New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2018.00053 http://hdl.handle.net/11449/170726 |
Resumo: | The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species. |
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New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip dataBubalus bubalisDomesticationEvolutionary historyGenomic diversityRiver buffaloSNPSwamp buffaloThe domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.Dipartimento di Scienze Animali della Nutrizione e degli Alimenti Università Cattolica del Sacro CuoreCentro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA)Department of Support Production and Animal Health School of Veterinary Medicine São Paulo State UniversityInternational Atomic Energy Agency (IAEA) Colaborating Centre on Animal Genomics and BioinformaticsPTP Science ParkLGS-AIA Associazione Italiana AllevatoriDipartimento di Scienze Biomediche Biotecnologiche e Traslazionali Università degli Studi di ParmaCell Biology Department Genetic Engineering and Biotechnology Research Division National Research CentrePhilippine Carabao CentreKey Laboratory of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education Huazhong Agricultural UniversityDepartment of Animal Husbandry Southwest UniversityInstitute of Animal Genetics and Breeding Sichuan Agricultural UniversityCollege of Veterinary Medicine Hunan Agricultural UniversityCollege of Animal Science Guizhou UniversityEnshi Technology CollegeDepartment of Animal Science Faculty of Agricultural Science Urmia UniversityCollege of Animal Science and Technology Yangzhou UniversityCollege of Life Science China Jiliang UniversityDepartment of Animal Genetics Faculty of Animal Science and Biotechnologies University of Agricultural Sciences and Veterinary MedicineDepartment of Agriculture University of Naples Federico IICOMSATS Institute of Information TechnologyDepartment of Animal Science Faculty of Agriculture Namik Kemal UniversitySchool of Biotechnology Suranaree University of TechnologyDepartment of Preventive Veterinary Medicine and Animal Reproduction School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp.)Faculdade de Medicina Veterinária e Zootecnia Universidade de São PauloInstituto de Biociências Letras e Ciências Exatas Universidade Estadual PaulistaRandD DepartmentCentre for Research and Conservation Royal Zoological Society of AntwerpIUCN SSC Asian Wild Cattle Specialist Group and Chester ZooRoyal (Dick) School of Veterinary Studies and The Roslin Institute University of EdinburghNRF/DST Centre of Excellence for Biomedical TB Research MRC Centre for TB Research and Division of Molecular Biology and Human Genetics Stellenbosch UniversityResearch Centre for Biotechnology Indonesian Institute of SciencesIndonesian Buffalo Conservation and Breeding CentreDepartment of Animal Production and Technology Bogor Agricultural University (IPB)Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia AgrariaDipartimento per l'Innovazione nei Sistemi Biologici Agroalimentari e Forestali DIBAF Università della TusciaThe Davies Research Centre School of Animal and Veterinary Science University of AdelaideDepartment of Support Production and Animal Health School of Veterinary Medicine São Paulo State UniversityDepartment of Preventive Veterinary Medicine and Animal Reproduction School of Agricultural and Veterinarian Sciences São Paulo State University (Unesp.)Instituto de Biociências Letras e Ciências Exatas Universidade Estadual PaulistaUniversità Cattolica del Sacro CuoreCentro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA)Universidade Estadual Paulista (Unesp)Colaborating Centre on Animal Genomics and BioinformaticsPTP Science ParkLGS-AIA Associazione Italiana AllevatoriUniversità degli Studi di ParmaNational Research CentrePhilippine Carabao CentreHuazhong Agricultural