Towards lice-resistant salmon: functional genetics and genome editing to enhance disease resistance in aquaculture
Lead Research Organisation:
University of Stirling
Department Name: Institute of Aquaculture
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Improving genetic resistance of farmed salmon stocks is a promising but underutilised component of preventing the economic and animal welfare burden caused by sea lice. While selective breeding incrementally increases host resistance, it is restricted to utilising genomic variants segregating in the broodstock. Genome editing approaches offer new opportunities to create de novo resistance alleles, or to introgress resistance alleles from closely related species. Therefore, understanding and harnessing within and across species variation in sea lice resistance in salmonids is a key goal.
While Atlantic salmon are susceptible to lice, certain Pacific salmon such as coho are highly resistant. This resistance is mediated by a localised epithelial hyperplasia coupled with immune cell infiltration in the first few days after louse attachment. This project focusses on understanding and exploiting the functional mechanisms underpinning this response. Harnessing large scale disease challenge and pedigree data provided by the industrial partner Benchmark, the team will map and characterise genes underpinning host resistance in Atlantic salmon. This will be coupled by a detailed temporal profiling of the localised host response using single cell RNA sequencing of attachment sites in resistant and susceptible fish, within and across species. Putative targets for immunomodulation by the parasite will also be identified using a yeast-two-hybrid approach with known louse secretory proteins.
The high-throughput genomic data will provide a list of putative key resistance genes and pathways for further filtering using CRISPR editing in a primary cell culture model system. This will culminate in high priority targets for in vivo editing, followed by assessment of the relative resistance to sea lice in edited salmon versus unedited controls. A successful outcome of an edited Atlantic salmon with resistance to sea lice has potential to transform global aquaculture.
While Atlantic salmon are susceptible to lice, certain Pacific salmon such as coho are highly resistant. This resistance is mediated by a localised epithelial hyperplasia coupled with immune cell infiltration in the first few days after louse attachment. This project focusses on understanding and exploiting the functional mechanisms underpinning this response. Harnessing large scale disease challenge and pedigree data provided by the industrial partner Benchmark, the team will map and characterise genes underpinning host resistance in Atlantic salmon. This will be coupled by a detailed temporal profiling of the localised host response using single cell RNA sequencing of attachment sites in resistant and susceptible fish, within and across species. Putative targets for immunomodulation by the parasite will also be identified using a yeast-two-hybrid approach with known louse secretory proteins.
The high-throughput genomic data will provide a list of putative key resistance genes and pathways for further filtering using CRISPR editing in a primary cell culture model system. This will culminate in high priority targets for in vivo editing, followed by assessment of the relative resistance to sea lice in edited salmon versus unedited controls. A successful outcome of an edited Atlantic salmon with resistance to sea lice has potential to transform global aquaculture.
Publications

Elumalai P
(2023)
Fish Vaccines - Health Management for Sustainable Aquaculture

Robinson NA
(2023)
Applying genetic technologies to combat infectious diseases in aquaculture.
in Reviews in aquaculture

