VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity.

Denoyelle, Laure; Talouarn, Estelle; Bardou, Philippe; Colli, Licia; Alberti, Adriana; Danchin, Coralie; Del Corvo, Marcello; Engelen, Stéfan; Orvain, Céline; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Salavati, Mazdak; Amills, Marcel; Clark, Emily; Crepaldi, Paola; Faraut, Thomas; Masiga, Clet Wandui; Pompanon, François; Rosen, Benjamin D; ... (2021). VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity. Genetics, selection, evolution, 53(1), p. 86. BioMed Central 10.1186/s12711-021-00659-6

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 610 Medicine & health
600 Technology > 630 Agriculture

ISSN:

1297-9686

Publisher:

BioMed Central

Language:

English

Submitter:

Cord Drögemüller

Date Deposited:

18 Nov 2021 09:34

Last Modified:

21 Nov 2021 01:48

Publisher DOI:

10.1186/s12711-021-00659-6

PubMed ID:

34749642

Additional Information:

Member of The VarGoats Consortium: Cord Drögemüller

BORIS DOI:

10.48350/161220

URI:

https://boris.unibe.ch/id/eprint/161220

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