Towards the causal factors underlying the genetic resistance of Atlantic salmon to infectious disease

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

Abstract

The sustainable production of fish through aquaculture faces a serious and persistent threat due to infectious disease outbreaks. Of particular relevance to the UK is the impact on Atlantic salmon of viral disease such as Infectious Pancreatic Necrosis (IPN) and Pancreas Disease (PD). For both these diseases, we see clear genetic differences between fish in their resistance, which can be exploited to reduce the incidence of disease, and its impact on production. The overall aim of this research is to use novel approaches to gain an understanding of host genetic resistance, focusing on the exemplar of a major locus underlying resistance to IPN. IPN is known to impact at two distinct windows of the salmon lifecycle; firstly in freshwater shortly after hatching, and secondly shortly after transfer to seawater. Our previous research has demonstrated that the genetic resistance to IPN across both windows of susceptibility is under the control of a single region of the genome (QTL). We have also begun to unravel the important genes and pathways underlying this QTL effect, through gene expression studies of disease-challenged fish of different genotypes. The rapid development of 'next-generation' sequencing technology offers novel opportunities to move towards locating and understanding the causal factors underlying this QTL. In doing so, the research will significantly advance our understanding of the salmon genome, and lead to advances in the fundamental understanding of disease resistance, providing an example of a hypothesised single mutation in the host genome with dramatically altered disease consequences. To achieve these goals, the proposed research will focus on creating the resources required to (i) identify the genes underlying the IPN QTL effects, (ii) determine the regions of the genome that affect resistance to PD, and (iii) to gain further understanding of the salmon genome and its inheritance. Firstly, a novel application of high-throughput DNA sequencing will be applied to fish of known QTL genotype to facilitate marker generation, and mapping of the QTL to a smaller region of the genome. Secondly, the gene expression profile of salmon will be characterised through cutting-edge sequencing techniques applied to genetically resistant and susceptible fish. Investigation of the genes, pathways and networks differing between the fish of alternative genotypes will yield information on the mode of action of the QTL . Thirdly, these results will be integrated through mapping relevant markers and sequences onto the salmon genome sequence. This will lead to putative functional disease resistance genes and genetic variation, which will be tested for causality. The resources generated will also be applied to map QTL underlying the resistance of salmon to PD, to investigate genetic signatures of selection in salmon, and aspects of the residual tetraploidy observed in the salmon genome. The outcomes of the research will include advances in knowledge of the mechanisms through which disease resistance loci drastically alter the outcome of infection, with implications for the interaction of host and pathogen genomes and their evolutionary arms race. The large-scale generation of salmon sequence data will lead to an improved annotation of the genes in the forthcoming salmon genome sequence. Furthermore, elucidation of the genes underlying salmon resistance to viral disease will lead to the development of genetic tests for improved resistance, and opportunities for novel vaccines and diagnostics, which can be applied in the salmon aquaculture industry to reduce disease-related mortality. The collaboration with salmon breeding company Landcatch Natural Selection Ltd ensures a clear route for the exploitation of the results.

Technical Summary

The sustainability of fish production in the UK is dependent on effective control of infectious disease outbreaks in aquaculture. Viral disease such as Infectious Pancreatic Necrosis (IPN) and Pancreas Disease (PD) can cause significant morbidity and mortality in Atlantic salmon production. The proposed research will focus on gaining an understanding of the polymorphisms, genes, pathways and networks explaining host genetic resistance to viral disease, with an initial focus on characterising a major QTL affecting IPN resistance. The resources to achieve this aim will be generated by capitalising on the rapid advances in high-throughput sequencing. Specifically, the novel application of deep sequencing to restriction enzyme associated DNA (RAD Tag technique) will facilitate the generation of large number of SNPs which will be applied for QTL fine mapping and LD analysis. Additionally, the salmon transcriptome will be characterised through digital profiling and sequencing techniques, and a focussed genetical genomics approach will be applied to investigate the effect of the alternative QTL genotypes on gene expression before and after infection. These results will be integrated through alignment with the salmon genome sequence, expected to be available in late 2010, facilitating the identification and functional testing of putative causal genes within that region. The data and resources generated are expected to assist with genome annotation, and will be applied later in the project to map QTL affecting resistance to PD, and to gain fundamental insight into the salmon genome and its inheritance. Knowledge of how perturbations in host genomic factors affect the dynamics of the host-pathogen relationship will significantly advance this area of science and lead to future collaborative projects. Furthermore, there is an immediate route of application of results to the salmon breeding industry through improved selection tools for disease resistance.

