Genomic Selection Applied to Pisciricketsia salmonis Resistance in Chilean Atlantic Salmon

Disease resistance is one of the major breeding goals of the Chilean salmon industry, in particular to one endemic bacteria Pisciricketsia salmonis. Implementing breeding programs including disease resistance is complicated using pedigree analysis only, considering sanitary constraints and relatively large rates of inbreeding under BLUP. In this paper, we are aiming at predicting which are the genetic factors explaining disease resistance, using genomic selection approaches in order to know the effects of a large number of SNPs segregating in a commercial breeding population. We further characterize the transcriptome of Salmo salar differing in their genetic (familiar) susceptibility. The heritability of the binary trait was significant with a posterior mode of about 0.65, a value that is very similar to what is obtained using of marker effects only (0.55). After applying Bayes Cpi genomic selection approach using uniform priors, seven markers show strong evidence of having significant effects. The GO of the sequence surrounding the significant SNPs, gave evidence that immunology genes as well as metabolism and cellular components drive disease resistance. This is also consistent with the RNAseq data, such that immunological genes that are differentially expressed play a significant role in disease resistance, between families showing different genetic resistance to P. salmonis. The results show that a thorough understanding of disease resistance requires a unified approach, which uses jointly information from phenotypic, transcriptomic and genomic variability. Fondecyt 1120608