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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Online Access: | https://doi.org/10.5061/dryad.53b58 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::67dc701fc3005e9590c4deb64a93598d 2023-05-15T15:31:06+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 2016-01-01 https://doi.org/10.5061/dryad.53b58 undefined unknown http://dx.doi.org/10.5061/dryad.53b58 https://dx.doi.org/10.5061/dryad.53b58 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:96291 10.5061/dryad.53b58 oai:easy.dans.knaw.nl:easy-dataset:96291 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture Population Genetics - Empirical quantitative genetics Adaptation Bay of Fundy envir anthro-se Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2016 fttriple https://doi.org/10.5061/dryad.53b58 2023-01-22T16:52:13Z 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_textraw 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. Dataset Atlantic salmon Salmo salar Unknown Canada |
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Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture Population Genetics - Empirical quantitative genetics Adaptation Bay of Fundy envir anthro-se |
spellingShingle |
Life sciences medicine and health care Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture Population Genetics - Empirical quantitative genetics Adaptation Bay of Fundy envir anthro-se 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 Captive Populations Genomics/Proteomics Salmo salar Contemporary Evolution Aquaculture Population Genetics - Empirical quantitative genetics Adaptation Bay of Fundy envir anthro-se |
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_textraw 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 |
Dataset |
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 |
https://doi.org/10.5061/dryad.53b58 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:96291 10.5061/dryad.53b58 oai:easy.dans.knaw.nl:easy-dataset:96291 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.53b58 https://dx.doi.org/10.5061/dryad.53b58 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.53b58 |
_version_ |
1766361586572722176 |