Epigenetic management of stress and disease resistance in Atlantic salmon

World fish consumption is expected to reach c. 180 million tons by 2015, most of which will have to come from farmed fish, as the majority of wild fisheries are either stagnant or grossly over-exploited. To meet future global food demands, aquaculture is expected to intensify production, delivering fish that will have to thrive at high densities on less water, less food and less space. However, stress during intensification can compromise the capacity of organisms to respond to pathogens, making them more susceptible to infectious diseases, though the underlying mechanisms are poorly understood.

We will combine the expertise of salmon biologists, geneticists, bioinformaticians and parasitologists to determine how stress experienced during early life affects immune-competence and fitness of Atlantic salmon later in life, enabling them to cope with pathogens and respond to subsequent stressors. To achieve this we will manipulate stress during embryo development combining a brief cold shock and air exposure, and assess the relative roles of immune-related genes and epigenetic programming (DNA methylation) on subsequent resistance to Saprolegnia parasitica, a pervasive fish pathogen that costs the salmon farming industry tens of millions of pounds in losses every year and that can also cause considerable damage to wild salmon populations.

Ultimately, the aim of our research is to investigate how knowledge of the effects of early life conditions on the epigenome could be incorporated into programmes for stress management and disease resistance in fish farming, thereby facilitating aquaculture intensification while minimising impacts on wild stocks.

To meet global food demands, aquaculture is expected to intensify fish production, but stress during intensification can also compromise animal health, particularly during early life when the teleost immune system is being formed. Many farmed fish are already highly inbred and further intensification will likely make them more susceptible to infectious diseases and pathogens more detrimental. Stress during intensification could change the expression of genes via epigenetic programming, but knowledge of fish epigenomes is very limited.

To address this knowledge gap, information is required on how stress experienced during early life can change the epigenome and subsequently affect the ability of fish to respond to pathogens. We will employ a BACI design to manipulate stress in Atlantic salmon during embryogenesis and assess its effects on subsequent gut health and fitness of three month old fry by carrying out a gut bacterial community profiling using targeted 16S rDNA sequencing followed by gut metagenomics. As a fitness indicator we will examine fluctuating asymmetry. We will then use the standardised ami-momi procedure to challenge fry with Saprolegnia parasitica, a pervasive fish pathogen, and monitor fry survival in relation to expression of immune-related genes through RNAseq, and patterns of DNA methylation in head kidney by Restricted Representation bisulphite sequencing (RRBS) on the same individuals. By following fish from fertilization to first feeding, we will be able to relate the effects of early stress to (1) health, (2) an indicator of fitness and (3) resistance to Saprolegnia, and examine these in relation to variation in the genome and the epigenome of different families.

This will be the first study to quantify the effects of stress during embryogenesis on gut health, developmental instability, and resistance to Saprolegnia infections in fish using an epigenomic approach.

The work we propose has great potential for improving the economic competitiveness of the UK fish farming industry, by providing practical, evidence-based advice in relation to stress management and disease resistance of young fish. Results from our study will pave the way for incorporating knowledge of the epigenome into intensive fish farming, and should advance on the domestication of fishes, improving production while maintaining good welfare in the face of emerging threats posed by pathogens that may become more detrimental under predicted climate change scenarios.

An anticipated outcome of the research we propose will be development of guidelines and best-practice for the epigenetic management of stress and disease resistance in fish embryos. Better control of stress levels may result in reduced infection and higher productivity for the fish farmer, and potentially reduced costs in the supermarket for the consumer. Likewise, knowledge on the relative roles of genetic and non-genetic mechanisms underlying disease resistance will increase productivity and welfare. Our research will also have environmental benefits. By improving the extent of genetic and epigenetic adaptation in captivity, farmed fish are likely to become increasingly maladapted to survive in the wild. In turn, this will decrease the probability of escapees becoming established and may mitigate for some of the negative impacts of aquaculture on wild populations. Our research could also benefit conservation programs, where careful consideration of the effects of conditions during early life may in the naturalization of hatchery fish and aid in reintroduction programmes. Our research will also have significant animal-welfare benefits. Identifying epigenetic and genetic mechanisms underlying disease resistance could lead to the development of better fish breeding practices.

We envisage that research developed in this proposal will make a significant contribution to the development of more sustainable ways of feeding the planet. Some current practises of livestock production are unlikely to be sustainable in the future. The genetic depauperation of gene pools in aquaculture is an epidemiological "time-bomb", making stocks more susceptible to the outbreak of infectious disease. Indeed, as resistance breaking of crop pathogens has shown, farming of similar genotypes through monoculture is an increasingly unpredictable and precarious undertaking, rendering our society prone to potential food shortages in the future. We expect our research to be instrumental in developing breeding protocols of genetically diverse, and hence, more resistant populations, leading to a paradigm shift in the aquaculture industry. Because our proposed work spans across the life sciences, our results will also be of interest to workers studying the effects of early stress on diseases of livestock and humans , with clear medical benefits.

The societal impact of our proposed research is demonstrated by the explicit support of two industrial partners who are key players within the UK aquaculture industry: LandCatch Hendrix-Genetics, a global, multi-species provider of sustainable genetic solutions for the production of animal protein, including fish, and Marine Harvest, the largest producer of Atlantic salmon, and the second largest seafood company in the world. We also have the support of Sainsuburys' and are beginning a collaboration with LCG, an international life sciences measurement and testing company (www.lgcgroup.com/os), to develop innovative solutions for measuring fish stress with applications on fish farming.