Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins
International audience Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquacu...
Published in: | Evolutionary Applications |
---|---|
Main Authors: | , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2018
|
Subjects: | |
Online Access: | https://hal.inrae.fr/hal-02921349 https://hal.inrae.fr/hal-02921349/document https://hal.inrae.fr/hal-02921349/file/P31.Lopez-etal-EVA-2018.pdf https://doi.org/10.1111/eva.12689 |
id |
ftccsdartic:oai:HAL:hal-02921349v1 |
---|---|
record_format |
openpolar |
institution |
Open Polar |
collection |
Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
op_collection_id |
ftccsdartic |
language |
English |
topic |
selective sweeps single nucleotide polymorphisms Salmo salar [SDV.GEN]Life Sciences [q-bio]/Genetics |
spellingShingle |
selective sweeps single nucleotide polymorphisms Salmo salar [SDV.GEN]Life Sciences [q-bio]/Genetics López, Maria, Benestan, Laura Moore, Jean-Sébastien Perrier, Charles Gilbey, John Genova, Alex, Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
topic_facet |
selective sweeps single nucleotide polymorphisms Salmo salar [SDV.GEN]Life Sciences [q-bio]/Genetics |
description |
International audience Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps. |
author2 |
Universidad de Chile = University of Chile Santiago (UCHILE) Institut de Biologie Intégrative et des Systèmes Québec (IBIS) Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD France-Sud ) Marine Scotland Science (MSS) SOAFD Freshwater Fisheries Laboratory Faskally Center for Mathematical Modeling (CMM) Center for Genome Regulation Santiago (CGR) Aquainnovo Núcleo Milenio de Salmónidos Invasores (INVASAL) Financial support was provided by CORFO (11IEI-12843 and 12PIE17669). We are grateful to Doctoral scholarship from CONICYT (21120382), Government of Chile; Canada–Chile Leadership Exchange Scholarship program, Government of Canada. JMY is supported by Núcleo Milenio INVASAL funded by Chile’s government program, Iniciativa Científica Milenio from Ministerio de Economía, Fomento y Turismo. |
format |
Article in Journal/Newspaper |
author |
López, Maria, Benestan, Laura Moore, Jean-Sébastien Perrier, Charles Gilbey, John Genova, Alex, Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José |
author_facet |
López, Maria, Benestan, Laura Moore, Jean-Sébastien Perrier, Charles Gilbey, John Genova, Alex, Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José |
author_sort |
López, Maria, |
title |
Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_short |
Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_full |
Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_fullStr |
Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_full_unstemmed |
Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins |
title_sort |
comparing genomic signatures of domestication in two atlantic salmon (salmo salar l.) populations with different geographical origins |
publisher |
HAL CCSD |
publishDate |
2018 |
url |
https://hal.inrae.fr/hal-02921349 https://hal.inrae.fr/hal-02921349/document https://hal.inrae.fr/hal-02921349/file/P31.Lopez-etal-EVA-2018.pdf https://doi.org/10.1111/eva.12689 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
ISSN: 1752-4563 EISSN: 1752-4571 Evolutionary Applications https://hal.inrae.fr/hal-02921349 Evolutionary Applications, Blackwell, 2018, 12 (1), pp.137-156. ⟨10.1111/eva.12689⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/eva.12689 info:eu-repo/semantics/altIdentifier/pmid/30622641 hal-02921349 https://hal.inrae.fr/hal-02921349 https://hal.inrae.fr/hal-02921349/document https://hal.inrae.fr/hal-02921349/file/P31.Lopez-etal-EVA-2018.pdf doi:10.1111/eva.12689 WOS: 000454198200012 PUBMED: 30622641 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1111/eva.12689 |
container_title |
Evolutionary Applications |
container_volume |
12 |
container_issue |
1 |
container_start_page |
137 |
op_container_end_page |
156 |
_version_ |
1766362392292229120 |
spelling |
ftccsdartic:oai:HAL:hal-02921349v1 2023-05-15T15:31:54+02:00 Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins López, Maria, Benestan, Laura Moore, Jean-Sébastien Perrier, Charles Gilbey, John Genova, Alex, Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José Universidad de Chile = University of Chile Santiago (UCHILE) Institut de Biologie Intégrative et des Systèmes Québec (IBIS) Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD France-Sud ) Marine Scotland Science (MSS) SOAFD Freshwater Fisheries Laboratory Faskally Center for Mathematical Modeling (CMM) Center for Genome Regulation Santiago (CGR) Aquainnovo Núcleo Milenio de Salmónidos Invasores (INVASAL) Financial support was provided by CORFO (11IEI-12843 and 12PIE17669). We are grateful to Doctoral scholarship from CONICYT (21120382), Government of Chile; Canada–Chile Leadership Exchange Scholarship program, Government of Canada. JMY is supported by Núcleo Milenio INVASAL funded by Chile’s government program, Iniciativa Científica Milenio from Ministerio de Economía, Fomento y Turismo. 2018 https://hal.inrae.fr/hal-02921349 https://hal.inrae.fr/hal-02921349/document https://hal.inrae.fr/hal-02921349/file/P31.Lopez-etal-EVA-2018.pdf https://doi.org/10.1111/eva.12689 en eng HAL CCSD Blackwell info:eu-repo/semantics/altIdentifier/doi/10.1111/eva.12689 info:eu-repo/semantics/altIdentifier/pmid/30622641 hal-02921349 https://hal.inrae.fr/hal-02921349 https://hal.inrae.fr/hal-02921349/document https://hal.inrae.fr/hal-02921349/file/P31.Lopez-etal-EVA-2018.pdf doi:10.1111/eva.12689 WOS: 000454198200012 PUBMED: 30622641 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1752-4563 EISSN: 1752-4571 Evolutionary Applications https://hal.inrae.fr/hal-02921349 Evolutionary Applications, Blackwell, 2018, 12 (1), pp.137-156. ⟨10.1111/eva.12689⟩ selective sweeps single nucleotide polymorphisms Salmo salar [SDV.GEN]Life Sciences [q-bio]/Genetics info:eu-repo/semantics/article Journal articles 2018 ftccsdartic https://doi.org/10.1111/eva.12689 2021-11-21T00:39:24Z International audience Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps. Article in Journal/Newspaper Atlantic salmon Salmo salar Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Evolutionary Applications 12 1 137 156 |