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dc.contributor.authorHouston, Ross Den_UK
dc.contributor.authorTaggart, Johnen_UK
dc.contributor.authorCezard, Timothéen_UK
dc.contributor.authorBekaert, Michaëlen_UK
dc.contributor.authorLowe, Natalie Ren_UK
dc.contributor.authorDowning, Alisonen_UK
dc.contributor.authorTalbot, Richard Ten_UK
dc.contributor.authorBishop, Stephen Cen_UK
dc.contributor.authorArchibald, Alan Len_UK
dc.contributor.authorBron, Jamesen_UK
dc.contributor.authorPenman, Daviden_UK
dc.contributor.authorDavassi, Alessandroen_UK
dc.contributor.authorBrew, Fionaen_UK
dc.contributor.authorTinch, Alan Een_UK
dc.contributor.authorGharbi, Karimen_UK
dc.contributor.authorHamilton, Alastairen_UK
dc.description.abstractBackgroundDense 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.en_UK
dc.publisherBioMed Central Ltden_UK
dc.relationHouston 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.
dc.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.en_UK
dc.subjectAtlantic salmonen_UK
dc.subjectSalmo salaren_UK
dc.subjectSingle nucleotide polymorphism, SNPen_UK
dc.subjectNext-generation sequencingen_UK
dc.subjectGenome duplicationen_UK
dc.titleDevelopment and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)en_UK
dc.typeJournal Articleen_UK
dc.citation.jtitleBMC Genomicsen_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationAffymetrix UK Ltden_UK
dc.contributor.affiliationAffymetrix UK Ltden_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationLandcatch Natural Selection Ltden_UK
dc.relation.funderprojectDissecting structural and functional genomic factors underlying the resistance of the Atlantic salmon fry to infectious pancreatic necrosisen_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
local.rioxx.authorHouston, Ross D|en_UK
local.rioxx.authorTaggart, John|0000-0002-3843-9663en_UK
local.rioxx.authorCezard, Timothé|en_UK
local.rioxx.authorBekaert, Michaël|0000-0002-1206-7654en_UK
local.rioxx.authorLowe, Natalie R|en_UK
local.rioxx.authorDowning, Alison|en_UK
local.rioxx.authorTalbot, Richard T|en_UK
local.rioxx.authorBishop, Stephen C|en_UK
local.rioxx.authorArchibald, Alan L|en_UK
local.rioxx.authorBron, James|0000-0003-3544-0519en_UK
local.rioxx.authorPenman, David|0000-0001-8608-6631en_UK
local.rioxx.authorDavassi, Alessandro|en_UK
local.rioxx.authorBrew, Fiona|en_UK
local.rioxx.authorTinch, Alan E|en_UK
local.rioxx.authorGharbi, Karim|en_UK
local.rioxx.authorHamilton, Alastair|en_UK
local.rioxx.projectBB/F001959/1|Biotechnology and Biological Sciences Research Council|
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