Family-based genome wide association analysis for salmon lice (Lepeophtheirus salmonis) resistance in North American Atlantic salmon using a 50 K SNP array

The salmon louse, Lepeophtheirus salmonis, is an economically important parasite on aquaculture stocks of Atlantic salmon grown in sea cages. The aim of this study was to perform a family-based genome wide association study to identify the genomic architecture of salmon louse resistance in a commercial population of Atlantic salmon using five year classes of data. A total of 1756 fish were genotyped from 248 families, which were experimentally infected with L. salmonis copepodids, using a 50 K SNP array designed specifically for North American Atlantic salmon. A within family-based association test for quantitative traits was run using QFAM in PLINK with salmon lice counts pre-adjusted for contemporary group as the phenotype. Salmon lice counts varied significantly among families and salmon lice resistance had an estimated heritability of 0.21 ± 0.03. After correcting for multiple testing, seven SNPs from three chromosomes surpassed a suggestive chromosome wide level. Ssa04 had the most suggestive SNP, and four other suggestive SNPs within a close range on the chromosome. A single SNP was suggestive on each of Ssa14 and Ssa20. The most suggestive SNP, and two suggestive tag SNPs, were located near a predicted gene on Ssa04 that codes for ceramide-1-phophate transfer protein which is involved with pathophysiological functions such as cell survival and inflammation. No loci with major effects were detected suggesting a polygenic trait architecture. However, several loci were detected which could be included directly in models used to estimate genomic breeding values. Therefore, genomic selection should continue to be used to breed Atlantic salmon naturally more resistant to L. salmonis infection.