Genomic selection and association mapping of Atlantic salmon populations

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Aquaculture now produces all the Atlantic salmon consumed by Canadians and a significant amount for export. However, disease is a major constraint affecting the sustainability and profitability of this industry. Foremost is disease in marine farmed stock. Disease has a direct impact on farm income through inventory losses and an indirect impact by influencing consumer demand. For example, some consumers are reluctant to buy farmed salmon because they believe they would be supporting an industry which is contributing to disease and parasitism in wild salmon stocks. Fortunately the rate of genetic improvement for functional traits such as disease resistance can be greatly improved by using a new method of animal breeding called genomic selection. This technique uses thousands of "SNP" genetic markers to determine which of the offspring produced by a disease-resistant family have inherited the disease-resistant alleles. Research using dairy bulls at the University of Guelph has shown that this technique increases the response to selection per generation per dollar spent for traits that can only be measured in the relatives of potential breeders. We are proposing to test whether genomic selection can improve growth rate in saltwater, rapid adaptation to seawater, disease resistance and delay sexual maturity relative to a conventional breeding program currently used at Cooke Aquaculture Inc. in New Brunswick. We anticipate that we accomplish this within a three year period using DNA samples and estimated breeding values (EVB) archived over a four year period from past broodstock and their full sib relatives, as well as the performance of their harvested offspring in seawater farm cages. We can then predict genetic changes in economically important traits that would accrue from the use of genomic selection, and compare this to current selection programs. Disease resistance will be determined by challenge of post smolts in the quarantine lab at