Utilising functional genomic variation for improved disease resistance in Chilean salmon aquaculture

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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.