Development and use of DNA markers for increased viral resistance in Atlantic salmon breeding programmes

In this project, we seek to identify DNA markers associated with the two viral diseases Infectious Pancreatic Necrosis (IPN) and Pancreas Disease (PD), currently the most problematic diseases in European Atlantic salmon aquaculture. The IPN part of the st udy will build upon an earlier project in which a highly significant QTL was found, explaining the majority of genetic variation in IPN resistance in both post-smolts and fry. This QTL has been mapped to a 4 cM interval on linkage group 21. Here, we aim a t using an upcoming Atlantic salmon SNP-chip to identify additional markers in the QTL region. The SNPs will be used to screen an existing BAC-library, whereupon BAC contigs mapping to the region will be bridged by contig walking. BAC end sequence, availa ble from the cGRASP initiative, will be captured and re-sequenced in 2x3 animals representing the QQ and qq genotypes, respectively. Re-sequencing will reveal additional SNP, which will be genotyped on a set of 73 QTL-heterozygous animals to identify SNP s in perfect linkage disequilibrium (LD) with the causative mutation. SNP data will be combined with sequence annotation to fine-map the QTL and to identify candidates for the causative gene/polymorphism. The PD part of the study will be based on a fiel d trial for PD-resistance, since a functional challenge test has not been developed. Twelve thousand animals representing 400 full-sib groups will be placed in a PD-exposed area. The SNP-chip will be used to genotype 1 200 of these animals, the choice of analysis methodology depending upon the mortality rate of the test and other factors. Given the large number of SNPs on the chip (16 500), this strategy could map and fine-map QTL for PD-resistance in one operation. In the final part of the study, a one -step genotype test will be developed in order to simultaneously test for IPN- and PD-resistance, and possibly other traits, in a cost-effective manner.