TY - JOUR
T1 - VarGoats project
T2 - a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity
AU - Denoyelle, Laure
AU - Talouarn, Estelle
AU - Bardou, Philippe
AU - Colli, Licia
AU - Alberti, Adriana
AU - Danchin, Coralie
AU - Del Corvo, Marcello
AU - Engelen, Stéfan
AU - Orvain, Céline
AU - Palhière, Isabelle
AU - Rupp, Rachel
AU - Sarry, Julien
AU - Salavati, Mazdak
AU - Amills, Marcel
AU - Clark, Emily
AU - Crepaldi, Paola
AU - Faraut, Thomas
AU - Masiga, Clet Wandui
AU - Pompanon, François
AU - Rosen, Benjamin D.
AU - Stella, Alessandra
AU - Van Tassell, Curtis P.
AU - Tosser-Klopp, Gwenola
AU - Kijas, James
AU - Guldbrandtsen, Bernt
AU - Kantanen, Juha
AU - Duby, Dylan
AU - Martin, Pierre
AU - Danchin, Coralie
AU - Duclos, Delphine
AU - Allain, Daniel
AU - Arquet, Rémy
AU - Mandonnet, Nathalie
AU - Naves, Michel
AU - Palhière, Isabelle
AU - Rupp, Rachel
AU - Pompanon, François
AU - Pompanon, François
AU - Carolan, Sean
AU - Foran, Maeve
AU - Ajmone-Marsan, Paolo
AU - Colli, Licia
AU - Crisà, Alessandra
AU - Marletta, Donata
AU - Crepaldi, Paola
AU - Ottino, Michele
AU - Randi, Ettore
AU - Benjelloun, Badr
AU - Lenstra, Hans
AU - Moaeen-ud-Din, Muhammad
AU - Reecy, Jim
AU - Goyache, Felix
AU - Alvarez, Isabel
AU - Amills, Marcel
AU - Amills, Marcel
AU - Capote, Juan
AU - Jordana, Jordi
AU - Pons, Agueda
AU - Martínez, Amparo
AU - Molina, Antonio
AU - Rosen, Benjamin
AU - Rosen, Benjamin
AU - Drögemüller, Cord
AU - Luikart, Gordon
AU - Masiga, Clet Wandui
AU - Masiga, Clet Wandui
AU - Mruttu, Hassan Ally
AU - Gondwe, Timothy
AU - Sikosana, Joseph
AU - Taela, Maria Da Gloria
AU - Nash, Oyekan
AU - The VarGoats Consortium
N1 - © 2021. The Author(s).
PY - 2021/11/8
Y1 - 2021/11/8
N2 - 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.
AB - 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.
KW - Animals
KW - Domestication
KW - Genetic Variation
KW - Genome
KW - Genome-Wide Association Study
KW - Genomics
KW - Goats/genetics
UR - http://www.scopus.com/inward/record.url?scp=85121651836&partnerID=8YFLogxK
U2 - 10.1186/s12711-021-00659-6
DO - 10.1186/s12711-021-00659-6
M3 - Short communication
C2 - 34749642
AN - SCOPUS:85121651836
SN - 0999-193X
VL - 53
JO - Genetics Selection Evolution
JF - Genetics Selection Evolution
IS - 1
M1 - 86
ER -