Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs 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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ftdryad:oai:v1.datadryad.org:10255/dryad.131811 2023-05-15T15:31:31+02:00 Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace Bay of Fundy 2016-11-22T15:56:43Z http://hdl.handle.net/10255/dryad.131811 https://doi.org/10.5061/dryad.53b58 unknown doi:10.5061/dryad.53b58/1 doi:10.1111/eva.12450 doi:10.5061/dryad.53b58 Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG (2017) 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. Evolutionary Applications 10(3): 276–296. 1752-4571 http://hdl.handle.net/10255/dryad.131811 Aquaculture Contemporary Evolution Population Genetics - Empirical Quantitative Genetics Adaptation Captive Populations Genomics/Proteomics Article 2016 ftdryad https://doi.org/10.5061/dryad.53b58 https://doi.org/10.5061/dryad.53b58/1 https://doi.org/10.1111/eva.12450 2020-01-01T15:43:29Z 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, 3 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, non-founder 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 Dryad Digital Repository (Duke University) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Aquaculture Contemporary Evolution Population Genetics - Empirical Quantitative Genetics Adaptation Captive Populations Genomics/Proteomics |
spellingShingle |
Aquaculture Contemporary Evolution Population Genetics - Empirical Quantitative Genetics Adaptation Captive Populations Genomics/Proteomics Liu, Lei Ang, Keng Pee Elliott, J. A. K. Kent, Matthew Peter Lien, Sigbjørn MacDonald, Danielle Boulding, Elizabeth Grace Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
topic_facet |
Aquaculture Contemporary Evolution Population Genetics - Empirical Quantitative Genetics Adaptation Captive Populations Genomics/Proteomics |
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, 3 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, non-founder 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 |
Article in Journal/Newspaper |
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 |
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
title_short |
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
title_full |
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
title_fullStr |
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
title_full_unstemmed |
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits |
title_sort |
data from: a genome scan for selection signatures comparing farmed atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and qtls for production traits |
publishDate |
2016 |
url |
http://hdl.handle.net/10255/dryad.131811 https://doi.org/10.5061/dryad.53b58 |
op_coverage |
Bay of Fundy |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
doi:10.5061/dryad.53b58/1 doi:10.1111/eva.12450 doi:10.5061/dryad.53b58 Liu L, Ang KP, Elliott JAK, Kent MP, Lien S, MacDonald D, Boulding EG (2017) 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. Evolutionary Applications 10(3): 276–296. 1752-4571 http://hdl.handle.net/10255/dryad.131811 |
op_doi |
https://doi.org/10.5061/dryad.53b58 https://doi.org/10.5061/dryad.53b58/1 https://doi.org/10.1111/eva.12450 |
_version_ |
1766362043998273536 |