Application of Genomics to Selective Breeding of Atlantic Salmon

Study of the genetic basis of economically-important traits in Atlantic salmon has been transformed by high-throughput genomics tools. Genome-wide marker data - typically tens or hundreds of thousands of SNPs - can now be generated on a population scale. We have applied genotyping by sequencing (RAD sequencing), and developed a high-density Atlantic salmon SNP array for this purpose. When combined with the large full-sibling families in commercial salmon populations, this high marker density enables powerful studies of complex traits. Using these genomic tools and the amenable family structure, we have studied genetic resistance to a number of commercially-important diseases. Host resistance to these diseases is consistently heritable, but the genetic architecture of resistance varies. The range includes the nearly-monogenic inheritance of resistance to the Infectious Pancreatic Necroris virus, the polygenic inheritance of sea lice resistance, and the intermediate nature of resistance to Pancreas Disease (salmonid alphavirus). The underlying genetic architecture impacts on the strategy for application of results into breeding programs, i.e. either using QTL-targeted markers or genomic selection approaches. In addition, gene expression profiling of resistant and susceptible fish using RNA sequencing and micorarrays has given insight into the causative factors underlying genetic resistance. Genetic improvement in resistance to multiple pathogens and parasites in Atlantic salmon farming can now be readily achieved via the application of genetic markers in breeding programmes.