Gene variant detection
For identification of polymorphisms in the Finnish Large White transcriptome, we used the Genome Analysis Toolkit (GATK) (Depristo et al. 2011; McKenna et al. 2010; van der Auwera et al. 2013) program and SNP and Variation Suite v7 (Golden Helix, Inc., Bozeman, MT; www.goldenhelix.com) for filtering and annotation of the identified variants. The data were filtered based on the read depth (>5), genotype quality (>20), and quality score (>80). The possible effect of amino acid substitutions on protein function was analyzed using SIFT (http://www.ensembl.org/Tools/VEP), and the effect on the secondary structure of the protein was analyzed using the CFSSP (http://www.biogem.org/tool/chou-fasman/) prediction tool.