Evaluation of an Atlantic salmon SNP chip as a genomic tool for the application in a Tasmanian Atlantic salmon (Salmo salar) breeding population

Ninety-five genomic DNA samples were extracted from fin clips of Tasmanian Atlantic salmon and genotyped using a 15,225 single nucleotide polymorphism (SNP) chip for Atlantic salmon, which was developed by the Center for Integrative Genetics (CIGENE) in Norway. Infinium assay intensity data suggested that 2991 polymorphic SNPs were single copy and another 952 polymorphic SNPs were present in two copies. A further 467 SNPs would fail quality control thresholds. However, the majority of SNPs that failed quality control departed from Hardy–Weinberg equilibrium. It is discussed that with a larger sample the threshold might need to be re-evaluated to ensure that quality control only removes SNPs for technical not biological reasons. Moderate linkage disequilibrium (LD) indicates the usefulness of loci pairs for whole genome selection. Pairwise LD was calculated between all of the 2991 loci from unique regions, with 9004 pairs of SNP loci found to be in moderate LD, which is significantly more than the 2078 expected by chance (established by permutation testing). The low numbers of SNPs that were evaluated to be useful make an LD-based genome-wide selection approach unfeasible with the resources available. However, the population structure of large numbers of offspring with phenotypic records within large numbers of families is ideally suited for a reference population design that capitalises on linkage information from the SNPs for within-family selection.