A1 Refereed original research article in a scientific journal
From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
Authors: Aykanat T, Lindqvist M, Pritchard VL, Primmer CR
Publisher: WILEY-BLACKWELL
Publication year: 2016
Journal: Journal of Fish Biology
Journal name in source: JOURNAL OF FISH BIOLOGY
Journal acronym: J FISH BIOL
Volume: 89
Issue: 6 (SI)
First page : 2658
Last page: 2679
Number of pages: 22
ISSN: 0022-1112
eISSN: 1095-8649
DOI: https://doi.org/10.1111/jfb.13149
Abstract
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 (N-SNP = 150), examining functional genetic variation associated with sea age at maturity (N-SNP = 5), and for performing genetic subpopulation assignment (N-SNP = 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. (C) 2016 The Fisheries Society of the British Isles
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 (N-SNP = 150), examining functional genetic variation associated with sea age at maturity (N-SNP = 5), and for performing genetic subpopulation assignment (N-SNP = 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. (C) 2016 The Fisheries Society of the British Isles
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