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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ftdryad:oai:v1.datadryad.org:10255/dryad.132277 2023-05-15T15:31:22+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 L. Primmer, Craig R. Finland 2016-11-28T16:31:48Z http://hdl.handle.net/10255/dryad.126101 http://hdl.handle.net/10255/dryad.132277 https://doi.org/10.5061/dryad.g0870.2 unknown doi:10.5061/dryad.g0870.2/1.2 doi:10.1111/jfb.13149 PMID:27709620 doi:10.5061/dryad.g0870.2 Aykanat T, Lindqvist M, Pritchard VL, Primmer CR (2016) From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. Journal of Fish Biology 89(6): 2658-2679. http://hdl.handle.net/10255/dryad.126101 http://hdl.handle.net/10255/dryad.132277 diagnostic SNPs genotyping by sequencing multiplex primer design sea age at maturity Article 2016 ftdryad https://doi.org/10.5061/dryad.g0870.2 https://doi.org/10.5061/dryad.g0870.2/1.2 https://doi.org/10.1111/jfb.13149 2020-01-01T15:43:39Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Dryad Digital Repository (Duke University) Teno ENVELOPE(25.690,25.690,68.925,68.925) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
diagnostic SNPs genotyping by sequencing multiplex primer design sea age at maturity |
spellingShingle |
diagnostic SNPs genotyping by sequencing multiplex primer design sea age at maturity Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria L. Primmer, Craig R. 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 |
diagnostic SNPs genotyping by sequencing multiplex primer design sea age at maturity |
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. |
format |
Article in Journal/Newspaper |
author |
Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria L. Primmer, Craig R. |
author_facet |
Aykanat, Tutku Lindqvist, Meri Pritchard, Victoria L. Primmer, Craig R. |
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://hdl.handle.net/10255/dryad.126101 http://hdl.handle.net/10255/dryad.132277 https://doi.org/10.5061/dryad.g0870.2 |
op_coverage |
Finland |
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.g0870.2/1.2 doi:10.1111/jfb.13149 PMID:27709620 doi:10.5061/dryad.g0870.2 Aykanat T, Lindqvist M, Pritchard VL, Primmer CR (2016) From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. Journal of Fish Biology 89(6): 2658-2679. http://hdl.handle.net/10255/dryad.126101 http://hdl.handle.net/10255/dryad.132277 |
op_doi |
https://doi.org/10.5061/dryad.g0870.2 https://doi.org/10.5061/dryad.g0870.2/1.2 https://doi.org/10.1111/jfb.13149 |
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