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 pathogens) 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
Gratacap RL
(2019)
Potential of Genome Editing to Improve Aquaculture Breeding and Production.
in Trends in genetics : TIG
Houston R
(2017)
Future directions in breeding for disease resistance in aquaculture species
in Revista Brasileira de Zootecnia
Kriaridou C
(2020)
Genomic Prediction Using Low Density Marker Panels in Aquaculture: Performance Across Species, Traits, and Genotyping Platforms.
in Frontiers in genetics
Palaiokostas C
(2018)
Genome-wide approaches to understanding and improving complex traits in aquaculture species.
in CABI Reviews
Robledo D
(2020)
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing.
in BMC genomics
Robledo D
(2018)
Applications of genotyping by sequencing in aquaculture breeding and genetics.
in Reviews in aquaculture
Robledo D
(2018)
Genome-Wide Association and Genomic Selection for Resistance to Amoebic Gill Disease in Atlantic Salmon.
in G3 (Bethesda, Md.)
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Simm G
(2021)
Genetic improvement of farmed animals
Tsai HY
(2017)
Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon.
in G3 (Bethesda, Md.)
Tsai HY
(2015)
Verification of SNPs Associated with Growth Traits in Two Populations of Farmed Atlantic Salmon.
in International journal of molecular sciences
Tsai HY
(2016)
Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations.
in Genetics, selection, evolution : GSE
Tsairidou S
(2020)
Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon.
in G3 (Bethesda, Md.)
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 | 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 | 04/2019 |
End | 04/2022 |
Description | BBSRC Responsive Mode |
Amount | £1,640,000 (GBP) |
Funding ID | BB/V009818/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2021 |
End | 08/2025 |
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 | 03/2018 |
End | 03/2021 |
Description | Direct funding from Industry (Hendrix Genetics) - Genome editing for resistance to IPNV in salmon |
Amount | £180,892 (GBP) |
Organisation | Hendrix Genetics |
Sector | Private |
Country | Netherlands |
Start | 06/2016 |
End | 03/2019 |
Description | Genome editing for resistance to viral disease in rainbow trout |
Amount | £161,786 (GBP) |
Organisation | Hendrix Genetics |
Sector | Private |
Country | Netherlands |
Start | 11/2020 |
End | 02/2022 |
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 | 04/2017 |
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 | 04/2017 |
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 | 03/2018 |
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 | 08/2018 |
End | 12/2022 |
Description | Scottish Aquaculture Innovation Centre |
Amount | £1,000,000 (GBP) |
Organisation | Scottish Aquaculture Innovation Centre |
Sector | Multiple |
Country | United Kingdom |
Start | 03/2018 |
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 | 04/2018 |
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 |
Country | United Kingdom |
Sector | Private |
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 | Roslin and Worldfish have a strategic research partnership since 2018 which focuses on selective breeding of Nile tilapia, one of the world's most important farmed fish species. Roslin scientists are developing genomic tools, and investigating how those genomic tools can be used to improve disease resistance of tilapia via breeding. |
Collaborator Contribution | The partners WorldFish run a tilapia breeding programme which provides samples and data to support the research undertaken at Roslin. This breeding programme also provides the route to impact by which the improved strains can be disseminated to benefit low and middle income country fish farmers. |
Impact | This has led to a peer reviewed publication https://www.sciencedirect.com/science/article/pii/S0044848619331837 describing genetic resistance to tilapia lake virus, which is one of the most problematic pathogens for global aquaculture. The story was presented in news form via the University of Edinburgh https://www.ed.ac.uk/edinburgh-infectious-diseases/news/news/genetic-resistance-to-lethal-virus-in-farmed-fish and also Science magazine https://www.sciencemag.org/news/2020/03/emerging-virus-killing-farmed-fish-breeders-can-help-them-fight-back |
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 | New Scientist Future of Food Webinar |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Ross Houston took part in the New Scientist Future of Food and Agriculture workshop by taking part in a panel discussion on genome editing. |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.newscientist.com/science-events/future-food-agriculture/ |
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 |