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 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.

Fig. 1

Geographical distribution of the 1159 sampled Capra individuals included in the dataset. The geographical origin of each sequenced animal is indicated both for the country (exterior circle) and the continent (interior circle). For each location, the number of sequenced individuals and their percentage in the overall dataset is indicated

Fig. 2

Analysis of the AdaptMap samples. a Concordance rates of the 457 AdaptMap individuals with 50 K chip and sequence data calculated on the basis of 44,691 common SNPs. b PCA to ascertain the breed of outlier animals

Fig. 3

Geographic distribution of European breeds. Breeds are represented by three letters corresponding to the breed code (see Additional file 1: Table S1). If a breed is present in multiple countries, the breed code is followed by the country code (2 letters). Each combination of color and symbol corresponds to domestic goats in a single country. Wild goats are identified with a specific color and symbol

Fig. 4

Geographic distribution of African breeds. Breeds are represented by three letters corresponding to the breed code (see Additional file 1: Table S1). If a breed is present in multiple countries, the breed code is followed by the country code (2 letters). Each combination of color and symbol corresponds to domestic goats in a single country

Fig. 5

Geographic distribution of Asian and Oceanian breeds. Breeds are represented by three letters corresponding to the breed code (see Additional file 1: Table S1). If a breed is present in multiple countries, the breed code is followed by the country code (2 letters). Each combination of color and symbol corresponds to domestic goats in a single country. Wild goats are identified with a specific color and symbol

Fig. 6

Neighbor-joining tree representing the genetic diversity of domestic goat populations analysed in the context of the VarGoats project. The three-letter breed code (see Additional file 1: Table S1) is used, followed by the two-letter country code if needed. Colors allow the identification of geographical origin