Applying genomics to establish mechanisms of disease resistance against a virus impacting on a globally farmed fish, the Common Carp (Cyprinus carpio)

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With a growing global population, the demand for food is increasing rapidly. Wild fish stocks have been subjected to unsustainable over exploitation, resulting in major population declines, and we are increasingly reliant on aquaculture (the farming of fish) to meet our global needs. Aquaculture provides over 50% of the supply of harvested aquatic organisms for consumption (over 70 million tons), and is an important source of animal protein for billions of people. The contribution of aquaculture is predicted to rise to over 60% by 2030. However, further intensification will increase the risk of disease due to high stocking densities, low genetic diversity in brood-stocks, and increased pathogen dispersal associated with international trade. Traditionally, disease in farming is managed by pesticides/antibiotics or vaccines. These however offer only a short term and unsustainable solution to disease prevention as pathogens/vectors can evolve resistance to medications, resulting in re-emerging infectious diseases. The security of aquaculture is of paramount importance and so new disease control methods must be developed to ensure global food security.Cutting edge DNA research offers an approach to help manage disease in aquaculture. DNA provides the blueprint for how living cells function and interact, and DNA variation results in the diversity of life we observe, controlling key biological characteristics such as appearance, behaviour, and disease susceptibility. The objective of my research proposal is to identify the differences in DNA between individuals of an important aquaculture fish species, the Common Carp (Cyprinus carpio), that are either resistant or susceptible to the deadly Koi Herpesvirus (KHV). Importantly, this is the first project to characterize global DNA variation in carp and KHV, which is an essential component in understanding and managing disease. Understanding host defence systems and the variable genomic components in the DNA that confer disease resistance, may offer part of the solution to the problems facing aquaculture, enabling farmers to create diverse brood-stocks with resistance to local pathogens. The analysis tools developed in this BBSRC fellowship can be applied to other emerging infectious diseases of carp, and the research can be used as a blueprint for other species in aquaculture.Common Carp is the third most farmed fish globally and is worth billions of pounds per annum. Aside from its global importance as a protein source for millions of people, it is also farmed in the UK and Europe for angling and as an ornamental strain (Koi). Alone, the carp fishing industry in the UK is worth over two billion pounds per annum. Huge financial losses have occurred in the carp industry through the rapid global spread of KHV. Despite the global value of carp and its vulnerability to viral outbreaks, genetically informed selective breeding is non-existent. This is a major limitation for the expansion of the industry and surprising given strong recommendations from the Food and Agriculture Organization (FAO) for intensified understanding and control of carp diseases (2004), and the fact that genomic techniques are now available to apply to such problems.By testing individuals from around the world for gene variants that promote resistance, and understanding the geographic patters of viral diversity, carp can be artificially selected by farmers to produce fish that are robust to infection from local strains of deadly viruses. Research focused purely on controlled laboratory infection trials in single host and viral strains, will produce findings that may be of little relevance to real-world aquaculture that comprises many strains of both host and pathogen. As such, I will pioneer a global plan for immuno-genomics informed selective breeding in carp aquaculture, which will contribute to promoting food security in this important species of fish.