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

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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.
 
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