Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Detalhes bibliográficos
Autor(a) principal: Porto-Neto, Laercio R.
Data de Publicação: 2013
Outros Autores: Sonstegard, Tad S., Liu, George E., Bickhart, Derek M., Da Silva, Marcos V. B., Machado, Marco A., Utsunomiya, Yuri T. [UNESP], Garcia, José Fernando [UNESP], Gondro, Cedric, Van Tassell, Curtis P.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1186/1471-2164-14-876
http://hdl.handle.net/11449/111550
Resumo: Background: Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F-ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.Results: Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F-ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F-ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:similar to 50 Mb and BTA14:similar to 25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F-ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:similar to 24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.Conclusions: Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.
id UNSP_1df7ec3c018065e6ba6fcaf6f4867c23
oai_identifier_str oai:repositorio.unesp.br:11449/111550
network_acronym_str UNSP
network_name_str Repositório Institucional da UNESP
repository_id_str 2946
spelling Genomic divergence of zebu and taurine cattle identified through high-density SNP genotypingBosTaurusIndicusFSTSelectionSpeciationBackground: Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F-ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.Results: Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F-ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F-ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:similar to 50 Mb and BTA14:similar to 25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F-ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:similar to 24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.Conclusions: Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.Next-Generation BioGreen 21 Program, Rural Development Administration, Republic of KoreaFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)USDA Agricultural Research ServiceNational Research Initiative Competitive Grant from the USDA National Institute of Food and AgricultureUniv Queensland, Sch Vet Sci, Anim Genet Lab, Gatton, Qld 4343, AustraliaUniv New England, Sch Environm & Rural Sci, Armidale, NSW 2351, AustraliaARS, USDA, Bovine Funct Genom Lab, Beltsville, MD 20705 USAUniv Estadual Paulista, UNESP, Aracatuba, SP, BrazilEmbrapa Dairy Cattle, Bioinformat & Anim Genom Lab, Juiz De Fora, MG, BrazilUniv Estadual Paulista, UNESP, Aracatuba, SP, BrazilNext-Generation BioGreen 21 Program, Rural Development Administration, Republic of KoreaPJ008196FAPESP: 10/52030-2CNPq: 475914/2010-4USDA Agricultural Research Service1265-31000-104-00DNational Research Initiative Competitive Grant from the USDA National Institute of Food and Agriculture2008-35205-18846Biomed Central Ltd.Univ QueenslandUniv New EnglandARSUniversidade Estadual Paulista (Unesp)Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Porto-Neto, Laercio R.Sonstegard, Tad S.Liu, George E.Bickhart, Derek M.Da Silva, Marcos V. B.Machado, Marco A.Utsunomiya, Yuri T. [UNESP]Garcia, José Fernando [UNESP]Gondro, CedricVan Tassell, Curtis P.2014-12-03T13:08:45Z2014-12-03T13:08:45Z2013-12-13info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://dx.doi.org/10.1186/1471-2164-14-876Bmc Genomics. London: Biomed Central Ltd, v. 14, 12 p., 2013.1471-2164http://hdl.handle.net/11449/11155010.1186/1471-2164-14-876WOS:000328649800001WOS000328649800001.pdf9991374083045897Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBMC Genomics3.7302,110info:eu-repo/semantics/openAccess2024-09-04T19:14:58Zoai:repositorio.unesp.br:11449/111550Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462024-09-04T19:14:58Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
title Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
spellingShingle Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
Porto-Neto, Laercio R.
Bos
Taurus
Indicus
FST
Selection
Speciation
title_short Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
title_full Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
title_fullStr Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
title_full_unstemmed Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
title_sort Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
author Porto-Neto, Laercio R.
author_facet Porto-Neto, Laercio R.
Sonstegard, Tad S.
Liu, George E.
Bickhart, Derek M.
Da Silva, Marcos V. B.
Machado, Marco A.
Utsunomiya, Yuri T. [UNESP]
Garcia, José Fernando [UNESP]
Gondro, Cedric
Van Tassell, Curtis P.
author_role author
author2 Sonstegard, Tad S.
Liu, George E.
Bickhart, Derek M.
Da Silva, Marcos V. B.
Machado, Marco A.
Utsunomiya, Yuri T. [UNESP]
Garcia, José Fernando [UNESP]
Gondro, Cedric
Van Tassell, Curtis P.
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Univ Queensland
Univ New England
ARS
Universidade Estadual Paulista (Unesp)
Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.contributor.author.fl_str_mv Porto-Neto, Laercio R.
Sonstegard, Tad S.
Liu, George E.
Bickhart, Derek M.
Da Silva, Marcos V. B.
Machado, Marco A.
Utsunomiya, Yuri T. [UNESP]
Garcia, José Fernando [UNESP]
Gondro, Cedric
Van Tassell, Curtis P.
dc.subject.por.fl_str_mv Bos
Taurus
Indicus
FST
Selection
Speciation
topic Bos
Taurus
Indicus
FST
Selection
Speciation
description Background: Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos taurus taurus more adapted to temperate climates and the tropically adapted Bos taurus indicus. After domestication, human selection exponentially intensified these differences. To better understand the genetic differences between these subspecies and detect genomic regions potentially under divergent selection, animals from the International Bovine HapMap Experiment were genotyped for over 770,000 SNP across the genome and compared using smoothed F-ST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds.Results: Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal components analyses and unsupervised clustering confirmed the well-characterized main division of domestic cattle. The top 1% smoothed F-ST, potentially associated to positive selection, contained 48 genomic regions across 17 chromosomes. Nearly half of the top F-ST signals (n = 22) were previously detected using a lower density SNP assay. Amongst the strongest signals were the BTA7:similar to 50 Mb and BTA14:similar to 25 Mb; both regions harboring candidate genes and different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. The bottom 1% of the smoothed F-ST values, potentially associated to balancing selection, included 24 regions across 13 chromosomes. These regions often overlap with copy number variants, including the highly variable region at BTA23:similar to 24 Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated with a significant overrepresentation of immune related pathways.Conclusions: Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.
publishDate 2013
dc.date.none.fl_str_mv 2013-12-13
2014-12-03T13:08:45Z
2014-12-03T13:08:45Z
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/10.1186/1471-2164-14-876
Bmc Genomics. London: Biomed Central Ltd, v. 14, 12 p., 2013.
1471-2164
http://hdl.handle.net/11449/111550
10.1186/1471-2164-14-876
WOS:000328649800001
WOS000328649800001.pdf
9991374083045897
url http://dx.doi.org/10.1186/1471-2164-14-876
http://hdl.handle.net/11449/111550
identifier_str_mv Bmc Genomics. London: Biomed Central Ltd, v. 14, 12 p., 2013.
1471-2164
10.1186/1471-2164-14-876
WOS:000328649800001
WOS000328649800001.pdf
9991374083045897
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv BMC Genomics
3.730
2,110
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12
application/pdf
dc.publisher.none.fl_str_mv Biomed Central Ltd.
publisher.none.fl_str_mv Biomed Central Ltd.
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 repositoriounesp@unesp.br
_version_ 1810021364531200000