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Mol Ecol Resour. 2016 Jul;16(4):1002-11. doi: 10.1111/1755-0998.12503. Epub 2016 Mar 1.

Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations.

Author information

1
Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile.
2
Aquainnovo, Talca 60, Puerto Montt, Chile.
3
Genus plc, 100 Bluegrass Commons Blvd. Suite 2200, Hendersonville, TN 37075, USA.
4
Faculty of Agricultural Sciences, University of Chile, Av. Santa Rosa 11315, Santiago, Chile.
5
Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, Scotland, UK.
6
Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada.
7
Marine Harvest, Kindrum, Fanad, C. Donegal, Ireland.
8
Data2Bio LLC, Ames, IA 50011, USA.
9
Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
10
Genus plc, 1525 River Road, DeForest, WI 53532, USA.
11
Fondap Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.
12
Mathomics Bioinformatics Laboratory, Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Av. Blanco Encalada 2120, 7th floor, Santiago, Chile.
13
Department of Mathematical Engineering, University of Chile, Av. Blanco Encalada 2120, 5th floor, Santiago, Chile.

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.

KEYWORDS:

SNP array; Salmo salar; genomic selection; next-generation sequencing; pseudo-tetraploid

PMID:
26849107
DOI:
10.1111/1755-0998.12503
[Indexed for MEDLINE]

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