, p. 5, 2015.1664-8021http://hdl.handle.net/11449/13130810.3389/fgene.2015.00005PMC4310349.pdf25688258PMC4310349PubMedreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers In Genetics4.1512,274info:eu-repo/semantics/openAccess2023-11-11T06:08:41Zoai:repositorio.unesp.br:11449/131308Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-11-11T06:08:41Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
title |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
spellingShingle |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes Zavarez, Ludmilla B. [UNESP] Bos indicus Cattle Disease resistance Fertility Runs of homozygosity Selection |
title_short |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
title_full |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
title_fullStr |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
title_full_unstemmed |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
title_sort |
Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes |
author |
Zavarez, Ludmilla B. [UNESP] |
author_facet |
Zavarez, Ludmilla B. [UNESP] Utsunomiya, Yuri T. [UNESP] Carmo, Adriana S. [UNESP] Neves, Haroldo H. R. [UNESP] Carvalheiro, Roberto [UNESP] Ferenčaković, Maja Pérez O'Brien, Ana M. Curik, Ino Cole, John B. Van Tassell, Curtis P. Silva, Marcos V. G. B. da Sonstegard, Tad S. Sölkner, Johann Garcia, José F. [UNESP] |
author_role |
author |
author2 |
Utsunomiya, Yuri T. [UNESP] Carmo, Adriana S. [UNESP] Neves, Haroldo H. R. [UNESP] Carvalheiro, Roberto [UNESP] Ferenčaković, Maja Pérez O'Brien, Ana M. Curik, Ino Cole, John B. Van Tassell, Curtis P. Silva, Marcos V. G. B. da Sonstegard, Tad S. Sölkner, Johann Garcia, José F. [UNESP] |
author2_role |
author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Department of Animal Science, Faculty of Agriculture, University of Zagreb Zagreb, Croatia. Division of Livestock Sciences, Department of Sustainable Agricultural Systems, BOKU - University of Natural Resources and Life Sciences Vienna, Austria. Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) |
dc.contributor.author.fl_str_mv |
Zavarez, Ludmilla B. [UNESP] Utsunomiya, Yuri T. [UNESP] Carmo, Adriana S. [UNESP] Neves, Haroldo H. R. [UNESP] Carvalheiro, Roberto [UNESP] Ferenčaković, Maja Pérez O'Brien, Ana M. Curik, Ino Cole, John B. Van Tassell, Curtis P. Silva, Marcos V. G. B. da Sonstegard, Tad S. Sölkner, Johann Garcia, José F. [UNESP] |
dc.subject.por.fl_str_mv |
Bos indicus Cattle Disease resistance Fertility Runs of homozygosity Selection |
topic |
Bos indicus Cattle Disease resistance Fertility Runs of homozygosity Selection |
description |
The use of relatively low numbers of sires in cattle breeding programs, particularly on those for carcass and weight traits in Nellore beef cattle (Bos indicus) in Brazil, has always raised concerns about inbreeding, which affects conservation of genetic resources and sustainability of this breed. Here, we investigated the distribution of autozygosity levels based on runs of homozygosity (ROH) in a sample of 1,278 Nellore cows, genotyped for over 777,000 SNPs. We found ROH segments larger than 10 Mb in over 70% of the samples, representing signatures most likely related to the recent massive use of few sires. However, the average genome coverage by ROH (>1 Mb) was lower than previously reported for other cattle breeds (4.58%). In spite of 99.98% of the SNPs being included within a ROH in at least one individual, only 19.37% of the markers were encompassed by common ROH, suggesting that the ongoing selection for weight, carcass and reproductive traits in this population is too recent to have produced selection signatures in the form of ROH. Three short-range highly prevalent ROH autosomal hotspots (occurring in over 50% of the samples) were observed, indicating candidate regions most likely under selection since before the foundation of Brazilian Nellore cattle. The putative signatures of selection on chromosomes 4, 7, and 12 may be involved in resistance to infectious diseases and fertility, and should be subject of future investigation. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015-12-07T15:33:42Z 2015-12-07T15:33:42Z 2015 |
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/10.3389/fgene.2015.00005 Frontiers In Genetics, v. 6, p. 5, 2015. 1664-8021 http://hdl.handle.net/11449/131308 10.3389/fgene.2015.00005 PMC4310349.pdf 25688258 PMC4310349 |
url |
http://dx.doi.org/10.3389/fgene.2015.00005 http://hdl.handle.net/11449/131308 |
identifier_str_mv |
Frontiers In Genetics, v. 6, p. 5, 2015. 1664-8021 10.3389/fgene.2015.00005 PMC4310349.pdf 25688258 PMC4310349 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers In Genetics 4.151 2,274 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
5 application/pdf |
dc.publisher.none.fl_str_mv |
Frontiers In Genetics |
publisher.none.fl_str_mv |
Frontiers In Genetics |
dc.source.none.fl_str_mv |
PubMed 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 |
|
_version_ |
1799964890522189824 |