title: Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.
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.
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France ; National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research Beni-Mellal, Morocco.
authors.forename: Badr
authors.initials: B
authors.lastname: Benjelloun
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France.
authors.forename: Florian J
authors.initials: FJ
authors.lastname: Alberto
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Streeter
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Stucki
authors.affiliation: National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research Beni-Mellal, Morocco.
authors.forename: Mohammed
authors.initials: M
authors.lastname: BenBati
authors.affiliation: Regional Centre of Agronomic Research Errachidia, National Institute of Agronomic Research (INRA Maroc) Errachidia, Morocco.
authors.forename: Mustapha
authors.initials: M
authors.lastname: Ibnelbachyr
authors.affiliation: Regional Centre of Agronomic Research Tangier, National Institute of Agronomic Research (INRA Maroc) Tangier, Morocco.
authors.forename: Mouad
authors.initials: M
authors.lastname: Chentouf
authors.affiliation: Regional Centre of Agronomic Research Oujda, National Institute of Agronomic Research (INRA Maroc) Oujda, Morocco.
authors.forename: Abdelmajid
authors.initials: A
authors.lastname: Bechchari
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Kevin
authors.initials: K
authors.lastname: Leempoel
authors.affiliation: Centre National de Séquençage, CEA-Institut de Génomique Genoscope, Évry, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: Centre National de Séquençage, CEA-Institut de Génomique Genoscope, Évry, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Engelen
authors.affiliation: Regional Centre of Agronomic Research Errachidia, National Institute of Agronomic Research (INRA Maroc) Errachidia, Morocco.
authors.forename: Abdelkader
authors.initials: A
authors.lastname: Chikhi
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK.
authors.forename: Laura
authors.initials: L
authors.lastname: Clarke
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute Hinxton, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne Lausanne, Switzerland.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Joost
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble-Alpes Grenoble, France ; Laboratoire d'Ecologie Alpine, Centre National de la Recherche Scientifique Grenoble, France.
authors.forename: François
authors.initials: F
authors.lastname: Pompanon
keywords: Capra hircus; Morocco; WGS; genomic diversity; indigenous populations; population genomics; selection signatures