The dissection of the molecular basis of relevant traits in farmed Atlantic salmon and the implementation of genomic selection schemes require a considerable number of single nucleotide polymorphisms (SNPs). In this study we performed a de novo SNP discovery and developed an Affymetrix Axiom® myDesign Custom Array, taking genome duplication and across continents genetic variation into account. 9,736,473 non-redundant SNPs were identified across a panel of 20 fish by whole genome sequencing. After applying six filtering steps, 200K SNPs were selected and genotyped in 480 fish representing wild and farmed fish from Europe, North America and Chile. Nearly 79.6% (159,099) SNPs had probes belonging to good quality categories according clustering properties. This array provides the platform for the dissection of economically important traits, assisting breeding programs through genomic selection and genetic studies in wild populations using high-resolution genome-wide information.

José M Yáñez, Sudhir Naswa, María E López, Liane Bassini, María E Cabrejos, John Gilbey, Louis Bernatchez, Ashie Norris, Carlos Soto, John Eisenhart, Barry Simpson, Roberto Neira, Jean P Lhorente, Patrick Schnable, Scott Newman, Alan Mileham, Nader Deeb

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Species Breeding: Breeding in aquaculture species, , 263, 2014
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