VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity
Abstract Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the conseque...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2021-11-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-021-00659-6 |
| _version_ | 1819002997917614080 |
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| author | Laure Denoyelle Estelle Talouarn Philippe Bardou Licia Colli Adriana Alberti Coralie Danchin Marcello Del Corvo Stéfan Engelen Céline Orvain Isabelle Palhière Rachel Rupp Julien Sarry Mazdak Salavati Marcel Amills Emily Clark Paola Crepaldi Thomas Faraut Clet Wandui Masiga François Pompanon Benjamin D. Rosen Alessandra Stella Curtis P. Van Tassell Gwenola Tosser-Klopp The VarGoats Consortium |
| author_facet | Laure Denoyelle Estelle Talouarn Philippe Bardou Licia Colli Adriana Alberti Coralie Danchin Marcello Del Corvo Stéfan Engelen Céline Orvain Isabelle Palhière Rachel Rupp Julien Sarry Mazdak Salavati Marcel Amills Emily Clark Paola Crepaldi Thomas Faraut Clet Wandui Masiga François Pompanon Benjamin D. Rosen Alessandra Stella Curtis P. Van Tassell Gwenola Tosser-Klopp The VarGoats Consortium |
| author_sort | Laure Denoyelle |
| collection | DOAJ |
| description | Abstract Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies. |
| first_indexed | 2024-12-20T23:14:00Z |
| format | Article |
| id | doaj.art-eba4a13e89084fd49785587ca3dcf7cf |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-12-20T23:14:00Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-eba4a13e89084fd49785587ca3dcf7cf2022-12-21T19:23:40ZdeuBMCGenetics Selection Evolution1297-96862021-11-0153111410.1186/s12711-021-00659-6VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversityLaure Denoyelle0Estelle Talouarn1Philippe Bardou2Licia Colli3Adriana Alberti4Coralie Danchin5Marcello Del Corvo6Stéfan Engelen7Céline Orvain8Isabelle Palhière9Rachel Rupp10Julien Sarry11Mazdak Salavati12Marcel Amills13Emily Clark14Paola Crepaldi15Thomas Faraut16Clet Wandui Masiga17François Pompanon18Benjamin D. Rosen19Alessandra Stella20Curtis P. Van Tassell21Gwenola Tosser-Klopp22The VarGoats ConsortiumGenPhySE, Université de Toulouse, INRAE, ENVTGenPhySE, Université de Toulouse, INRAE, ENVTGenPhySE, Université de Toulouse, INRAE, ENVTDipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro CuoreGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayInstitut de L’Elevage, Maison Nationale Des EleveursDipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti, BioDNA Centro Di Ricerca Sulla Biodiversità E Sul DNA Antico, Facoltà Di Scienze Agrarie, Alimentari E Ambientali, Università Cattolica del Sacro CuoreGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayGénomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-SaclayGenPhySE, Université de Toulouse, INRAE, ENVTGenPhySE, Université de Toulouse, INRAE, ENVTGenPhySE, Université de Toulouse, INRAE, ENVTThe Roslin Institute and R(D)SVS, University of EdinburghCentre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de BarcelonaThe Roslin Institute and R(D)SVS, University of EdinburghDepth. Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanGenPhySE, Université de Toulouse, INRAE, ENVTTropical Institute of Development Innovations (TRIDI)Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECAAnimal Genomics and Improvement Laboratory, BARC, USDA-ARSIstituto Di Biologia E Biotecnologia Agraria, Consiglio Nazionale Delle RicercheAnimal Genomics and Improvement Laboratory, BARC, USDA-ARSGenPhySE, Université de Toulouse, INRAE, ENVTAbstract Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies.https://doi.org/10.1186/s12711-021-00659-6 |
| spellingShingle | Laure Denoyelle Estelle Talouarn Philippe Bardou Licia Colli Adriana Alberti Coralie Danchin Marcello Del Corvo Stéfan Engelen Céline Orvain Isabelle Palhière Rachel Rupp Julien Sarry Mazdak Salavati Marcel Amills Emily Clark Paola Crepaldi Thomas Faraut Clet Wandui Masiga François Pompanon Benjamin D. Rosen Alessandra Stella Curtis P. Van Tassell Gwenola Tosser-Klopp The VarGoats Consortium VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity Genetics Selection Evolution |
| title | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity |
| title_full | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity |
| title_fullStr | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity |
| title_full_unstemmed | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity |
| title_short | VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity |
| title_sort | vargoats project a dataset of 1159 whole genome sequences to dissect capra hircus global diversity |
| url | https://doi.org/10.1186/s12711-021-00659-6 |
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