RCUK-CONICYT: Utilising functional genomic variation for improved disease resistance in Chilean salmon aquaculture

The economic burden of infectious disease hinders sustainable farmed Atlantic salmon production in Chile, and most aquaculture species worldwide. Targeting production of resistant stocks by selective breeding is a long term goal, and will contribute to disease control at a population level. Enabled by advanced genomics tools and technology, genetic improvement of disease resistance can be accelerated using genetic marker data to identify resistant parent fish in breeding programs. Further, the large families and the practical feasibility of large scale disease challenge experiments make salmon excellent models to discover genes and mutations underpinning host response to pathogens. Focusing on two of Chile's most problematic diseases (sea lice and Salmon Rickettsial Syndrome; SRS) in Atlantic salmon, this project will harness these genomic tools to (i) discover genes and functional variants affecting host response to infectious disease in farmed salmon and (ii) improve the use of genomic tools in breeding programs to increase population-level disease resistance via genomic prediction, and reduce the negative impact of outbreaks.

There is now a substantial genomic toolbox now available for Atlantic salmon (e.g. an advanced reference genome assembly and high density genetic marker arrays), this offers an unprecedented resource to locate specific genes and causative genomic variation underpinning host response to pathogens. In the proposed project, we will utilise data and samples previously collected from two large-scale disease challenge experiments (sea lice and SRS challenges. Genome-wide genetic marker data will be generated for all animals, and locating functional variants for resistance to each of the diseases will be achieved using the complementary approaches of (i) high power genome-wide association analysis; (ii) RNA-Seq (gene expression) comparison of the most resistant (R) and susceptible (S) individuals; (iii) Whole genome resequencing of pools of the R and pools of the S individuals combined with functional annotation. In addition to improving knowledge of the fundamental biology of host response to pathogens, these results have potential commercial relevance in at least two important fields. Firstly, the genes identified and their encoded proteins are potential drug or vaccination targets. Secondly, genomic regions and specific variants can be incorporated into selective breeding schemes, via improvement of the accuracy and cost-efficiency of genomic prediction of disease resistance. These results and techniques will lead to improved control of disease in Chilean aquaculture, and also provide a paradigm for tackling infectious disease problems via selective breeding in other farmed aquatic species worldwide.

The primary goal of this project is to tackle infectious diseases impacting on Chilean salmon aquaculture via improvements in host genetic resistance. This will be achieved via a multi-faceted genomics approach based on data and samples collected from previous large scale disease challenge experiments in commercial Chilean salmon populations. Our direct links with the salmon breeding and production industries mean that the outcomes of this project are likely to be immediately and enthusiastically translated into practice for positive economic impact. There will also be downstream beneficial impact for the scientific community via the tools and knowledge developed within the project, particularly contributions to the fields of disease biology and selective breeding. Finally, the general public and policy makers will benefit from improved efficiency and sustainability of salmon production, and the project is likely to have wider ranging impacts on the production of other aquatic species worldwide.

Industry: The bacterial disease SRS and the ectoparasitic sea lice are the two largest disease threats to stable and sustainable Chilean salmon aquaculture. Sea lice present the biggest problem for salmon farming globally, causing issues relating to fish health and welfare and the environment, in addition to large negative financial impact. Therefore, routes to tackle lice and SRS are clear industry priorities. The outcomes of this project have both direct and long term potential for positive impact by reducing the number and severity of outbreaks of these diseases, in Chile but with potential for global application. This will be achieved firstly by the application of the cost-efficient genomic prediction for resistance in commercial salmon populations in Chile, via the link with AquaInnovo. The specific functional variants identified may have wider applications as molecular genetic tests for resistance that can be utilised by other breeders and producers. Further, the knowledge of the genes and mutations underpinning host resistance may guide vaccination and drug studies, or at least provide potential targets worthy of further research.

Scientific Community: The project outcomes will be of considerable interest and value for researchers in several related fields. The first and most obvious impact will be fundamental knowledge of the host response to SRS and sea lice in salmon. Since disease challenge experiments in aquaculture species tend to be undertaken on a scale that is not practical / possible in other species, the results may have significant value for improving understanding of host-pathogen interaction, and the causal factors underlying genetic variation in resistance. The incorporation of functional variation into genomic prediction models also presents an exciting avenue of research of potential interest to quantitative geneticists and animal breeders. Further, the project will provide substantial training for the PDRA as well as project management development opportunities for the team as a whole.

General Public and Policy Makers: The improvement of infectious disease control in aquaculture increases the stability and sustainability of a high quality protein product, potentially resulting in health benefits to society. In addition, the economic benefits to the industry will help support the tens of thousands of jobs that rely on aquaculture in Chile. The project also has potential to transform the control of infectious disease on a global aquaculture scale, through innovations in tools and techniques applied to selective breeding, including in developing countries. Government policy makers are likely to benefit from the research through its contribution to a sustainable aquaculture industry. The research will be communicated to the public via interaction with the media, presentations, publications, exhibitions and schools activities - supported by a policy of clear and open communication and public engagement.