Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2018.00737 http://hdl.handle.net/11449/184279 |
Resumo: | Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of Sao Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix AxiomR (R) 600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments. |
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Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditionschickensenvironmentselection signaturesadaptationimmune systemExtreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of Sao Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix AxiomR (R) 600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments.Ensminger Endowment, State of IowaUSDA-NIFAAFRI Climate Change AwardHatch fundingIowa State Univ, Dept Anim Sci, Ames, IA 50011 USAUniv Peradeniya, Dept Anim Sci, Fac Agr, Kandy, Sri LankaSao Paulo State Univ, Dept Anim Sci, Coll Agr & Vet Sci, Jaboticabal, BrazilAnim Prod Res Inst, Dept Anim Biotechnol, Giza, EgyptUniv Delaware, Anim & Food Sci, Newark, DE USASao Paulo State Univ, Dept Anim Sci, Coll Agr & Vet Sci, Jaboticabal, BrazilUSDA-NIFAAFRI Climate Change Award: 2011-67003-30228Frontiers Media SaIowa State UnivUniv PeradeniyaUniversidade Estadual Paulista (Unesp)Anim Prod Res InstUniv DelawareWalugembe, MuhammedBertolini, FrancescaDematawewa, Chandraratne Mahinda B.Reis, Matheus P. [UNESP]Elbeltagy, Ahmed R.Schmidt, Carl J.Lamont, Susan J.Rothschild, Max F.2019-10-04T11:56:24Z2019-10-04T11:56:24Z2019-01-14info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13http://dx.doi.org/10.3389/fgene.2018.00737Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 13 p., 2019.1664-8021http://hdl.handle.net/11449/18427910.3389/fgene.2018.00737WOS:000455670100001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers In Geneticsinfo:eu-repo/semantics/openAccess2021-10-22T19:39:21Zoai:repositorio.unesp.br:11449/184279Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-22T19:39:21Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
title |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
spellingShingle |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions Walugembe, Muhammed chickens environment selection signatures adaptation immune system |
title_short |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
title_full |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
title_fullStr |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
title_full_unstemmed |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
title_sort |
Detection of Selection Signatures Among Brazilian, Sri Lankan, and Egyptian Chicken Populations Under Different Environmental Conditions |
author |
Walugembe, Muhammed |
author_facet |
Walugembe, Muhammed Bertolini, Francesca Dematawewa, Chandraratne Mahinda B. Reis, Matheus P. [UNESP] Elbeltagy, Ahmed R. Schmidt, Carl J. Lamont, Susan J. Rothschild, Max F. |
author_role |
author |
author2 |
Bertolini, Francesca Dematawewa, Chandraratne Mahinda B. Reis, Matheus P. [UNESP] Elbeltagy, Ahmed R. Schmidt, Carl J. Lamont, Susan J. Rothschild, Max F. |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Iowa State Univ Univ Peradeniya Universidade Estadual Paulista (Unesp) Anim Prod Res Inst Univ Delaware |
dc.contributor.author.fl_str_mv |
Walugembe, Muhammed Bertolini, Francesca Dematawewa, Chandraratne Mahinda B. Reis, Matheus P. [UNESP] Elbeltagy, Ahmed R. Schmidt, Carl J. Lamont, Susan J. Rothschild, Max F. |
dc.subject.por.fl_str_mv |
chickens environment selection signatures adaptation immune system |
topic |
chickens environment selection signatures adaptation immune system |
description |
Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal's immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt = Arid) and in non-indigenous chickens that derived from human migration events to the generally tropical State of Sao Paulo, Brazil. To do so, analyses were conducted using fixation index (Fst) and hapFLK analyses. Chickens from Brazil (n = 156), Sri Lanka (n = 92), and Egypt (n = 96) were genotyped using the Affymetrix AxiomR (R) 600k Chicken Genotyping Array. Pairwise Fst analyses among countries did not detect major regions of divergence between chickens from Sri Lanka and Brazil, with ecotypes/breeds from Brazil appearing to be genetically related to Asian-Indian (Sri Lanka) ecotypes. However, several differences were detected in comparisons of Egyptian with either Sri Lankan or Brazilian populations, and common regions of difference on chromosomes 2, 3 and 8 were detected. The hapFLK analyses for the three separate countries suggested unique regions that are potentially under selection on chromosome 1 for all three countries, on chromosome 4 for Sri Lankan, and on chromosomes 3, 5, and 11 for the Egyptian populations. Some of identified regions under selection with hapFLK analyses contained genes such as TLR3, SOCS2, EOMES, and NFAT5 whose biological functions could provide insights in understanding adaptation mechanisms in response to arid and tropical environments. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-04T11:56:24Z 2019-10-04T11:56:24Z 2019-01-14 |
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.2018.00737 Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 13 p., 2019. 1664-8021 http://hdl.handle.net/11449/184279 10.3389/fgene.2018.00737 WOS:000455670100001 |
url |
http://dx.doi.org/10.3389/fgene.2018.00737 http://hdl.handle.net/11449/184279 |
identifier_str_mv |
Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 9, 13 p., 2019. 1664-8021 10.3389/fgene.2018.00737 WOS:000455670100001 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers In Genetics |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
13 |
dc.publisher.none.fl_str_mv |
Frontiers Media Sa |
publisher.none.fl_str_mv |
Frontiers Media Sa |
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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1803047195208843264 |