Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle
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.2019.00442 http://hdl.handle.net/11449/184512 |
Resumo: | Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N'Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N'Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance. |
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Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu CattleAfrican Bos taurusMHCdisease resistanceheat tolerancecomparative genomicsLike most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N'Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N'Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.Livestock CGIAR - CRPNational Biotechnology Development Agency (NABDA), NigeriaUniv Nottingham, Cells Organisms & Mol Genet, Sch Life Sci, Univ Pk Campus, Nottingham, EnglandNatl Biotechnol Dev Agcy, Ctr Genom Res & Innovat, Abuja, NigeriaInt Livestock Res Inst, Addis Ababa, EthiopiaSao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, Sao Paulo, BrazilUniv Nigeria, Fac Agr, Dept Anim Sci, Nsukka, NigeriaSao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, Sao Paulo, BrazilFrontiers Media SaUniv NottinghamNatl Biotechnol Dev AgcyInt Livestock Res InstUniversidade Estadual Paulista (Unesp)Univ NigeriaTijjani, AbdulfataiUtsunomiya, Yuri Tani [UNESP]Ezekwe, Arinze G.Nashiru, OyekanmiHanotte, Olivier2019-10-04T12:14:13Z2019-10-04T12:14:13Z2019-06-04info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article18http://dx.doi.org/10.3389/fgene.2019.00442Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 10, 18 p., 2019.1664-8021http://hdl.handle.net/11449/18451210.3389/fgene.2019.00442WOS:000470237100001Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers In Geneticsinfo:eu-repo/semantics/openAccess2021-10-23T04:16:27Zoai:repositorio.unesp.br:11449/184512Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T19:50:59.292934Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
title |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
spellingShingle |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle Tijjani, Abdulfatai African Bos taurus MHC disease resistance heat tolerance comparative genomics |
title_short |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
title_full |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
title_fullStr |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
title_full_unstemmed |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
title_sort |
Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle |
author |
Tijjani, Abdulfatai |
author_facet |
Tijjani, Abdulfatai Utsunomiya, Yuri Tani [UNESP] Ezekwe, Arinze G. Nashiru, Oyekanmi Hanotte, Olivier |
author_role |
author |
author2 |
Utsunomiya, Yuri Tani [UNESP] Ezekwe, Arinze G. Nashiru, Oyekanmi Hanotte, Olivier |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Univ Nottingham Natl Biotechnol Dev Agcy Int Livestock Res Inst Universidade Estadual Paulista (Unesp) Univ Nigeria |
dc.contributor.author.fl_str_mv |
Tijjani, Abdulfatai Utsunomiya, Yuri Tani [UNESP] Ezekwe, Arinze G. Nashiru, Oyekanmi Hanotte, Olivier |
dc.subject.por.fl_str_mv |
African Bos taurus MHC disease resistance heat tolerance comparative genomics |
topic |
African Bos taurus MHC disease resistance heat tolerance comparative genomics |
description |
Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N'Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N'Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-04T12:14:13Z 2019-10-04T12:14:13Z 2019-06-04 |
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.2019.00442 Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 10, 18 p., 2019. 1664-8021 http://hdl.handle.net/11449/184512 10.3389/fgene.2019.00442 WOS:000470237100001 |
url |
http://dx.doi.org/10.3389/fgene.2019.00442 http://hdl.handle.net/11449/184512 |
identifier_str_mv |
Frontiers In Genetics. Lausanne: Frontiers Media Sa, v. 10, 18 p., 2019. 1664-8021 10.3389/fgene.2019.00442 WOS:000470237100001 |
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 |
18 |
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 |
|
_version_ |
1808129128317059072 |