UniversitySouthwest UniversitySichuan Agricultural UniversityHunan Agricultural UniversityGuizhou UniversityEnshi Technology CollegeUrmia UniversityYangzhou UniversityChina Jiliang UniversityUniversity of Agricultural Sciences and Veterinary MedicineUniversity of Naples Federico IICOMSATS Institute of Information TechnologyNamik Kemal UniversitySuranaree University of TechnologyUniversidade de São Paulo (USP)RandD DepartmentRoyal Zoological Society of AntwerpIUCN SSC Asian Wild Cattle Specialist Group and Chester ZooUniversity of EdinburghStellenbosch UniversityIndonesian Institute of SciencesIndonesian Buffalo Conservation and Breeding CentreBogor Agricultural University (IPB)Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia AgrariaUniversità della TusciaUniversity of AdelaideColli, LiciaMilanesi, Marco [UNESP]Vajana, EliaIamartino, DanielaBomba, LorenzoPuglisi, FrancescoCorvo, Marcello DelNicolazzi, Ezequiel L.Ahmed, Sahar S.E.Herrera, Jesus R.V.Cruz, LibertadoZhang, ShujunLiang, AixinHua, GuohuaYang, LiguoHao, XingjieZuo, FuyuanLai, Song-JiaWang, ShuilianLiu, RuyuGong, YundengMokhber, MahdiMao, YongjiangGuan, FengVlaic, AugustinVlaic, BogdanRamunno, LuigiCosenza, GianfrancoAhmad, AliSoysal, IhsanÜnal, Emel Ö.Ketudat-Cairns, MarienaGarcia, José F. [UNESP]Utsunomiya, Yuri T. [UNESP]Baruselli, Pietro S.Amaral, Maria E.J. [UNESP]Parnpai, RangsunDrummond, Marcela G.Galbusera, PeterBurton, JamesHoal, EileenYusnizar, YulnawatiSumantri, CeceMoioli, BiancaValentini, AlessioStella, AlessandraWilliams, John L.Ajmone-Marsan, Paolo2018-12-11T16:52:11Z2018-12-11T16:52:11Z2018-03-02info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://dx.doi.org/10.3389/fgene.2018.00053Frontiers in Genetics, v. 9, n. MAR, 2018.1664-8021http://hdl.handle.net/11449/17072610.3389/fgene.2018.000532-s2.0-850427068952-s2.0-85042706895.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Genetics2,274info:eu-repo/semantics/openAccess2023-11-05T06:11:27Zoai:repositorio.unesp.br:11449/170726Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:59:11.624741Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
title |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
spellingShingle |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data Colli, Licia Bubalus bubalis Domestication Evolutionary history Genomic diversity River buffalo SNP Swamp buffalo |
title_short |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
title_full |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
title_fullStr |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
title_full_unstemmed |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
title_sort |
New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data |
author |
Colli, Licia |
author_facet |
Colli, Licia Milanesi, Marco [UNESP] Vajana, Elia Iamartino, Daniela Bomba, Lorenzo Puglisi, Francesco Corvo, Marcello Del Nicolazzi, Ezequiel L. Ahmed, Sahar S.E. Herrera, Jesus R.V. Cruz, Libertado Zhang, Shujun Liang, Aixin Hua, Guohua Yang, Liguo Hao, Xingjie Zuo, Fuyuan Lai, Song-Jia Wang, Shuilian Liu, Ruyu Gong, Yundeng Mokhber, Mahdi Mao, Yongjiang Guan, Feng Vlaic, Augustin Vlaic, Bogdan Ramunno, Luigi Cosenza, Gianfranco Ahmad, Ali Soysal, Ihsan Ünal, Emel Ö. Ketudat-Cairns, Mariena Garcia, José F. [UNESP] Utsunomiya, Yuri T. [UNESP] Baruselli, Pietro S. Amaral, Maria E.J. [UNESP] Parnpai, Rangsun Drummond, Marcela G. Galbusera, Peter Burton, James Hoal, Eileen Yusnizar, Yulnawati Sumantri, Cece Moioli, Bianca Valentini, Alessio Stella, Alessandra Williams, John L. Ajmone-Marsan, Paolo |
author_role |
author |
author2 |
