Genotyping of Atlantic Cod Populations

In total, 5 × 96 well plates of selected DNA samples were genotyped using the two Illumina Golden Gate panels. Two plates consisted of two references families, B33 and B87 with two parents and 91 progeny. The three remaining plates consisted of wild cod populations. In total, seven populations of Atlantic cod were genotyped for this study, with an average of 23 fish genotyped per population. The geographic location of collections covers the North Atlantic with a more detailed sampling for Atlantic Canadian populations. DNA extraction methods have been described previously [46 ]. In summary, fin clips or muscle tissue samples were taken and placed in 95% ethanol. DNA was extracted using the Qiagen DNAeasy 96 extraction kit (Qiagen, Mississauga, ON). The kit protocol utilizes a buffer containing proteinase K to lyse the tissue. The lysate was loaded onto a plate where the DNA binds to a silica membrane in the presence of chaotropic salt. Proteins and other contaminants were washed from the bound DNA using wash buffers and centrifugation. DNA was then eluted in water.
High-throughput genotyping was performed at the McGill/Genome Quebec Innovation Centre using the GoldenGate assay.