A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits
Abstract Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North Ame...
Published in: | Evolutionary Applications |
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Online Access: | http://dx.doi.org/10.1111/eva.12450 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12450 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12450 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.12450 |
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crwiley:10.1111/eva.12450 2024-09-15T17:56:11+00:00 A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace Genome Canada Natural Sciences and Engineering Research Council of Canada 2016 http://dx.doi.org/10.1111/eva.12450 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12450 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12450 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.12450 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Evolutionary Applications volume 10, issue 3, page 276-296 ISSN 1752-4571 1752-4571 journal-article 2016 crwiley https://doi.org/10.1111/eva.12450 2024-08-09T04:30:11Z Abstract Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci ( QTL s) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL . We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection. Article in Journal/Newspaper Atlantic salmon Wiley Online Library Evolutionary Applications 10 3 276 296 |
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Open Polar |
collection |
Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci ( QTL s) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL . We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection. |
author2 |
Genome Canada Natural Sciences and Engineering Research Council of Canada |
format |
Article in Journal/Newspaper |
author |
Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace |
spellingShingle |
Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
author_facet |
Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace |
author_sort |
Liu, Lei |
title |
A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
title_short |
A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
title_full |
A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
title_fullStr |
A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
title_full_unstemmed |
A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
title_sort |
genome scan for selection signatures comparing farmed atlantic salmon with two wild populations: testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits |
publisher |
Wiley |
publishDate |
2016 |
url |
http://dx.doi.org/10.1111/eva.12450 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12450 https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12450 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.12450 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Evolutionary Applications volume 10, issue 3, page 276-296 ISSN 1752-4571 1752-4571 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/eva.12450 |
container_title |
Evolutionary Applications |
container_volume |
10 |
container_issue |
3 |
container_start_page |
276 |
op_container_end_page |
296 |
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1810432400972316672 |