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.

Highlights

  • Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest

  • The existing 6 K SNP array [3] has been applied for mapping quantitative trait loci (QTL) [14,15] and differentiating between populations [16,17]

  • SNPs were discovered in representative samples of the Atlantic salmon breeding company Landcatch Natural Selection Ltd (LNS, Stirling, UK) while the representation sequencing (RR-Seq) included a pool of wild fish from diverse geographical sources and a single haploid Atlantic salmon embryo for the purpose of paralogous sequence variants (PSV) exclusion (See Methods and Table 1 for details)

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Summary

Introduction

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. Atlantic salmon is considered a model species for the other members of the Salmonidae family and as such is the target of an on-going genome sequencing and assembly project [2] This genome sequence and its interrogation will be important for understanding the genetic regulation of complex traits in salmonids, with applications for improvement of aquaculture breeding programs and for population and evolutionary genetics studies. The existing 6 K SNP array [3] has been applied for mapping QTL [14,15] and differentiating between populations [16,17]

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