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

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.

Over 50% of harvested aquatic biomass comes from aquaculture, which may rise to 60% by 2030. Intensifying aquaculture will increase pandemics associated with high stocking densities, low genetic diversity in brood-stocks, and increased pathogen dispersal with international trade. New disease prevention methods are needed for global aquatic food security. I will examine global variation in the genome associated with disease resistance to Koi Herpesvirus (KHV) in a widely farmed fish, the Common Carp (Cyprinus carpio). I will use whole genome sequencing and develop a powerful candidate gene approach, sampling carp survivors and non-survivors of KHV outbreaks in populations, also utilizing experimental data. The data derived can be applied directly to reduce viral pandemics and promote aquatic food security through selective breeding of carp for increased immuno-competence.
The objectives of my fellowship are:
1: Characterize genome-wide patterns of immuno-genetic evolution and resistance to KHV in carp using novel using novel PacBio and HiSeqX based genome assemblies of KHV resistant and non-resistant individuals. Additionally, utilizing published genomic resources this will significantly improve understanding of the evolution of the immune system though identifying causal SNPs, LGs, and CNV. It will enable examination of mechanisms that facilitate disease resistance at the genomic level (e.g. DNA recombination).
2: Characterize global patterns of diversity and KHV resistance among carp strains using targeted sequencing (MyBaits, HiSeq2500) of ~1000 immune, and immune related genes in 600 individuals by mapping SNPs to the new high-quality carp genome assemblies to identify haplotypes, LGs, CNV and genomic regions associated with KHV resistance.
3: Using targeted sequencing (MYBaits, HiSeq2500), characterize geographic distribution of genome-wide variation of KHV strains to quantifying speed/mode of evolution, and transmission routes.

My fellowship will produce high-impact outputs of social and economic importance across a wide range of beneficiaries.

Who will benefit?
Aquaculture Industry: The global value of finfish aquaculture is over £80 billion. Farming of carp species accounts for over 40% of the global aquaculture production, and 70% of freshwater production. Common Carp account for over 10% of freshwater production, and are a focus of future expansion to meet global food requirements. Carp are farmed for consumption in over 100 countries, and Koi are reared globally.

Biotech Industry: Development of novel disease detection and management strategies is important for food security during increased intensification of aquaculture. Application of host and viral genomic information for field based disease monitoring technologies is high on the agenda for Biotech companies.

Third Sector: Non-profit organisations aim to reduce world hunger though promoting aquaculture security in lower to middle income counties (LMICs). For example, WorldFish (www.worldfishcenter.org/) is an international, non-profit research organization that harnesses the potential of fisheries and aquaculture to reduce hunger and poverty.

Policy makers: Understanding the genetics of farmed species is recognized as key in promoting and preserving agriculture and aquaculture. Informed decisions can only be made by policy makers with a sufficient knowledge of national/global brood-stocks and populations.

The Public: Carp are a source of protein for millions of people around the world. Farmers in LMICs operate small scale/subsistence production, with a local workforce. Carp promote financial security and social stability in local/rural areas in many countries, and is an "ecologically sustainable" farmed species omitting the need for expensive fish-based feed. In Europe, fishing is among the top social pastimes, and so tens of millions of anglers in Europe will also benefit from carp preservation.

How will they benefit?
Aquaculture Industry: Rapid spread of KHV around the globe caused huge financial loses. In the UK and Europe KHV outbreaks increase each year. The application of genomic data could significantly improve disease resistance in in farmed carp strains though selective breeding. This can curtail viral outbreaks, further economic impacts, and promote security of this important finfish.

Biotech Industry: Understanding the genomics of KHV resistance could lead to simple genetic assays to test for KHV resistance, and detect KHV infection, improving management of valuable populations. Given the size of the carp aquaculture market, there is considerable scope for Biotech companies to deploy novel field based detection methods of viral strains. This would protect both industrial and subsistence sized farmers, and the angling industry.

Third Sector: Non-profit research organizations (e.g. WorldFish) would benefit by access to results and engagement in dissemination activities, thereby promoting food security, quality of life and economic benefits in the poorest nations. They also distribute carp brood stocks and so would benefit greatly from gaining access to genetically diverse and disease resistant brood stocks.

Policy makers: Legislation and recommendations can be informed by understanding the genomic composition and functionality of farmed fish populations. Access to genomic data which characterizes disease resistance of host and patterns of pathogen spread can help to inform practices of international trade, and local management strategies to improve disease management.

The public: Protecting carp production promotes food, financial and environmental security for many societies. Angling in the UK alone is worth billions of pounds per annum and protecting this industry will promote job security and preservation of a popular recreation. Promoting the understanding of carp disease and their preservation will be of significant cultural value in Europe.