Planned Impact

Who will benefit from this research? The research proposed will have a diverse range of benefits for the scientific community and the salmon aquaculture industry. Furthermore, consumers and the general public will benefit from the effective implementation of the results, and the results will also be disseminated to policy makers to illustrate how this research can contribute to a sustainable aquaculture industry. How will they benefit from this research? Scientific community: The research will make an important contribution to the characterisation of the salmon genome, with downstream benefits for many genomics researchers. The refinement of cutting-edge next generation sequencing techniques for complex genome characterisation will also benefit a wide community, and increase my range of research skills and knowledge. Also, the improvement in fundamental knowledge of genetic resistance to disease and the host-pathogen interaction will advance several fields, including immunology, virology and evolutionary biology. Industry: This research program will lead directly to exploitable outputs within the aquaculture industry. The close collaboration with UK salmon breeding company Landcatch Natural Selection Ltd (LNS) will ensure the rapid application of mutations underlying disease resistance, and associated markers, as selection tools to improve disease resistance in commercial salmon populations. This will contribute to the economic output and overall sustainability of the aquaculture industry - a particularly important employer in rural economies - and help to advance the position of the UK as a global leader in salmon production. General Public and Policy Makers: The benefits to the salmon aquaculture industry described above will ensure the provision of high quality protein product and essential Omega-3 fatty acids to the public at reasonable cost, with the ensuing health benefits to society. The resulting improvements in fish health and welfare associated with the reduction of the impact of infectious diseases will improve the public perception of the acceptability of salmon production through aquaculture. Government policy makers will also benefit from the research through its contribution to a sustainable aquaculture industry. What will be done to ensure that they benefit from this research? Scientific community: The primary means for dissemination of the research results, and hence their benefits to the scientific community, will be publication in high-impact journals. In addition, I will present the results at a broad range of scientific meetings and seminars to disseminate the findings to audiences from alternative areas of science. Industry: I will arrange regular meetings with LNS throughout the project results and their implementation plans. Previous BBSRC-funded research by our group has led to LNS pioneering the application of marker-assisted selection within aquaculture, which will serve as an exemplar for future research exploitation. The results will also be communicated to the wider industrial community by taking part in various initiatives aiming to encourage academic-industrial communication. For example, the animal breeding and animal health sector of the Biosciences Knowledge Transfer Network (KTN) are located at Roslin, and assist with the application of research to industry through regular events and initiatives. Such opportunities should lead to new collaboration in other areas of aquaculture, animal breeding and animal health. General Public and Policy Makers: The research and results will be communicated to the public through various forums, including interaction with the media, presentations, publications, exhibitions and schools activities - supported by the Roslin Institute's policy of clear and open communication and public engagement. Regular participation in government-led initiatives will ensure effective communication with relevant policy makers.

Publications

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Gorjanc G (2015) Potential of genotyping-by-sequencing for genomic selection in livestock populations. in Genetics, selection, evolution : GSE

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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

 
Description The sustainable production of fish through aquaculture faces a serious and persistent threat due to infectious disease outbreaks. Of particular relevance to the UK is the impact on Atlantic salmon of viral disease such as Infectious Pancreatic Necrosis (IPN) and Pancreas Disease (PD). For both these diseases, we see clear genetic differences between fish in their resistance, which can be exploited via selective breeding to reduce the incidence of disease, and its impact on production. The overall aim of this research was to use high-throughput genomics approaches to gain an understanding of host genetic resistance, focusing on the exemplar of a major locus underlying resistance to IPN. IPN is known to impact at two distinct windows of the salmon lifecycle; firstly in freshwater shortly after hatching, and secondly shortly after transfer to seawater. Our previous research has demonstrated that the genetic resistance to IPN across both windows of susceptibility is under the control of a single region of the genome (QTL). In this fellowship project, restriction site associated sequencing (RAD-Seq) was applied to fine map the major locus to a smaller region of the genome, and to identify SNP markers associated with resistance at the population level. These SNP markers have been applied in marker-assisted selection to drastically reduce the prevalence of IPN on commercial salmon farms; one of the major success stories for genetic control of disease resistance in farmed animals.

