Comparing genomic signatures of domestication in two Atlantic salmon (
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 wa...
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Online Access: | https://doi.org/10.1111/eva.12689 https://pubmed.ncbi.nlm.nih.gov/30622641 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304691/ |
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ftpubmed:30622641 2024-05-12T08:01:19+00:00 Comparing genomic signatures of domestication in two Atlantic salmon ( López, Maria E Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M 2019 Jan https://doi.org/10.1111/eva.12689 https://pubmed.ncbi.nlm.nih.gov/30622641 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304691/ eng eng PubMed Central https://doi.org/10.1111/eva.12689 https://pubmed.ncbi.nlm.nih.gov/30622641 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304691/ Evol Appl ISSN:1752-4571 Volume:12 Issue:1 Salmo salar selective sweeps single nucleotide polymorphisms Journal Article 2019 ftpubmed https://doi.org/10.1111/eva.12689 2024-04-13T16:02:00Z 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 PubMed Central (PMC) Evolutionary Applications 12 1 137 156 |
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PubMed Central (PMC) |
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language |
English |
topic |
Salmo salar selective sweeps single nucleotide polymorphisms |
spellingShingle |
Salmo salar selective sweeps single nucleotide polymorphisms López, Maria E Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M Comparing genomic signatures of domestication in two Atlantic salmon ( |
topic_facet |
Salmo salar selective sweeps single nucleotide polymorphisms |
description |
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. |
format |
Article in Journal/Newspaper |
author |
López, Maria E Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M |
author_facet |
López, Maria E Benestan, Laura Moore, Jean-Sebastien Perrier, Charles Gilbey, John Di Genova, Alex Maass, Alejandro Diaz, Diego Lhorente, Jean-Paul Correa, Katharina Neira, Roberto Bernatchez, Louis Yáñez, José M |
author_sort |
López, Maria E |
title |
Comparing genomic signatures of domestication in two Atlantic salmon ( |
title_short |
Comparing genomic signatures of domestication in two Atlantic salmon ( |
title_full |
Comparing genomic signatures of domestication in two Atlantic salmon ( |
title_fullStr |
Comparing genomic signatures of domestication in two Atlantic salmon ( |
title_full_unstemmed |
Comparing genomic signatures of domestication in two Atlantic salmon ( |
title_sort |
comparing genomic signatures of domestication in two atlantic salmon ( |
publisher |
PubMed Central |
publishDate |
2019 |
url |
https://doi.org/10.1111/eva.12689 https://pubmed.ncbi.nlm.nih.gov/30622641 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304691/ |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Evol Appl ISSN:1752-4571 Volume:12 Issue:1 |
op_relation |
https://doi.org/10.1111/eva.12689 https://pubmed.ncbi.nlm.nih.gov/30622641 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304691/ |
op_doi |
https://doi.org/10.1111/eva.12689 |
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Evolutionary Applications |
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12 |
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1 |
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137 |
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156 |
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