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

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

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 thogens) will be improved. The outputs of the project will have positive economic, animal welfare and environmental implications for the UK salmon farming industry.

Technical Summary

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.

Planned Impact

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.

Publications

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Houston R (2017) Future directions in breeding for disease resistance in aquaculture species in Revista Brasileira de Zootecnia

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Palaiokostas C (2017) Genome-wide approaches to understanding and improving complex traits in aquaculture species. in CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources

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Tsai HY (2015) Verification of SNPs Associated with Growth Traits in Two Populations of Farmed Atlantic Salmon. in International journal of molecular sciences

 
Description In our research funded on this grant, we performed experiments to investigate genetic resistance to Amoebic Gill Disease (AGD), which is a major problem for Atlantic salmon production in the UK and other salmon farming countries. We surveyed the genomes of salmon which had undergone a challenge with the causative agent of AGD (Neoparamoeba perurans). Using these data, we discovered that host resistance to this disease (which is measured by surveying gill damage and by quantification of the pathogen in gill tissue) is heritable, and therefore selective breeding might be a viable option for improving resistance. Further, we discovered a QTL affecting resistance on chromosome 18 of the salmon genome. Finally, we discovered that genomic selection is a highly effective approach for improving breeding for resistance to AGD, giving a significantly higher accuracy than traditional approaches based on pedigree records. These findings were published recently in Robledo et al. (2018): http://www.g3journal.org/content/early/2018/02/02/g3.118.200075. These results are being applied in the salmon aquaculture industry to help improve the resistance of farmed salmon to AGD.
Exploitation Route The results are already being applied by the industrial partner Hendrix Genetics to improve their breeding program. The delivery of salmon eggs with higher resistance to AGD will reduce requirements for treatments, which are potentially damaging to the environment and the welfare of the fish. The results from the testing of genomic selection approaches will have broader applications and uptake by salmon breeding companies and potentially breeders for other commercially important aquaculture species.
Sectors Agriculture, Food and Drink

URL https://www.ed.ac.uk/roslin/news-events/archive/2016/breakthrough-in-amoebic-gill-disease-control
 
Description In this award we have gained novel insights into the genetic basis of resistance to Amoebic Gill Disease (AGD) in salmon. AGD is one of the most serious threats to the sustainable production of farmed salmon. The impact on UK salmon production includes reduced growth, substantial treatment and management costs, increased susceptibility to other pathogens and potentially mortality. We worked with salmon breeding company Landcatch (part of Hendrix Genetics) to identify regions of the genome that impact resistance to salmon. A novel finding was a QTL on Chromosome 18 that explained a significant proportion of the genetic variation in resistance. We then tested novel methods of implementing genomic selection to improved resistance via selective breeding; results which have been published recently (Robledo et al. 2018, G3) and also implemented in the industry to help tackle this serious problem for salmon production (https://www.hendrix-genetics.com/en/news/improving-breeding-combat-amoebic-gill-disease-salmon/). These results have led to new methods of tackling a long term disease problem in aquaculture, and the methods used are likely to be utilized to tackle other important diseases, potentially in other aquaculture species. The award has also helped lead to a long term strategic partnership between Roslin and Hendrix Genetics in the area of aquaculture breeding and genetics.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Societal,Economic,Policy & public services

 
Description Advisory to European Food Safety Authority
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Impact I was involved as an expert adviser to the European Food Safety Authority regarding the potential of a DNA based vaccine for Pancreas Disease in salmon to integrate into the genome of the salmon. The review outcome contributed to a decision that the first DNA vaccine was approved for use in salmon in Europe, with positive impact on disease control, environment, economy, and animal welfare.
URL https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2017.4689
 
Description Advancing European Aquaculture by Genome Functional Annotation
Amount € 6,000,000 (EUR)
Funding ID 817923 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2019 
End 04/2022
 
Description BBSRC Responsive Mode
Amount £900,000 (GBP)
Funding ID BB/R008612/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description Genomic and nutritional innovations for genetically superior farmed fish to improve efficiency in European aquaculture
Amount € 6,149,963 (EUR)
Funding ID 818367 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 01/2019 
End 12/2022
 
