Improving resistance to infectious salmon anaemia using genome editing: Novel approaches to tackling viral disease in aquaculture

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


Farmed salmon is a major source of high quality protein and fatty acids essential for human health. Salmon aquaculture is worth approximately £1Bn to the UK economy, and supports many rural and coastal communities. However, disease outbreaks have a major negative effect on salmon production and animal welfare. Infectious salmon anaemia (ISA) is one such disease, and is sometimes dubbed 'salmon flu' because it is caused by a virus (ISAV) that is similar in to influenza. At present, ISA is a notifiable disease in the UK, meaning farmers are obliged to cull their stock in the event of an outbreak. Vaccination and biosecurity cannot fully prevent outbreaks, and developing disease resistant strains of salmon is high priority.

Selective breeding can result in moderate improvements in disease resistance of salmon stocks and may take many generations. However, a revolutionary approach known as genome editing has potential to rapidly increase the rate at which disease resistant salmon can be produced. Genome editing involves the use of "gene scissors" to precisely cut the genome at a specific location, leading to small-scale targeted changes in the DNA sequence. In this proposal, genome editing technology will be used to investigate genes underlying resistance to ISAV, and potentially to produce a disease-resistant salmon.

The first stage of the project is to identify target genes that will be edited. This will be achieved by measuring the ISAV resistance in a selective breeding program. Genetic markers dispersed throughout the salmon genome will then be used to map individual genes that contribute to variation in resistance in the population. Salmon from resistant and susceptible families will also be sequenced and to identify candidate genes and mutations causing this genetic effect on resistance to ISAV.

In parallel to the 'forward genetic' approach described above, a 'reverse genetic' approach to identifying ISAV resistance candidates will be employed using cell culture models. A genome editing method known as CRISPR-Cas9 will be applied to destroy the function of key candidate ISAV resistance genes in the cell lines. Two methods of choosing candidate genes will be used. The first is based on prior knowledge of the biology of the interaction between the virus and the host cell, partly harnessing extensive research which has been performed on ISAV's close relative influenza. The second is to use the genes affecting natural resistance identified in the forward genetic screen described above. These edited cell lines will be infected with ISAV, and the impact of the edited gene on ISAV resistance and cellular response to infection will be assessed. This will build on an ongoing project to develop genome editing for salmon cell lines.

Finally, genome editing will be used in Atlantic salmon embryos to test the highest priority ISAV resistance genes, especially where knockout of the gene has an impact on resistance in cell culture. Targeted editing of the genes will be performed by microinjecting newly fertilised embryos, which will be reared until the freshwater fry stage. These edited embryos, and unedited controls from the same family, will be challenged with ISAV. The nature and frequency of the edited genes in the resistant and susceptible salmon will be measured.

This proposal has potential to create Atlantic salmon with resistance to a problematic viral disease (ISA) using a novel breeding technology. As such, it could have major animal welfare and economic impacts via prevention of outbreaks and subsequent culling of stocks. The approaches will be directly relevant to other viral disease in fish aquaculture. While the regulatory landscape for application of edited animals in food production is uncertain, a successful outcome of this proposal will provide a high profile example of the power of this technology to understand biology and to improve food security and animal health.

Technical Summary

Salmon aquaculture is worth approximately £1 billion per annum to the UK economy and is the primary source of employment in many rural and coastal communities. Infectious disease epidemics constrain sustainability and expansion, and cause major negative economic and animal welfare impact. Infectious Salmon Anaemia Virus (ISAV) is a notifiable disease that requires culling of stocks for control. Improving genetic resistance of salmon stocks is a critical component of tackling ISAV. Genome editing raises the possibility of creating targeted and informed de novo disease resistance alleles (e.g. CD163 deletions for PRRS virus in pigs), and to test the causality of naturally-occurring variants, and potentially increase genetic gain in breeding programs. ISAV is a close relative of influenza, and knowledge of the conserved function of viral binding, internalisation and replication across orthomyxoviridae is one route to identifying target genes for editing.

This proposal will use forward and reverse genetics to identify genome editing targets for resistance to ISAV in Atlantic salmon. Harnessing large scale disease challenge and pedigree data provided by the industrial partner Benchmark, the team will map and characterise genes underpinning host resistance. Genome editing will be applied in cell culture to screen putative functional resistance candidate genes, with targets including 'naturally-occurring' variants, and de novo targets with a predicted key role in the ISAV host-cell interaction. These approaches will deliver high priority candidates for in vivo genome editing of salmon embryos, followed by an ISAV challenge to assess the resistance of the edited fish. The outcomes will include fundamental knowledge of mechanisms of genetic resistance to ISAV, and potential novel strategies to combat viral diseases impacting on salmon aquaculture. As such, it is aligned to the BBSRC priorities on 'Sustainably enhancing agricultural production' and 'Animal health'.

