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

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.

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.

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.