Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for mu...
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ftdans:oai:easy.dans.knaw.nl:easy-dataset:118713 2023-07-02T03:31:42+02:00 Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria Primmer, Craig 2016-10-11T14:11:29.000+02:00 http://nbn-resolving.org/urn:nbn:nl:ui:13-n2-07w9 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:118713 unknown doi:10.5061/dryad.g0870.1/1.1 doi:10.1111/jfb.13149 PMID:27709620 http://nbn-resolving.org/urn:nbn:nl:ui:13-n2-07w9 doi:10.5061/dryad.g0870.1 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:118713 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.g0870.1/1.110.1111/jfb.1314910.5061/dryad.g0870.1 2023-06-13T13:34:29Z A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species. Other/Unknown Material Atlantic salmon Salmo salar Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) Teno ENVELOPE(25.690,25.690,68.925,68.925) |
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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 Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria Primmer, Craig Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
topic_facet |
Life sciences medicine and health care |
description |
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species. |
author |
Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria Primmer, Craig |
author_facet |
Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria Primmer, Craig |
author_sort |
Aykanat, Tutku |
title |
Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
title_short |
Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
title_full |
Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
title_fullStr |
Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
title_full_unstemmed |
Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar |
title_sort |
data from: from population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in atlantic salmon salmo salar |
publishDate |
2016 |
url |
http://nbn-resolving.org/urn:nbn:nl:ui:13-n2-07w9 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:118713 |
long_lat |
ENVELOPE(25.690,25.690,68.925,68.925) |
geographic |
Teno |
geographic_facet |
Teno |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
doi:10.5061/dryad.g0870.1/1.1 doi:10.1111/jfb.13149 PMID:27709620 http://nbn-resolving.org/urn:nbn:nl:ui:13-n2-07w9 doi:10.5061/dryad.g0870.1 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:118713 |
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.g0870.1/1.110.1111/jfb.1314910.5061/dryad.g0870.1 |
_version_ |
1770271081920200704 |