Development and Validation of a High Density SNP Genotyping Array for Atlantic Salmon (Salmo salar)

Dense single nucleotide polymorphism (SNP) genotyping arrays rapidly provide extensive information on genome-wide polymorphic variation. Such information can be applied to study the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding programs. In Atlantic salmon (Salmo salar), a partially tetraploid species, these goals have been hampered by the lack of a high-density SNP genotyping platform. SNPs for such a high-density genotyping array were  discovered using extensive sequencing of Reduced Representation (RR-Seq), Restriction site-Associated DNA (RAD-Seq) and mRNA (RNA-Seq) libraries derived from farmed and wild salmon samples (n = 283), resulting in 286,021 putative SNPs. An Affymetrix Axiom genotyping array was designed and tested on animals of disparate wild and farmed origin (n = 96). Automated clustering and genotype assignment was used to type 132,033 polymorphic high resolution SNPs with high call rate, good cluster separation and stable Mendelian inheritance. 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 salmon allowed the mapping of 40,252 SNPs distributed across all 29 pairs of chromosomes, highlighting the extensive genome-wide coverage of the SNPs. Identity-by-state clustering analysis revealed that the array can clearly distinguish between salmon populations, both farmed and wild. Further, Y-specific probes on the array provide an accurate molecular genetic test for sex. This publicly-available SNP array can be used for high-resolution genetics research and in aquaculture breeding programs via genomic selection.