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
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 Atl...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322405/ https://doi.org/10.1111/eva.12450 |
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ftpubmed:oai:pubmedcentral.nih.gov:5322405 2023-05-15T15:31:24+02:00 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 2016-12-29 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322405/ https://doi.org/10.1111/eva.12450 en eng John Wiley and Sons Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322405/ http://dx.doi.org/10.1111/eva.12450 © 2016 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. CC-BY Original Articles Text 2016 ftpubmed https://doi.org/10.1111/eva.12450 2017-03-05T01:28:12Z 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 (QTLs) 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. Text Atlantic salmon PubMed Central (PMC) Evolutionary Applications 10 3 276 296 |
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Original Articles |
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Original Articles 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 |
topic_facet |
Original Articles |
description |
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 (QTLs) 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. |
format |
Text |
author |
Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace |
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 |
John Wiley and Sons Inc. |
publishDate |
2016 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322405/ https://doi.org/10.1111/eva.12450 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322405/ http://dx.doi.org/10.1111/eva.12450 |
op_rights |
© 2016 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1111/eva.12450 |
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Evolutionary Applications |
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10 |
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3 |
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276 |
op_container_end_page |
296 |
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1766361903906422784 |