Description Horizon 2020 - Food security, sustainable agriculture and forestry, marine and maritime and inland water research - Ross Houston - Mediterranean Aquaculture Integrated Development
Amount £290,823 (GBP)
Funding ID 727315 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2017 
End 04/2021
 
Description Horizon 2020 Call H2020-SFS-2016-2
Amount € 7,000,000 (EUR)
Funding ID 727315 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2017 
End 04/2021
 
Description Industry Partnership Award (TR) - Ross Houston - Improving resistance to infectious salmon anaemia using genome editing: Novel approaches to tackling viral disease in aquaculture
Amount £566,189 (GBP)
Funding ID BB/R008612/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description Newton International Fellowship
Amount £96,501 (GBP)
Funding ID NF160037 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2017 
End 02/2019
 
Description RCUK Newton-Picarte UK-Chile
Amount £339,925 (GBP)
Funding ID BB/N024044/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2016 
End 12/2018
 
Description Research Grant - Ross Houston - Genomic selection to enhance tilapia breeding
Amount £449,897 (GBP)
Organisation Worldfish 
Sector Charity/Non Profit
Country Malaysia
Start 09/2018 
End 12/2022
 
Description Scottish Aquaculture Innovation Centre
Amount £1,000,000 (GBP)
Organisation Scottish Aquaculture Innovation Centre 
Sector Multiple
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Scottish Aquaculture Innovation Centre (SAIC) (TR) - Ross Houston - Genomic breeding for gill health and lice resistance in salmon: Towards a step improvement in accuracy and affordability
Amount £314,771 (GBP)
Funding ID 4640007 
Organisation Government of Scotland 
Department Scottish Funding Council
Sector Public
Country United Kingdom
Start 05/2018 
End 05/2020
 
Description Standard - Ross Houston - ROBUST-SMOLT Impact of early life history in freshwater Recirculation Aquaculture Systems on A. salmon robustness and susceptibility to disease at sea
Amount £202,913 (GBP)
Funding ID BB/S00436X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021
 
Description Standard Grant - Ross Houston - AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production
Amount £403,285 (GBP)
Funding ID BB/S004343/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021
 
Description Collaboration with Benchmark PLC in salmon gene editing 
Organisation Benchmark Holdings
PI Contribution This collaboration has been to develop a successful Industrial Partnership Award proposal for BBSRC into gene editing for disease resistance in salmon. Our team have developed gene editing facilities and capability in house for salmon (cell culture and embryos), and worked together with Benchmark to codevelop the project which begins on 1 April 2018. The reference code is BB/R008612/1.
Collaborator Contribution The partners are bringing substantial in kind contribution, cash contribution and expertise to the project. This includes access to samples and data from their salmon breeding programme in Norway, and access to year-round salmon gametes for gene editing experiments.
Impact Outputs include the successful award of project BB/R008612/1
Start Year 2017
 
Description Strategic research partnership with WorldFish 
Organisation Worldfish
Country Malaysia 
Sector Charity/Non Profit 
PI Contribution A strategic research partnership has been established between Roslin and WorldFish. This partnership is initially focussed on use of advanced genetic and genomic technology to improve selective breeding of tilapia - one of the world's most important foodfish. Our contribution has included development of a research programme that builds on research performed in Atlantic salmon to inform strategies and techniques to implement genomic selection in WorldFish tilapia breeding programme.
Collaborator Contribution WorldFish run a family based selective breeding programme for tilapia and will provide data and samples from this programme to inform the research.
Impact This is a multidisciplinary partnership involving researchers involved in tilapia health, genetics, molecular biology and bioinformatics.
Start Year 2017
 
Description Organised a British Council Researcher Links conference in Mexico 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Co-organised a Researcher Links conference about Genomics in Aquaculture in Merida, Mexico in January 2017. This 5 day event featured around 40 scientists, with a mix of young researchers and mentors from both the UK and Mexico. This has already led to several collaborative links between UK and Mexico in this field.
Year(s) Of Engagement Activity 2017
URL https://sites.google.com/site/genomicsinaquaculturemxuk/home