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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ftzenodo:oai:zenodo.org:4983993 2024-09-15T17:56:03+00:00 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 2016-11-22 https://doi.org/10.5061/dryad.53b58 unknown Zenodo https://doi.org/10.1111/eva.12450 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.53b58 oai:zenodo.org:4983993 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture info:eu-repo/semantics/other 2016 ftzenodo https://doi.org/10.5061/dryad.53b5810.1111/eva.12450 2024-07-26T16:19:20Z 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. TOB VS STW populations_text raw dataset with 3980 SNP genotypes for two wild Atlantic salmon populations from the Tobique River and the Stewiacke River in the Bay of Fundy, Canada. Other/Unknown Material Atlantic salmon Salmo salar Zenodo |
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Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture |
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Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture 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 |
Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture |
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. TOB VS STW populations_text raw dataset with 3980 SNP genotypes for two wild Atlantic salmon populations from the Tobique River and the Stewiacke River in the Bay of Fundy, Canada. |
format |
Other/Unknown Material |
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 |
publisher |
Zenodo |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.53b58 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
https://doi.org/10.1111/eva.12450 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.53b58 oai:zenodo.org:4983993 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.53b5810.1111/eva.12450 |
_version_ |
1810432271029633024 |