Genomics as a tool for detecting selection in farm Atlantic salmon and interactions between escaped farm and wild salmon

Norway is of unique importance for the Atlantic salmon, both as the largest producer of farmed salmon and a main reservoir of wild stocks. However, escaped farmed fish make up a significant portion of spawners in the wild, and there is concern that the ge netic constitution of wild stocks is deteriorating due to gene flow from farmed populations selected for traits of commercial importance. The main objectives of this study are 1) to identify signatures of selection due to artificial selection in Atlanti c salmon; 2) to determine whether interbreeding with farm fish results in changes in allele frequency at non-neutral loci in Norwegian and Irish rivers at risk; and 3) to develop a platform for simulating mechanisms and consequences of such genetic intera ctions. Signatures of selection will be found by combining a "genome scan" with a "candidate gene" approach. 3000 SNP markers will be used in a genome scan on a collection of animals sampled from different Norwegian rivers and breeding programmes. The gen ome scan will be reinforced by a particular focus on regions harbouring QTL for traits under selection, as well as SNPs identified within candidate genes for growth rate. Non-neutral markers, and neutral markers, will be used to test for allelic diverge nce over time in rivers shown to be under strong pressure/no pressure from farm escapees. This experiment will indicate whether gene-flow from farmed to wild populations results in genetic changes at phenotype-controlling, or whether such changes are succ esfully mitigated by balancing selection. The simulation study will be based on the "Virtual Genome" platform of CIGENE, and will draw upon data from this and previous studies. We believe the study, by connecting research environments from the manageme nt- and aquaculture sides, will contribute to a more complete understanding of the workings of selection in aquaculture and in the wild as well as the consequences of farm/wild genetic interactions.