Marker-Assisted Selection for IPN resistance in Atlantic salmon

IPN is a major problem in salmon farming. DNA markers linked to resistance genes could be used to improve selection for resistance, through MAS. Here, we propose to combine experimental and theoretical approaches to lay the foundations for MAS on IPN in A tlantic salmon. Genetic material for the study will come from two IPN challenge tests. In the first test, each of 400 families constituting the Aqua Gen broodstock will be tested at the fry stage. Within-family variation for IPN resistance will be used t o select families for a second test, performed at the smolt stage. Here, fewer and larger families will be tested. A genome scan will be done using animals from the smolt test and 450 SNP markers from a dense SNP map. Large sample sizes and selective gen otyping will be used to ensure high power. QTL will be fine-mapped using combined linkage disequilibrium/linkage analysis (LDLA) and material from the fry test. In addition, strong candidate genes, such as genes in the Major Histocompatibility Complex (MH C) clusters, will be tested for association to the trait using fry test material. The Aqua Gen population will be simulated with markers and genes segregating. The efficiency of the current breeding scheme (family selection) will be compared with MAS and different schemes combining MAS with family selection. Both markers in LD and in linkage (equilibrium) will be considered. When ready, data on QTL from the experimental part of the study will replace simulated QTL. Simulations and experimental results wi ll be combined with relevant data from the industry to perform a cost-benefit analysis on MAS. Finally, we will perform a real-life pilot study on MAS. Matings will be designed based on parents? genotypes at IPN-controlling loci. The offspring will be ch allenge-tested for IPN and other diseases. The end-product of the study will be a recommendation to the salmonid industry on how and when (or if) MAS for IPN (or other disease traits) should be implemented.