Genomic selection for improved resistance to Amoebic Gill Disease in farmed Atlantic salmon

Atlantic salmon is the most valuable aquaculture species to the UK economy (£0.6 bn/annum) and provides a major source of employment in rural and coastal communities. Currently, Amoebic gill disease (AGD) is one of the most serious threats to the sustainable production of salmon. Infection can result in reduced growth, substantial treatment and management costs, increased susceptibility to other pathogens and, if untreated, mortality. Therefore, AGD presents a large economic and welfare burden. AGD has been a problem in Tasmania since 1980, where control costs are high ($1AUS/kg salmon). However, these costs are dwarfed by losses that would be incurred without treatment. The UK produced 162M kg of salmon in 2012, hence similar control costs here would cost ~£90M/year to the economy. Our previous TSB-funded work has led to the development of the first high-density SNP genotyping arrary for Atlantic salmon and enabled testing and application of genomic selection strategies in salmon breeding. In this project, we aim to apply this array and knowledge to improve AGD resistance in farmed salmon stocks using genomic selection. By performing a controlled AGD challenge experiment and utilising gill damage data collected in the farm environment, we aim to identify and benchmark accurate phenotypes and combine these data with dense genotype data to substantially improve AGD resistance. While genomic selection (utilising dense genetic marker information to predict breeding values for individual selection candidates) is routine in the terrestrial livestock sector, it has only recently been applied to aquaculture. LNS are already internationally recognised as pioneers in this area and this proposed project will further develop genomic selection as a route to accurate and effective selective breeding for disease resistance. While the intitial target trait is AGD resistance, other economically and environmentally important target traits (e.g. fillet quality, resistance to other pathogens) will be improved. The outputs of the project will have positive economic, animal welfare and environmental implications for the UK salmon farming industry.

Atlantic salmon is the most valuable aquaculture species to the UK economy (£0.6 bn/annum) and provides a major source of employment in rural and coastal communities. Currently, Amoebic gill disease (AGD) is one of the most serious threats to the sustainable production of salmon. Infection can result in reduced growth, substantial treatment and management costs, increased susceptibility to other pathogens and, if untreated, mortality. Therefore, AGD presents a large economic and welfare burden. AGD has been a problem in Tasmania since 1980, where control costs are high ($1AUS/kg salmon). However, these costs are dwarfed by losses that would be incurred without treatment. The UK produced 162M kg of salmon in 2012, hence similar control costs here would cost ~£90M/year to the economy. Our previous TSB-funded work has led to the development of the first high-density SNP genotyping arrary for Atlantic salmon and enabled testing and application of genomic selection strategies in salmon breeding. In this project, we aim to apply this array and knowledge to improve AGD resistance in farmed salmon stocks using genomic selection. By performing a controlled AGD challenge experiment and utilising gill damage data collected in the farm environment, we aim to identify and benchmark accurate phenotypes and combine these data with dense genotype data to substantially improve AGD resistance. While genomic selection (utilising dense genetic marker information to predict breeding values for individual selection candidates) is routine in the terrestrial livestock sector, it has only recently been applied to aquaculture. LNS are already internationally recognised as pioneers in this area and this proposed project will further develop genomic selection as a route to accurate and effective selective breeding for disease resistance, and other target traits.

The project is expected to result in multi-faceted positive impact. The major direct impacts for the commercial partner LNS include (i) the production of salmon eggs and juvenilles with improved resistance to AGD, and (ii) the development of genomic selection techniques for disease resistance. The former output derives from the project facilitating the immediate incorporation of genetic resistance to AGD into their UK-based, and potentially Chilean-based, salmon breeding programs. Currently, no company markets AGD-resistant stock and this new product is therefore likely to increase LNS's share of the world market as described above. In the medium term, applying genomic selection across the LNS broodstock will significantly reduce the requirement for disease challenge and sentinel testing. In addition, LNS will market and supply genomic selection technology to new and existing customers of their genomic services. The project outputs will be communicated to potential customers and the industry in general via marketing literature, presentations at industry conferences and 'trade' press. In the case where a specific gene or marker explains a high proportion of the variation in resistance, this marker/gene has potential to be sold as a genetic test product. In this case, the consortium will seek to protect the IP via a patenting strategy, subject to a cost-benefit evalutation. This will allow LNS to market such a test exclusively and therefore gain further competitive advantage. In addition to the commercial applications, the results and outputs of the project are likely to be of substantial interest to the academic community and, subject to IP agreements, the academic partners will disseminate these results rapidly through high-impact academic publications/conferences and public outreach channels. A good prior example of this is the previous TSB-funded project in which there were peer-reviewed publications and presentations at academic conferences. During the course of the project and in the period immediately after project completion, LNS anticipate substantial economic benefits from increased competitiveness and added-value of the LNS fish against the products of non-UK competitors. While the specifics of the benefit of AGD resistance are difficult to quantify due to the unpredicable nature of disease outbreaks, a parallel can be drawn with sea lice. Currently the industry's largest problem, sea lice and their treatment represent a large proportion of the costs of salmon production. It is likely that the benefits from the proposed project into AGD resistance will be similar and both direct benefits of improved salmon health and indirect benefits of reduced treatment costs will be observed. On a broader scale, improved resistance to AGD will help secure a profitable and sustainable salmon farming industry in the UK. This will contribute to the continued growth of a significant UK export. Much of the benefit will be in the rural communities which are reliant on salmon farming in the Highlands and Islands and the downstream social benefits in these communities will be substantial. Animal welfare and the environment will also benefit through the reduced impact and threat of AGD outbreaks. The avoidance or reduction of chemical treatments will lessen the impact of salmon farming on marine ecosystems, including wild salmonid populations. In turn, gains in production efficiency will lead to lower carbon emissions across the industry.