Planned Impact

This proposal is applying novel and innovative methods with potential to develop an Atlantic salmon with resistance to ISAV as a result of genome editing. This outcome, and the research that leads to it, is likely to have high impact for academic, industry, government and societal groups.

It is likely that the major impact of the proposal will be medium and long term, due to uncertainty over the regulatory landscape and public appetite for genome editing technologies. However, high profile success stories are key, and this proposal has high potential to deliver such success stories. Use of genome editing to produce a disease resistant food fish has animal welfare, environmental and economic benefits.

It should also be noted that intermediate impacts of the research will include improved methods of genomic selection for disease resistance in aquaculture breeding, improved knowledge of host-pathogen interaction for ISAV, and optimised methods of using CRISPR-Cas9 for animal bioscience research. The following groups can expect positive impact from the proposal:

(i) UK and global aquaculture industry: ISAV has a major negative impact on aquaculture production, and is a notifiable disease in the UK. This proposal has potential for developing disease-resistant strains of salmon within a relatively short timeframe, and major breeding companies such as Benchmark view genome editing as a high priority R&D activity. While the regulatory landscape for genome editing is uncertain at present, achievement of the aims of this proposal is likely to be a driver to incorporate this technology to benefit food production.

(ii) Animal breeding industry: The improved genomic selection arising from the identification of functional genomic variants will have short term impact on selective breeding programmes. In the longer term, aquaculture species such as salmon are amenable to genome editing due to their high fecundity and easily visible embryos, and may be a good model for other species.

(iii) UK economy: This project has potential for long term impact for the UK economy via improved sustainable production of a high quality food product with reduced environmental impact. There will be direct contribution to the UK treasury via improved market share for the project partner Benchmark, and downstream impacts on fish farming companies, and the communities that depend on these industries.

(iv) Academic community: The impact for academic groups will include improved knowledge of the genetic basis of resistance to ISAV in salmon, specific genes and mutations impacting resistance, and improvement in methods of effective genome editing of cell lines and embryos.

(v) UK science capacity. This project will enable capacity and expertise for application of genome editing technology to address (applied) biological questions via research programs in academia and industry. This should lead to the UK taking a leading global position in the application of this technology for animal research and production.

(vi) Political and regulatory bodies. The regulatory landscape of genome editing currently precludes its use for food production in the short term. Successful achievement of the objectives of this project will influence ethical and regulatory frameworks to encourage full exploitation of genome editing in an informed and responsible manner.

(vii) General public and society. This project has potential to influence societal attitudes to genome editing in aquaculture and, more broadly, in food production animals. In the longer term, there will be direct benefits to society via improved economic stability and reduced environmental impact of the aquaculture industry.
Description The key findings of this award to date have been (i) that resistance to Infectious Salmon Anaemia virus (ISAV) is a heritable trait in a commercial population of Atlantic salmon, (ii) regions of the salmon genome that explain genetic variation in resistance to ISAV, (iii) key differences in the gene expression response between resistant and susceptible fish when challenged with ISAV. In addition, methods for efficient genome editing of salmonid fish cell lines have been developed which have allowed effective testing of gene knockout approaches in several cell lines, followed by viral challenge to assess their impact. The project resulted in a high profile review paper published in Trends in Genetics about the potential of genome editing in aquaculture species. There have also been two publications related to the cell line CRISPR methods, and a paper under review highlighting the genetic and genomic basis of host response to ISAV.
Exploitation Route In the short term, the results allow the collaborating commercial partner Benchmark Genetics to improve genomic selection to enhance resistance to ISAV in salmon. In the medium term, the optimization of genome editing, and the improved knowledge of host resistance to ISAV in salmon, will help researchers in academia and industry to make further advances in the field. In the longer term, the results may lead to a genome edited salmon with improved resistance to ISAV. Further funding has been successfully achieved working with Benchmark Genetics to tackle sea lice using genomics and genome editing methods.
Sectors Agriculture, Food and Drink

Description This project and its partners have been actively involved in stakeholder engagement to discuss regulatory issues around the use of genome editing in aquaculture, including contribution to USDA, FSA, and Defra discussions on this topic.
Sector Agriculture, Food and Drink
Impact Types Societal,Policy & public services

Description Contribution to International Council for Exploration of the Sea, Working Group on Application of Genetics in Fisheries and Aquaculture
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a guidance/advisory committee
Description Scottish Salmon Producers' Organisation Industry Blueprint Workshop
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
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 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 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 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 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 and also Science magazine
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