Milanesi, Marco [UNESP] Vajana, Elia Iamartino, Daniela Bomba, Lorenzo Puglisi, Francesco Corvo, Marcello Del Nicolazzi, Ezequiel L. Ahmed, Sahar S.E. Herrera, Jesus R.V. Cruz, Libertado Zhang, Shujun Liang, Aixin Hua, Guohua Yang, Liguo Hao, Xingjie Zuo, Fuyuan Lai, Song-Jia Wang, Shuilian Liu, Ruyu Gong, Yundeng Mokhber, Mahdi Mao, Yongjiang Guan, Feng Vlaic, Augustin Vlaic, Bogdan Ramunno, Luigi Cosenza, Gianfranco Ahmad, Ali Soysal, Ihsan Ünal, Emel Ö. Ketudat-Cairns, Mariena Garcia, José F. [UNESP] Utsunomiya, Yuri T. [UNESP] Baruselli, Pietro S. Amaral, Maria E.J. [UNESP] Parnpai, Rangsun Drummond, Marcela G. Galbusera, Peter Burton, James Hoal, Eileen Yusnizar, Yulnawati Sumantri, Cece Moioli, Bianca Valentini, Alessio Stella, Alessandra Williams, John L. Ajmone-Marsan, Paolo |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Università Cattolica del Sacro Cuore Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA) Universidade Estadual Paulista (Unesp) Colaborating Centre on Animal Genomics and Bioinformatics PTP Science Park LGS-AIA Associazione Italiana Allevatori Università degli Studi di Parma National Research Centre Philippine Carabao Centre Huazhong Agricultural University Southwest University Sichuan Agricultural University Hunan Agricultural University Guizhou University Enshi Technology College Urmia University Yangzhou University China Jiliang University University of Agricultural Sciences and Veterinary Medicine University of Naples Federico II COMSATS Institute of Information Technology Namik Kemal University Suranaree University of Technology Universidade de São Paulo (USP) RandD Department Royal Zoological Society of Antwerp IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo University of Edinburgh Stellenbosch University Indonesian Institute of Sciences Indonesian Buffalo Conservation and Breeding Centre Bogor Agricultural University (IPB) Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Università della Tuscia University of Adelaide |
dc.contributor.author.fl_str_mv |
Colli, Licia Milanesi, Marco [UNESP] Vajana, Elia Iamartino, Daniela Bomba, Lorenzo Puglisi, Francesco Corvo, Marcello Del Nicolazzi, Ezequiel L. Ahmed, Sahar S.E. Herrera, Jesus R.V. Cruz, Libertado Zhang, Shujun Liang, Aixin Hua, Guohua Yang, Liguo Hao, Xingjie Zuo, Fuyuan Lai, Song-Jia Wang, Shuilian Liu, Ruyu Gong, Yundeng Mokhber, Mahdi Mao, Yongjiang Guan, Feng Vlaic, Augustin Vlaic, Bogdan Ramunno, Luigi Cosenza, Gianfranco Ahmad, Ali Soysal, Ihsan Ünal, Emel Ö. Ketudat-Cairns, Mariena Garcia, José F. [UNESP] Utsunomiya, Yuri T. [UNESP] Baruselli, Pietro S. Amaral, Maria E.J. [UNESP] Parnpai, Rangsun Drummond, Marcela G. Galbusera, Peter Burton, James Hoal, Eileen Yusnizar, Yulnawati Sumantri, Cece Moioli, Bianca Valentini, Alessio Stella, Alessandra Williams, John L. Ajmone-Marsan, Paolo |
dc.subject.por.fl_str_mv |
Bubalus bubalis Domestication Evolutionary history Genomic diversity River buffalo SNP Swamp buffalo |
topic |
Bubalus bubalis Domestication Evolutionary history Genomic diversity River buffalo SNP Swamp buffalo |
description |
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-12-11T16:52:11Z 2018-12-11T16:52:11Z 2018-03-02 |
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.2018.00053 Frontiers in Genetics, v. 9, n. MAR, 2018. 1664-8021 http://hdl.handle.net/11449/170726 10.3389/fgene.2018.00053 2-s2.0-85042706895 2-s2.0-85042706895.pdf |
url |
http://dx.doi.org/10.3389/fgene.2018.00053 http://hdl.handle.net/11449/170726 |
identifier_str_mv |
Frontiers in Genetics, v. 9, n. MAR, 2018. 1664-8021 10.3389/fgene.2018.00053 2-s2.0-85042706895 2-s2.0-85042706895.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Genetics 2,274 |
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info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
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UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
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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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1808128730630979584 |