Atlantic Salmon genome re-sequencing of individuals belonging to different populations farmed in Chile. Salmo salar

The elucidation of genotype-phenotype association, the dissection of the molecular basis of relevant traits in farmed Atlantic salmon and the implementation of genomic selection require a considerable number of single nucleotide polymorphisms (SNPs). In this study we performed de novo SNP discovery and developed an Affymetrix Axiom® myDesign Custom Array, taking genome duplication and across continent 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 were high quality according clustering properties. This novel SNP panel provides a 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.