Salisbury S
(2024)
Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon
in BMC Biology
Description | Enhanced capacity for conducting fish disease research at Cefas |
First Year Of Impact | 2024 |
Sector | Agriculture, Food and Drink,Environment |
Impact Types | Societal |
Description | Advisory meeting with Veterinary Medicines Directorate to discuss ways to improved health and welfare of farmed fish |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | Appointed to European Union workgroup on Listing and Categorisation of Aquatic Diseases |
Geographic Reach | Europe |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | Canadian Ministerial Roundtable on Aquaculture Science |
Geographic Reach | North America |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | Consultation with Chief Scientist Scotland |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | MSc education |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Panel on availability of vaccines for the aquaculture sector - discussion with Chief Scientific Adviser for Scotland |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | PhD Education - Appointment to EASTBIO Doctoral Training Partnership management group |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | PhD education |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Influenced training of practitioners or researchers |
Description | Development of a mucosally-delivered and active salmon louse vaccine for Atlantic salmon aquaculture |
Amount | £1,209,358 (GBP) |
Funding ID | BB/Y006534/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 03/2027 |
Description | Harnessing cross-species variation in sea lice resistance |
Amount | £3,384,347 (GBP) |
Funding ID | 901631 |
Organisation | FHF - Fiskeri- og havbruksnæringens forskningsfinansiering |
Sector | Private |
Country | Norway |
Start | 01/2021 |
End | 12/2024 |
Title | Flow-through challenge of coho salmon with sea lice |
Description | Developed a successful flow-through challenge model for infecting coho salmon with sea lice |
Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
Year Produced | 2024 |
Provided To Others? | No |
Impact | Impacts still pending analysis of research outcomes |
Title | Tissue samples for Coho and Atlantic salmon infected with sea lice |
Description | Timecourse samples of infected Atlantic salmon and Coho salmon tissues |
Type Of Material | Database/Collection of data |
Year Produced | 2024 |
Provided To Others? | No |
Impact | Impacts and availability to others pending initial analysis of tissues |
Description | Characterisation of function of parasite anti-host secretions |
Organisation | University of Bergen |
Country | Norway |
Sector | Academic/University |
PI Contribution | Providing knowledge, facilities, expertise, biological resources and biological samples for shared research interests |
Collaborator Contribution | Providing knowledge and expertise and analytical capabilities for shared research interests |
Impact | Shared knowledge and expertise |
Start Year | 2023 |
Description | Collaboration with Rothamstead |
Organisation | Rothamsted Research |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Expertise on sea lice and salmon tissue / mucus samples |
Collaborator Contribution | Expertise on semiochemicals in sea lice and other arthropod pests |
Impact | None yet |
Start Year | 2021 |
Description | Collaboration with University of Melbourne |
Organisation | University of Melbourne |
Country | Australia |
Sector | Academic/University |
PI Contribution | Expertise with sea lice, immunology and bioinformatics |
Collaborator Contribution | Expertise in genetics for selective resistance in livestock |
Impact | None yet |
Start Year | 2021 |
Description | Conducting disease-associated microbiome composition research in salmonids |
Organisation | University of Copenhagen |
Department | Faculty of Health and Medical Sciences |
Country | Denmark |
Sector | Academic/University |
PI Contribution | Providing resources, biological samples and expertise to help further research on disease-associated microbiome composition in salmonids |
Collaborator Contribution | Partners are conducting disease-associated microbiome composition research in salmonids and are able to use and analyse material and employ knowledge generated by challenge trials conducted under this award. |
Impact | Biological material has been jointly generated and sampled by collaborating parties. |
Start Year | 2023 |
Description | Enhanced understanding of transcriptome of infective sea louse stages exposed to host chemicals |
Organisation | Institute of Marine Research |
Country | Portugal |
Sector | Public |
PI Contribution | Transcriptomic research on sea louse responses to salmon host generated chemicals (kairomones) |
Collaborator Contribution | Partners provided facilities and expertise allowing us to obtain biological material for studying transcriptome of infectious stages exposed to host chemicals (kairomones) that ties in with their behavioural experiments |
Impact | Biological material collected in Norway and initial transcriptomics analysed. |
Start Year | 2023 |
Description | Aquaculture Mini-Conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Undergraduate students |
Results and Impact | Series of talks and debates concerning aquaculture between University of Stirling Researchers and undergraduate students. Students from diverse backgrounds, biology, computing business and economics reported enhanced awareness and understanding of aquaculture and its impact and potential. |
Year(s) Of Engagement Activity | 2024 |
Description | I'm a scientist get me out of here |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Text discussions with a variety of UK based primary and secondary school children concerning scientific careers and details of current research activities. Students and teachers reported high engagement and enhanced appreciation of science careers and research |
Year(s) Of Engagement Activity | 2024 |
URL | https://imascientist.org.uk/ |
Description | Press Release "Scots aim for lice-resistant salmon" |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Press release on "The Fish Site", which lists its readership as "...aquaculturists who are interested in sustainable production, general farming techniques and innovation" and "...Innovators, investors, suppliers, academics/researchers, NGOs and other change leaders". Readership estimated at >2.3 million unique users. |
Year(s) Of Engagement Activity | 2022 |
URL | https://thefishsite.com/articles/scots-aim-for-lice-resistant-salmon-genolice |