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Open Access Highly Accessed Research article

Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

Ross D Houston1*, John B Taggart2, Timothé Cézard3, Michaël Bekaert2, Natalie R Lowe1, Alison Downing4, Richard Talbot4, Stephen C Bishop1, Alan L Archibald1, James E Bron2, David J Penman2, Alessandro Davassi5, Fiona Brew5, Alan E Tinch6, Karim Gharbi3 and Alastair Hamilton6

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK

2 Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK

3 Edinburgh Genomics, Ashworth Laboratories, King’s Buildings, University of Edinburgh, Edinburgh, EH9 3JT, UK

4 Edinburgh Genomics, The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, UK

5 Affymetrix UK Ltd, Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH, UK

6 Landcatch Natural Selection Ltd., 15 Beta Centre, Stirling University Innovation Park, Stirling FK9 4NF, UK

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BMC Genomics 2014, 15:90  doi:10.1186/1471-2164-15-90

Published: 14 February 2014

Abstract

Background

Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), these goals are currently hampered by the lack of a high-density SNP genotyping platform. Therefore, the aim of the study was to develop and test a dense Atlantic salmon SNP array.

Results

SNP discovery was performed using extensive deep sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild Atlantic salmon samples (n = 283) resulting in the discovery of > 400 K putative SNPs. An Affymetrix Axiom® myDesign Custom Array was created and tested on samples of animals of wild and farmed origin (n = 96) revealing a total of 132,033 polymorphic SNPs with high call rate, good cluster separation on the array and stable Mendelian inheritance in our sample. At least 38% of these SNPs are from transcribed genomic regions and therefore more likely to include functional variants. Linkage analysis utilising the lack of male recombination in salmonids allowed the mapping of 40,214 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. An identity-by-state clustering analysis revealed that the array can clearly distinguish between fish of different origins, within and between farmed and wild populations. Finally, Y-chromosome-specific probes included on the array provide an accurate molecular genetic test for sex.

Conclusions

This manuscript describes the first high-density SNP genotyping array for Atlantic salmon. This array will be publicly available and is likely to be used as a platform for high-resolution genetics research into traits of evolutionary and economic importance in salmonids and in aquaculture breeding programs via genomic selection.

Keywords:
Atlantic salmon; Salmo salar; Polymorphism; Single nucleotide polymorphism, SNP; Next-generation sequencing; Array; Genomics; Mapping; Genome duplication