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...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | DE EN FR |
| Publicado: |
BMC
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/eba4a13e89084fd49785587ca3dcf7cf |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:eba4a13e89084fd49785587ca3dcf7cf |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:eba4a13e89084fd49785587ca3dcf7cf2021-11-14T12:28:38ZVarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity10.1186/s12711-021-00659-61297-9686https://doaj.org/article/eba4a13e89084fd49785587ca3dcf7cf2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12711-021-00659-6https://doaj.org/toc/1297-9686Abstract 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.Laure DenoyelleEstelle TalouarnPhilippe BardouLicia ColliAdriana AlbertiCoralie DanchinMarcello Del CorvoStéfan EngelenCéline OrvainIsabelle PalhièreRachel RuppJulien SarryMazdak SalavatiMarcel AmillsEmily ClarkPaola CrepaldiThomas FarautClet Wandui MasigaFrançois PompanonBenjamin D. RosenAlessandra StellaCurtis P. Van TassellGwenola Tosser-KloppThe VarGoats ConsortiumBMCarticleAnimal cultureSF1-1100GeneticsQH426-470DEENFRGenetics Selection Evolution, Vol 53, Iss 1, Pp 1-14 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
DE EN FR |
| topic |
Animal culture SF1-1100 Genetics QH426-470 |
| spellingShingle |
Animal culture SF1-1100 Genetics QH426-470 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 |
| 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. |
| format |
article |
| 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 |
| title |
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_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_sort |
vargoats project: a dataset of 1159 whole-genome sequences to dissect capra hircus global diversity |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/eba4a13e89084fd49785587ca3dcf7cf |
| work_keys_str_mv |
AT lauredenoyelle vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT estelletalouarn vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT philippebardou vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT liciacolli vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT adrianaalberti vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT coraliedanchin vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT marcellodelcorvo vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT stefanengelen vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT celineorvain vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT isabellepalhiere vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT rachelrupp vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT juliensarry vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT mazdaksalavati vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT marcelamills vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT emilyclark vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT paolacrepaldi vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT thomasfaraut vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT cletwanduimasiga vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT francoispompanon vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT benjamindrosen vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT alessandrastella vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT curtispvantassell vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT gwenolatosserklopp vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity AT thevargoatsconsortium vargoatsprojectadatasetof1159wholegenomesequencestodissectcaprahircusglobaldiversity |
| _version_ |
1718429202330419200 |