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...
Main Authors: | , , , , , , |
---|---|
Language: | unknown |
Published: |
2016
|
Subjects: | |
Online Access: | http://nbn-resolving.org/urn:nbn:nl:ui:13-nc-k5n4 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:96291 |
id |
ftdans:oai:easy.dans.knaw.nl:easy-dataset:96291 |
---|---|
record_format |
openpolar |
spelling |
ftdans:oai:easy.dans.knaw.nl:easy-dataset:96291 2023-07-02T03:31:42+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 2016-11-22T16:56:43.000+01:00 http://nbn-resolving.org/urn:nbn:nl:ui:13-nc-k5n4 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:96291 unknown doi:10.5061/dryad.53b58/1 doi:10.1111/eva.12450 http://nbn-resolving.org/urn:nbn:nl:ui:13-nc-k5n4 doi:10.5061/dryad.53b58 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:96291 OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf Life sciences medicine and health care 2016 ftdans https://doi.org/10.5061/dryad.53b58/110.1111/eva.1245010.5061/dryad.53b58 2023-06-13T13:23:59Z 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. Other/Unknown Material Atlantic salmon Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) |
institution |
Open Polar |
collection |
Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) |
op_collection_id |
ftdans |
language |
unknown |
topic |
Life sciences medicine and health care |
spellingShingle |
Life sciences medicine and health care 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 |
Life sciences medicine and health care |
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. |
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://nbn-resolving.org/urn:nbn:nl:ui:13-nc-k5n4 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:96291 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
doi:10.5061/dryad.53b58/1 doi:10.1111/eva.12450 http://nbn-resolving.org/urn:nbn:nl:ui:13-nc-k5n4 doi:10.5061/dryad.53b58 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:96291 |
op_rights |
OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf |
op_doi |
https://doi.org/10.5061/dryad.53b58/110.1111/eva.1245010.5061/dryad.53b58 |
_version_ |
1770271085864943616 |