title: Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.
abstract: A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.
authors: Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile.|Aquainnovo, Talca 60, Puerto Montt, Chile.
authors: J M
authors: JM
authors: Yáñez
authors: Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA.
authors: S
authors: S
authors: Naswa
authors: Aquainnovo, Talca 60, Puerto Montt, Chile.|Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile.
authors: M E
authors: ME
authors: López
authors: Aquainnovo, Talca 60, Puerto Montt, Chile.|Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile.
authors: L
authors: L
authors: Bassini
authors: Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile.|Aquainnovo, Talca 60, Puerto Montt, Chile.
authors: K
authors: K
authors: Correa
authors: Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, Scotland, UK.
authors: J
authors: J
authors: Gilbey
authors: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada.
authors: L
authors: L
authors: Bernatchez
authors: Marine Harvest, Kindrum, Fanad, C. Donegal, Ireland.
authors: A
authors: A
authors: Norris
authors: Aquainnovo, Talca 60, Puerto Montt, Chile.|Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile.
authors: R
authors: R
authors: Neira
authors: Aquainnovo, Talca 60, Puerto Montt, Chile.
authors: J P
authors: JP
authors: Lhorente
authors: Data2Bio LLC, Ames, IA 50011, USA.|Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
authors: P S
authors: PS
authors: Schnable
authors: Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA.
authors: S
authors: S
authors: Newman
authors: Genus plc, 1525 River Road, DeForest, WI 53532, USA.
authors: A
authors: A
authors: Mileham
authors: Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA.
authors: N
authors: N
authors: Deeb
authors: Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.|Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.
authors: A
authors: A
authors: Di Genova
authors: Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.|Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.|Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile.
authors: A
authors: A
authors: Maass
mesh_terms: D000569:Americas; D000818:Animals; D000835:Animals, Wild; D017756:Aquaculture; D019295:Computational Biology / Q000379:methods; D005060:Europe; D056726:Genetic Association Studies; D005828:Genetics, Population / Q000379:methods*; D060005:Genotyping Techniques / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D020317:Salmo salar / Q000145:classification* / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: SNP array; Salmo salar; genomic selection; next-generation sequencing; pseudo-tetraploid