Axiom 132k atlantic salmon snp chip

All samples were genotyped with the Affymetrix Axiom 132K Atlantic salmon SNP chip (Houston et al. 2014 (link)) such that genotypes were available for all animals for 78,362 high quality, mapped and ordered SNP markers. Families with > 5% and individuals with > 10% Mendelian errors were excluded using Plink/1.90-beta4.1 (Purcell et al. 2007 (link)). Further quality control was conducted for the offspring using the GenABEL package (Aulchenko et al. 2007 (link)) on R/3.1.2 (R Development Core Team 2008 ) with the following criteria: SNPs with a minor allele frequency (MAF) < 5%, call rates < 95%, or Hardy-Weinberg Equilibrium P-value < 10⁻⁵ were excluded. Individuals with a percentage of missing genotypes > 3% were also excluded. In total, 76,488 SNPs (hereafter referred to as the HD SNP panel), and 520 offspring passed all criteria, and were used to calculate the genomic relationship matrices for each SNP panel.

All samples were genotyped using the Affymetrix Axiom 132 K Atlantic salmon SNP chip developed by Houston et al. (2014) (link), as described in Tsai et al. (2015) (link). The quality control measures resulted in the exclusion of SNPs with Mendelian errors, minor allele frequency (MAF) <0.05, and proportion of individuals with missing genotypes >0.03. The MAF of SNPs were calculated using Plink 1.9 (Purcell et al. 2007 (link)). SNPs with a known and unique chromosome position on the Atlantic salmon reference genome [GenBank accession GCA_000233375.4, (Lien et al. 2016 (link))] were retained for analysis. After these filtering steps, 78,362 (78 K) SNPs were retained for the high density SNP panel (hereafter “HD SNP panel”). A subset of these SNPs [25,634 (25 K)] formed part of a second medium density Affymetrix Axiom array described in Tsai et al. (2015) (link), and these formed a medium density SNP panel (hereafter “MD SNP panel”). The details of the SNPs in the MD SNP panel and the HD SNP panel are provided in Supplemental Material, File S1 and File S2, respectively. As a result, all parents and offspring samples had genotypes for both SNP panels (the genotype data are provided in File S3), and these formed the basis of the imputation analyses.