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Signatures of selection and environmental adaptation across the goat genome post-domestication
BACKGROUND: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, appro...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240954/ https://www.ncbi.nlm.nih.gov/pubmed/30449276 http://dx.doi.org/10.1186/s12711-018-0421-y |
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author | Bertolini, Francesca Servin, Bertrand Talenti, Andrea Rochat, Estelle Kim, Eui Soo Oget, Claire Palhière, Isabelle Crisà, Alessandra Catillo, Gennaro Steri, Roberto Amills, Marcel Colli, Licia Marras, Gabriele Milanesi, Marco Nicolazzi, Ezequiel Rosen, Benjamin D. Van Tassell, Curtis P. Guldbrandtsen, Bernt Sonstegard, Tad S. Tosser-Klopp, Gwenola Stella, Alessandra Rothschild, Max F. Joost, Stéphane Crepaldi, Paola |
author_facet | Bertolini, Francesca Servin, Bertrand Talenti, Andrea Rochat, Estelle Kim, Eui Soo Oget, Claire Palhière, Isabelle Crisà, Alessandra Catillo, Gennaro Steri, Roberto Amills, Marcel Colli, Licia Marras, Gabriele Milanesi, Marco Nicolazzi, Ezequiel Rosen, Benjamin D. Van Tassell, Curtis P. Guldbrandtsen, Bernt Sonstegard, Tad S. Tosser-Klopp, Gwenola Stella, Alessandra Rothschild, Max F. Joost, Stéphane Crepaldi, Paola |
author_sort | Bertolini, Francesca |
collection | PubMed |
description | BACKGROUND: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12711-018-0421-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6240954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-62409542018-11-23 Signatures of selection and environmental adaptation across the goat genome post-domestication Bertolini, Francesca Servin, Bertrand Talenti, Andrea Rochat, Estelle Kim, Eui Soo Oget, Claire Palhière, Isabelle Crisà, Alessandra Catillo, Gennaro Steri, Roberto Amills, Marcel Colli, Licia Marras, Gabriele Milanesi, Marco Nicolazzi, Ezequiel Rosen, Benjamin D. Van Tassell, Curtis P. Guldbrandtsen, Bernt Sonstegard, Tad S. Tosser-Klopp, Gwenola Stella, Alessandra Rothschild, Max F. Joost, Stéphane Crepaldi, Paola Genet Sel Evol Research Article BACKGROUND: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12711-018-0421-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-11-19 /pmc/articles/PMC6240954/ /pubmed/30449276 http://dx.doi.org/10.1186/s12711-018-0421-y Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Bertolini, Francesca Servin, Bertrand Talenti, Andrea Rochat, Estelle Kim, Eui Soo Oget, Claire Palhière, Isabelle Crisà, Alessandra Catillo, Gennaro Steri, Roberto Amills, Marcel Colli, Licia Marras, Gabriele Milanesi, Marco Nicolazzi, Ezequiel Rosen, Benjamin D. Van Tassell, Curtis P. Guldbrandtsen, Bernt Sonstegard, Tad S. Tosser-Klopp, Gwenola Stella, Alessandra Rothschild, Max F. Joost, Stéphane Crepaldi, Paola Signatures of selection and environmental adaptation across the goat genome post-domestication |
title | Signatures of selection and environmental adaptation across the goat genome post-domestication |
title_full | Signatures of selection and environmental adaptation across the goat genome post-domestication |
title_fullStr | Signatures of selection and environmental adaptation across the goat genome post-domestication |
title_full_unstemmed | Signatures of selection and environmental adaptation across the goat genome post-domestication |
title_short | Signatures of selection and environmental adaptation across the goat genome post-domestication |
title_sort | signatures of selection and environmental adaptation across the goat genome post-domestication |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240954/ https://www.ncbi.nlm.nih.gov/pubmed/30449276 http://dx.doi.org/10.1186/s12711-018-0421-y |
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