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Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)
Author(s): Houston, Ross D
Taggart, John
Cezard, Timothé
Bekaert, Michaël
Lowe, Natalie R
Downing, Alison
Talbot, Richard T
Bishop, Stephen C
Archibald, Alan L
Bron, James
Penman, David
Davassi, Alessandro
Brew, Fiona
Tinch, Alan E
Gharbi, Karim
Hamilton, Alastair
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Keywords: Atlantic salmon
Salmo salar
Single nucleotide polymorphism, SNP
Next-generation sequencing
Genome duplication
Issue Date: 6-Feb-2014
Date Deposited: 6-May-2014
Citation: Houston RD, Taggart J, Cezard T, Bekaert M, Lowe NR, Downing A, Talbot RT, Bishop SC, Archibald AL, Bron J, Penman D, Davassi A, Brew F, Tinch AE, Gharbi K & Hamilton A (2014) Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). BMC Genomics, 15 (1), Art. No.: 90.
Abstract: BackgroundDense 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. ResultsSNP 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. ConclusionsThis 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.
DOI Link: 10.1186/1471-2164-15-90
Rights: © 2014 Houston et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
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