We sampled 316 Atlantic cod (Figure 1 and Table 1 ), consisting of 144 individuals from 5 locations from the Northwest Atlantic, 39 Frontal and 39 Coastal ecotype individuals from Iceland (classified by data storage tag (DST) profiles, see Pálsson and Thorsteinsson, 2003 ; Thorsteinsson et al., 2012 ), and 50 NEAC and 44 NCC individuals from the Northeast Atlantic.
DNA was extracted from muscle tissue using the E.Z.N.A Tissue DNA kit (Omega Bio-Tek, Norcross, GA, USA) and normalized to 100 ng μl−1. All samples were individually genotyped using a 12K Illumina SNP chip for which 8165 SNPs were polymorphic in this data set, had a call rate of >95% and showed Mendelian inheritance in a separate set of individuals with a pedigree. Out of these SNPs, 602 were close to selected candidate genes, 1470 were nonsynonymous SNPs and the remaining 5857 SNPs were randomly distributed throughout the 23 different linkage groups (LGs). Genotype clustering was performed in Genome Studio 2011.1 (Illumina Inc., San Diego, CA, USA). The nomenclature of the LGs follows Hubert et al. (2010) (link) and the order of the SNPs are as in Berg et al. (2016) (link). All 8165 SNPs used were mapped to the published Atlantic cod genome (ATLCOD1C) (Star et al., 2011 (link)) in the same way as in Berg et al. (2016) (link) and details are available in dbSNP (www.ncbi.nlm.nih.gov/snp ).
DNA was extracted from muscle tissue using the E.Z.N.A Tissue DNA kit (Omega Bio-Tek, Norcross, GA, USA) and normalized to 100 ng μl−1. All samples were individually genotyped using a 12K Illumina SNP chip for which 8165 SNPs were polymorphic in this data set, had a call rate of >95% and showed Mendelian inheritance in a separate set of individuals with a pedigree. Out of these SNPs, 602 were close to selected candidate genes, 1470 were nonsynonymous SNPs and the remaining 5857 SNPs were randomly distributed throughout the 23 different linkage groups (LGs). Genotype clustering was performed in Genome Studio 2011.1 (Illumina Inc., San Diego, CA, USA). The nomenclature of the LGs follows Hubert et al. (2010) (link) and the order of the SNPs are as in Berg et al. (2016) (link). All 8165 SNPs used were mapped to the published Atlantic cod genome (ATLCOD1C) (Star et al., 2011 (link)) in the same way as in Berg et al. (2016) (link) and details are available in dbSNP (
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