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

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 cosmopoli...

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Autores principales: Benjelloun, Badr, Alberto, Florian J., Streeter, Ian, Boyer, Frédéric, Coissac, Eric, Stucki, Sylvie, BenBati, Mohammed, Ibnelbachyr, Mustapha, Chentouf, Mouad, Bechchari, Abdelmajid, Leempoel, Kevin, Alberti, Adriana, Engelen, Stefan, Chikhi, Abdelkader, Clarke, Laura, Flicek, Paul, Joost, Stéphane, Taberlet, Pierre, Pompanon, François
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387958/
https://www.ncbi.nlm.nih.gov/pubmed/25904931
http://dx.doi.org/10.3389/fgene.2015.00107
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author Benjelloun, Badr
Alberto, Florian J.
Streeter, Ian
Boyer, Frédéric
Coissac, Eric
Stucki, Sylvie
BenBati, Mohammed
Ibnelbachyr, Mustapha
Chentouf, Mouad
Bechchari, Abdelmajid
Leempoel, Kevin
Alberti, Adriana
Engelen, Stefan
Chikhi, Abdelkader
Clarke, Laura
Flicek, Paul
Joost, Stéphane
Taberlet, Pierre
Pompanon, François
author_facet Benjelloun, Badr
Alberto, Florian J.
Streeter, Ian
Boyer, Frédéric
Coissac, Eric
Stucki, Sylvie
BenBati, Mohammed
Ibnelbachyr, Mustapha
Chentouf, Mouad
Bechchari, Abdelmajid
Leempoel, Kevin
Alberti, Adriana
Engelen, Stefan
Chikhi, Abdelkader
Clarke, Laura
Flicek, Paul
Joost, Stéphane
Taberlet, Pierre
Pompanon, François
author_sort Benjelloun, Badr
collection PubMed
description 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.
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spelling pubmed-43879582015-04-22 Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data Benjelloun, Badr Alberto, Florian J. Streeter, Ian Boyer, Frédéric Coissac, Eric Stucki, Sylvie BenBati, Mohammed Ibnelbachyr, Mustapha Chentouf, Mouad Bechchari, Abdelmajid Leempoel, Kevin Alberti, Adriana Engelen, Stefan Chikhi, Abdelkader Clarke, Laura Flicek, Paul Joost, Stéphane Taberlet, Pierre Pompanon, François Front Genet Genetics 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. Frontiers Media S.A. 2015-04-07 /pmc/articles/PMC4387958/ /pubmed/25904931 http://dx.doi.org/10.3389/fgene.2015.00107 Text en Copyright © 2015 Benjelloun, Alberto, Streeter, Boyer, Coissac, Stucki, BenBati, Ibnelbachyr, Chentouf, Bechchari, Leempoel, Alberti, Engelen, Chikhi, Clarke, Flicek, Joost, Taberlet, Pompanon and NextGen Consortium. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Benjelloun, Badr
Alberto, Florian J.
Streeter, Ian
Boyer, Frédéric
Coissac, Eric
Stucki, Sylvie
BenBati, Mohammed
Ibnelbachyr, Mustapha
Chentouf, Mouad
Bechchari, Abdelmajid
Leempoel, Kevin
Alberti, Adriana
Engelen, Stefan
Chikhi, Abdelkader
Clarke, Laura
Flicek, Paul
Joost, Stéphane
Taberlet, Pierre
Pompanon, François
Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title_full Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title_fullStr Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title_full_unstemmed Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title_short Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data
title_sort characterizing neutral genomic diversity and selection signatures in indigenous populations of moroccan goats (capra hircus) using wgs data
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387958/
https://www.ncbi.nlm.nih.gov/pubmed/25904931
http://dx.doi.org/10.3389/fgene.2015.00107
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