Parasites have a major impact on global finfish and shellfish aquaculture, having significant effects on farm production, sustainability and economic viability. Parasite infections and impacts can, according to pathogen and context, be considered to be either unpredictable/sporadic or predictable/regular. Although both types of infection may result in the loss of stock and incur costs associated with the control and management of infection, predictable infections can also lead to costs associated with prophylaxis and related activities. The estimation of the economic cost of a parasite event is frequently complicated by the complex interplay of numerous factors associated with a specific incident, which may range from direct production losses to downstream socio-economic impacts on livelihoods and satellite industries associated with the primary producer. In this study, we examine the world's major marine and brackish water aquaculture production industries and provide estimates of the potential economic costs attributable to a range of key parasite pathogens using 498 specific events for the purposes of illustration and estimation of costs. This study provides a baseline resource for risk assessment and the development of more robust biosecurity practices, which can in turn help mitigate against and/or minimise the potential impacts of parasite-mediated disease in aquaculture.

BackgroundExpansion of aquaculture is seriously limited by reductions in fish oil (FO) supply for aquafeeds. Terrestrial alternatives such as vegetable oils (VO) have been investigated and recently a strategy combining genetic selection with changes in diet formulations has been proposed to meet growing demands for aquaculture products. This study investigates the influence of genotype on transcriptomic responses to sustainable feeds in Atlantic salmon.ResultsA microarray analysis was performed to investigate the liver transcriptome of two family groups selected according to their estimated breeding values (EBVs) for flesh lipid content, 'Lean' or 'Fat', fed diets containing either FO or a VO blend. Diet principally affected metabolism genes, mainly of lipid and carbohydrate, followed by immune response genes. Genotype had a much lower impact on metabolism-related genes and affected mostly signalling pathways. Replacement of dietary FO by VO caused an up-regulation of long-chain polyunsaturated fatty acid biosynthesis, but there was a clear genotype effect as fatty acyl elongase (elovl2) was only up-regulated and desaturases (Δ5 fad and Δ6 fad) showed a higher magnitude of response in Lean fish, which was reflected in liver fatty acid composition. Fatty acid synthase (FAS) was also up-regulated by VO and the effect was independent of genotype. Genetic background of the fish clearly affected regulation of lipid metabolism, as PPARα and PPARβ were down-regulated by the VO diet only in Lean fish, while in Fat salmon SREBP-1 expression was up-regulated by VO. In addition, all three genes had a lower expression in the Lean family group than in the Fat, when fed VO. Differences in muscle adiposity between family groups may have been caused by higher levels of hepatic fatty acid and glycerophospholipid synthesis in the Fat fish, as indicated by the expression of FAS, 1-acyl-sn-glycerol-3-phosphate acyltransferase and lipid phosphate phosphohydrolase 2.ConclusionsThis study has identified metabolic pathways and key regulators that may respond differently to alternative plant-based feeds depending on genotype. Further studies are required but data suggest that it will be possible to identify families better adapted to alternative diet formulations that might be appropriate for future genetic selection programmes.

25The present study compared the effects of diets formulated with reduced fishmeal 26 (FM) content and either 100% fish oil (FO) or 100% of a vegetable oil (VO) blend in 27 post-smolts of three family groups of Atlantic salmon. Two groups were selected as 28 being either "Lean" or "Fat" based on estimated breeding values (EBV) for flesh 29 adiposity of their parents derived from a breeding programme, while the third group 30 (CAL) was a mix of non-pedigreed commercial families unrelated to the two groups 31 above. The VO blend comprised rapeseed, palm and a new product, Camelina oil in 32 a ratio of 5/3/2, and diets were fed to duplicate pens of each salmon group. After an 33 ongrowing period of 55 weeks, to reach a mean weight of 3kg, the fish from all 34 treatments were switched to a decontaminated FO for a further 24 weeks to follow 35 restoration of long-chain n-3 polyunsaturated fatty acids (LC-PUFA) in the fish 36 previously fed VO. Final weights were significantly affected by family group and 37 there was also an interaction between diet and group with Fat and Lean FO fish being 38 larger than the same fish fed VO. Specific growth rate (SGR) was highest in CAL 39 fish (1.01), feed conversion ratio (FCR) was highest in the Lean fish but there were 40 no significant effects on thermal growth coefficient (TGC). Condition Factor (CF) 41 was lowest in CAL fish while the hepato-somatic index (HSI) was highest in Lean 42 fish and viscero-somatic index (VSI) highest in Fat fish. Flesh and viscera lipid 43 content was affected by both family group and diet with a significant interaction 44 between the two. Flesh lipid in fish fed FO was in the order Fat > CAL > Lean 45 although this order was Fat = Lean > CAL when fed VO. Flesh fatty acid 46 compositions were affected mainly by diet although some minor fatty acids were also 47 3 influenced by group. Fish fed VO had n-3 LC-PUFA reduced by ~65% compared to 48 fish fed FO but this could be restored by a 16 week FO finishing diet phase. The 49 differences observed in lipid and fatty acid deposition suggested that genetics 50 affected lipid deposition and metabolism and that breeding programmes could select 51 for fish that retained more n-3 LC-PUFA in their flesh, particularly when fed diets 52 low in these fatty acids. 53 54

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The present study investigates the effects of genotype on responses to alternative feeds in Atlantic salmon. Microarray analysis of the liver transcriptome of two family groups, lean or fat, fed a diet containing either a fish oil (FO) or a vegetable oil (VO) blend indicated that pathways of cholesterol and lipoprotein metabolism might be differentially affected by the diet depending on the genetic background of the fish, and this was further investigated by real-time quantitative PCR, plasma and lipoprotein biochemical analysis. Results indicate a reduction in VLDL and LDL levels, with no changes in HDL, when FO is replaced by VO in the lean family group, whereas in fat fish fed FO, levels of apoB-containing lipoproteins were low and comparable with those fed VO in both family groups. Significantly lower levels of plasma TAG and LDL-TAG were measured in the fat group that was independent of diet, whereas plasma cholesterol was significantly higher in fish fed the FO diet in both groups. Hepatic expression of genes involved in cholesterol homeostasis, b-oxidation and lipoprotein metabolism showed relatively subtle changes. A significantly lower expression of genes considered anti-atherogenic in mammals (ATP-binding cassette transporter A1, apoAI, scavenger receptor class B type 1, lipoprotein lipase (LPL)b (TC67836) and LPLc (TC84899)) was found in lean fish, compared with fat fish, when fed VO. Furthermore, the lean family group appeared to show a greater response to diet composition in the cholesterol biosynthesis pathway, mediated by sterol-responsive element-binding protein 2. Finally, the presence of three different transcripts for LPL, with differential patterns of nutritional regulation, was demonstrated.