Fish diseases are a huge threat for the aquaculture industry and for global food security. Some of the most important disease-causing organisms in aquaculture are part of the oomycetes or watermoulds, in particular Saprolegnia parasitica, Saprolegnia diclina and Saprolegnia australis are causing serious fish losses. Collectively, these fungal-like organisms are responsible for at least 10% annual mortalities in most salmon hatcheries and freshwater sites. Consequently, Saprolegnia ranks among the most important pathogens of Atlantic salmon. Unfortunately, over the last few years the incidences of saprolegniosis outbreaks in Scottish farms have significantly increased. Indeed, some sites have had very high losses due to saprolegniosis. Whereas other farms have remained largely disease free. The reasons as to why some farms are badly affected and others seem to avoid disease outbreaks, with apparent identical welfare standards and husbandry management practises, are at present completely unclear and form the main rational for the current application. Our hypothesis is that several risk factors (pertaining to fish, pathogens and the environment) are playing a synergistic role in suppressing immunity in fish towards Saprolegnia, which lead to outbreaks of saprolegniosis. Therefore, we propose a concerted industry-wide, industry-led and industry-supported research programme to discover, map, model and understand the main drivers, risk factors, that allow saprolegniosis outbreaks. A "big data" resource will be created that will be scrutinised with statistical methods to identify the main risk factors and conditions for outbreaks of saprolegniosis. Undoubtedly, identifying the main, or a combination of, risk factors will greatly aid the salmon aquaculture industry to pre-empt any future outbreaks and would lead to an integrated approach to saprolegniosis management, which would result in increased welfare standards, improved fish health, fewer losses and a reduction in production and treatment costs.

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.