From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

• DOI: 10.1111/jfb.13149
• Publication Date: 2016-10-12T21:47:14Z
• Authors: T. Aykanat; M. Lindqvist; V. L. Pritchard; C. R. Primmer
• Keywords: SNP genotyping; Ion semiconductor sequencing; Molecular Inversion Probe; SNP

A genotyping assay for the Ion Torrent PGM platform was developed fast and cost-effective targeted of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised simple primer design step multiplex-polymerase chain reaction (PCR), followed by two rounds sequencing to empirically evaluate marker efficiency large multiplexes optimise or exclude them when necessary. Of 282 pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included sdy partial gene product determine genetic sex, as well three additional modules comprising SNPs assessing neutral variation (NSNP = 150), examining functional associated with sea age at maturity 5), performing subpopulation assignment 61). primarily monitor long-term changes S. salar from Teno River, but are likely suitable application wide range populations. Furthermore, versatile development pipeline offers strategy developing assays any species.