Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Badr Benjelloun,Florian J Alberto,Pierre Taberlet,Stã©Phane Joost,Stefan Engelen,Eric Coissac,Mohammed Benbati,Laura Clarke,Abdelkader Chikhi,Sylvie Stucki,Abdelmajid Bechchari,Adriana Alberti,Frã©Dã©Ric Boyer,Paul Flicek,Mustapha Ibnelbachyr,Kevin Leempoel,Mouad Chentouf,Franã§Ois Pompanon,Ian Streeter

doi:10.3389/fgene.2015.00107

Abstract

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

Highlights

Livestock species play a major socio-economic role in the world since they provide many goods and services to human populations
In an alternative complementary approach, the 481 bp length sequenced of the hyper variable segment (HVI) segment of the control region was extracted, and this revealed 64 polymorphic sites identifying 40 single haplotypes
The whole genome data and the wide geographic spread of animals allowed for a precise characterization of the distribution of genomic diversity in various populations

Summary

Introduction

Livestock species play a major socio-economic role in the world since they provide many goods and services to human populations. Following human migrations and trade routes, goats rapidly spread over the rest of the world, mainly in Eurasia and Africa (Taberlet et al, 2008; Tresset and Vigne, 2011) During this expansion, they became adapted to different climatic conditions and husbandry practices. Since mid-1900s, industrial breeding has become more widespread, backed by the progress of husbandry practices including the introduction of artificial insemination, embryo transfer, the improvements in feed technology and the use of vaccines and therapeutics against endemic diseases This has led breeders to progressively substitute the many locally-adapted indigenous breeds for very few highly productive cosmopolitan ones for short-term economic reasons (Taberlet et al, 2008). A part of the highly valuable genetic resources captured from the wilds and gradually accumulated over 98% of their common history with humans is threatened (Taberlet et al, 2008)

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