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. 2019 Feb;50(1):54-63.
doi: 10.1111/age.12752. Epub 2018 Dec 13.

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

C Oget  1 , B Servin  1 , I Palhière  1
Affiliations

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation

C Oget et al. Anim Genet. 2019 Feb.

Abstract

After domestication 11 000 years ago in Asia Minor, the goat followed human migration to Europe and Asia. It was then introduced in Africa and is now raised all over the world. In this study, we exploited a dataset composed of 54 000 SNPs (Illumina goat DNA chip) to analyze the genetic diversity of 223 individuals belonging to eight French breeds (Alpine, Angora, Corse, Fossés, Poitevine, Provençale, Pyrénées and Saanen). Analyses carried out included individual-based approaches (principal component analysis and population structure) and population-based approaches (phylogenetic tree constructions). The results of the genetic diversity analyses revealed that French breeds are clearly differentiated, in particular, the Angora breed that originates from south west Asia. The Provençale breed shows a very original genetic pattern that could be the result of ancient admixture. Then, selection signatures were detected by identifying regions of outlying genetic differentiation between populations. Five genomic regions were detected under selection on chromosomes 5, 6, 11, 13 and 20, revealing mainly soft selective sweeps and a few hard selective sweeps and highlighting candidate genes that had been selected for during the evolutionary history of these breeds. Among them, two coat coloration genes (ADAMTS20 and ASIP) and one gene related to milk composition (CSN1S1) were involved.

Keywords: Capra hircus; SNP; caprine; diversity; evolutionary history; selection signature.

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Figures

Figure 1
Figure 1
Representation of the first and second components of the principal component analysis. Breed abbreviations are given in Table 1.
Figure 2
Figure 2
Bayesian clustering performed with admixture software on genotyping data of the selected animals. Assignment of each individual (vertical bars) to different clusters (colors) when K = 8 hypothetical populations are assumed. Breed abbreviations are given in Table 1.
Figure 3
Figure 3
Maximum likelihood tree of the selected animals with Iranian goat (IRA) and Bezoar ibex (BEZ) populations and one unknown admixture event inferred. Breed abbreviations are given in Table 1.
Figure 4
Figure 4
Genome scan for selection signature in six French breeds genotyped. Color change represents transition from one chromosome to the next.
See this image and copyright information in PMC

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