To identify genes and networks underpinning resistance to the IPN virus, RNA and microRNA sequencing of resistant and susceptible salmon was performed. This highlighted a striking difference in response to viral infection between the genotypes, with susceptible fish demonstrating a large innate immune response that was substantially less in the resistant fish. Concurrently, pooled whole genome sequencing of resistant and susceptible salmon was used to discover and characterise all genomic variants within the region of the salmon genome containing the major resistance locus. Integrating these datasets with the salmon reference genome sequence enabled the identification of the most likely candidate causative SNPs, and experiments to assess their mechanism of action are underway using cell line models.

Additional outputs of the project included improved knowledge of salmon genome biology, and various genomics tools and resources for the study of salmon. These included high density linkage maps, a high density SNP array, genome annotation, and a microRNA database. In addition, a large scale experiment into the genetic basis of PD virus resistance resulted in mapping a second major resistance locus to chromosome 3 of salmon, and development of marker-based tests of resistance to this disease. Working alongside commercial partners has ensured that the results and technology developed in this fellowship have been rapidly applied in salmon aquaculture to help control viral disease outbreaks.
Exploitation Route Genetic markers to predict resistance will be used by the salmon aquaculture industry. The scientific discoveries relating to the genes and pathways contributing to disease resistance in salmon may form the basis for downstream studies into individual pathways and genes. The genomic resources (e.g. SNP markers, SNP array, genotyping-by-sequencing) will be widely applied by the academic community.
Sectors Agriculture, Food and Drink

URL http://www.biomedcentral.com/1471-2164/13/244
 
Description The main findings of this grant are related to genetic resistance of salmon to viral disease. This includes a genetic marker panel which is applied within commercial salmon breeding schemes to breed only from disease-resistant salmon. In addition, the grant has led to improved genomic resources for Atlantic salmon and has increase knowledge of the underlying factors contributing to genetic resistance. The research has contributed to a strategic research partnership between Roslin and Hendrix Genetics, which is building on the findings using new approaches to studying individual genes affecting resistance.
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
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 Response Mode
Amount £20,483 (GBP)
Funding ID BB/L024004/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2014 
End 07/2017
 
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 BBSRC Sustainable Aquaculture Call
Amount £249,324 (GBP)
Funding ID BB/M026140/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2015 
End 03/2017
 
Description European Commission 7th framework
Amount € 533,043 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 02/2014 
End 01/2019
 
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 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 NERC Aquaculture Innovation Award
Amount £202,253 (GBP)
Funding ID NE/P010695/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 12/2018
 
Description NERC Outline - Ross Houston - Vaccines for chronic viral pathogens in salmon- generation of interferon attenuated cell lines
Amount £26,843 (GBP)
Funding ID RG13822-10 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 12/2018
 
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 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 Technology Strategy Board Crop and Livestock Diseases
Amount £114,274 (GBP)
Funding ID 45266-329178 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 01/2015 
End 12/2017
 
Description Technology Strategy Board Genomes UK
Amount £110,149 (GBP)
Funding ID 5771-40229 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 08/2011 
End 07/2014
 
Title Atlantic salmon Illumina Sequencing 
Description Atlantic salmon microRNA raw Illumina sequence files (project 368) Atlantic salmon reduced representation Illumina sequence files (project 549) Atlantic salmon RNA-Seq raw Illumina sequence files (Project_607) 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
 
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
 
Title Genetic markers for disease resistant salmon 
Description Genetic markers were discovered that can predict whether Atlantic salmon are resistant to a viral disease, Infectious Pancreatic Necrosis. These are applied in salmon breeding programmes 
IP Reference  
Protection Protection not required
Year Protection Granted 2011
Licensed Yes
Impact The use of these markers was licensed to Landcatch Ltd which is a UK salmon breeding company. Their use of the test and marketing to other parties is covered by a licensing agreement and royalties are paid to University of Edinburgh.
 
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
 
Description School visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact This was a talk at a careers data at George Watson's school to inform pupils about life as a research scientist. The pupils were engaged and asked relevant questions, which led to interesting discussion about the possibilities for careers in biological science.
Year(s) Of Engagement Activity 2013