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Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed

Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajec...

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Autores principales: Boitard, Simon, Paris, Cyriel, Sevane, Natalia, Servin, Bertrand, Bazi-Kabbaj, Kenza, Dunner, Susana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901938/
https://www.ncbi.nlm.nih.gov/pubmed/33633776
http://dx.doi.org/10.3389/fgene.2021.575405
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author Boitard, Simon
Paris, Cyriel
Sevane, Natalia
Servin, Bertrand
Bazi-Kabbaj, Kenza
Dunner, Susana
author_facet Boitard, Simon
Paris, Cyriel
Sevane, Natalia
Servin, Bertrand
Bazi-Kabbaj, Kenza
Dunner, Susana
author_sort Boitard, Simon
collection PubMed
description Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity.
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spelling pubmed-79019382021-02-24 Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed Boitard, Simon Paris, Cyriel Sevane, Natalia Servin, Bertrand Bazi-Kabbaj, Kenza Dunner, Susana Front Genet Genetics Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity. Frontiers Media S.A. 2021-02-02 /pmc/articles/PMC7901938/ /pubmed/33633776 http://dx.doi.org/10.3389/fgene.2021.575405 Text en Copyright © 2021 Boitard, Paris, Sevane, Servin, Bazi-Kabbaj and Dunner. 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) and the copyright owner(s) 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
Boitard, Simon
Paris, Cyriel
Sevane, Natalia
Servin, Bertrand
Bazi-Kabbaj, Kenza
Dunner, Susana
Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title_full Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title_fullStr Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title_full_unstemmed Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title_short Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed
title_sort gene banks as reservoirs to detect recent selection: the example of the asturiana de los valles bovine breed
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901938/
https://www.ncbi.nlm.nih.gov/pubmed/33633776
http://dx.doi.org/10.3389/fgene.2021.575405
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