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Morais S.,University of Stirling | Taggart J.B.,University of Stirling | Guy D.R.,Landcatch Natural Selection Ltd | Bell J.G.,University of Stirling | Tocher D.R.,University of Stirling
BMC Genomics | Year: 2012

Background: Genetic selection of Atlantic salmon families better adapted to alternative feed formulations containing high levels of vegetable ingredients has been suggested to ensure sustainable growth of aquaculture. The present study aimed to identify molecular pathways that could underlie phenotypic differences in flesh n-3 long-chain polyunsaturated fatty acid (LC-PUFA) levels when fish are fed vegetable oil diets. Liver transcriptome was analyzed and compared in four families presenting higher or lower n-3 LC-PUFA contents at two contrasting flesh total lipid levels.Results: The main effect of n-3 LC-PUFA contents was in the expression of immune response genes (38% of all significantly affected genes), broadly implicated in the modulation of inflammatory processes and innate immune response. Although genetic evaluations of traits used in the breeding program revealed that the chosen families were not balanced for viral disease resistance, this did not fully explain the preponderance of immune response genes in the transcriptomic analysis. Employing stringent statistical analysis no lipid metabolism genes were detected as being significantly altered in liver when comparing families with high and low n-3 LC-PUFA flesh contents. However, relaxing the statistical analysis enabled identification of potentially relevant effects, further studied by RT-qPCR, in cholesterol biosynthesis, lipoprotein metabolism and lipid transport, as well as eicosanoid metabolism particularly affecting the lipoxygenase pathway. Total lipid level in flesh also showed an important effect on immune response and 8% of significantly affected genes related to lipid metabolism, including a fatty acyl elongase (elovl2), an acyl carrier protein and stearoyl-CoA desaturase.Conclusions: Inter-family differences in n-3 LC-PUFA content could not be related to effects on lipid metabolism, including transcriptional modulation of the LC-PUFA biosynthesis pathway. An association was found between flesh adiposity and n-3 LC-PUFA in regulation of cholesterol biosynthesis, which was most likely explained by variation in tissue n-3 LC-PUFA levels regulating transcription of cholesterol metabolism genes through srebp2. A preponderance of immune response genes significantly affected by n-3 LC-PUFA contents could be potentially associated with disease resistance, possibly involving anti-inflammatory actions of tissue n-3 LC-PUFA through eicosanoid metabolism. This association may have been fortuitous, but it is important to clarify if this trait is included in future salmon breeding programmes. © 2012 Morais et al.; licensee BioMed Central Ltd.


Morais S.,University of Stirling | Silva T.,University of Algarve | Cordeiro O.,University of Algarve | Rodrigues P.,University of Algarve | And 5 more authors.
BMC Genomics | Year: 2012

Background: Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in maintaining body homeostasis and health, its molecular response to replacement of dietary FO by VO has been little investigated. This study employed transcriptomic and proteomic analyses to study effects of dietary VO in two family groups of Atlantic salmon selected for flesh lipid content, 'Lean' or 'Fat'.Results: Metabolism, particularly of lipid and energy, was the functional category most affected by diet. Important effects were also measured in ribosomal proteins and signalling. The long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis pathway, assessed by fatty acid composition and gene expression, was influenced by genotype. Intestinal tissue contents of docosahexaenoic acid were equivalent in Lean salmon fed either a FO or VO diet and expression of LC-PUFA biosynthesis genes was up-regulated in VO-fed fish in Fat salmon. Dietary VO increased lipogenesis in Lean fish, assessed by expression of FAS, while no effect was observed on β-oxidation although transcripts of the mitochondrial respiratory chain were down-regulated, suggesting less active energetic metabolism in fish fed VO. In contrast, dietary VO up-regulated genes and proteins involved in detoxification, antioxidant defence and apoptosis, which could be associated with higher levels of polycyclic aromatic hydrocarbons in this diet. Regarding genotype, the following pathways were identified as being differentially affected: proteasomal proteolysis, response to oxidative and cellular stress (xenobiotic and oxidant metabolism and heat shock proteins), apoptosis and structural proteins particularly associated with tissue contractile properties. Genotype effects were accentuated by dietary VO.Conclusions: Intestinal metabolism was affected by diet and genotype. Lean fish may have higher responsiveness to low dietary n-3 LC-PUFA, up-regulating the biosynthetic pathway when fed dietary VO. As global aquaculture searches for alternative oils for feeds, this study alerts to the potential of VO introducing contaminants and demonstrates the detoxifying role of intestine. Finally, data indicate genotype-specific responses in the intestinal transcriptome and proteome to dietary VO, including possibly structural properties of the intestinal layer and defence against cellular stress, with Lean fish being more susceptible to diet-induced oxidative stress. © 2012 Morais et al.; licensee BioMed Central Ltd.


Houston R.D.,Roslin Institute | Davey J.W.,University of Edinburgh | Bishop S.C.,Roslin Institute | Lowe N.R.,Roslin Institute | And 9 more authors.
BMC Genomics | Year: 2012

Background: Restriction site-associated DNA sequencing (RAD-Seq) is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN) challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools.Results: Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified.Conclusions: We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD-Seq as a tool for rapid and efficient generation of QTL-targeted and genome-wide marker data in a large complex genome, and its possible utility in farmed animal selection programs. © 2012 Houston et al.; licensee BioMed Central Ltd; licensee BioMed Central Ltd.


Morais S.,University of Stirling | Pratoomyot J.,University of Stirling | Taggart J.B.,University of Stirling | Bron J.E.,University of Stirling | And 3 more authors.
BMC Genomics | Year: 2011

Background: Expansion 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.Results: A 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.Conclusions: This 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. © 2011 Morais et al; licensee BioMed Central Ltd.


Taylor J.F.,University of Stirling | Sambraus F.,University of Stirling | Mota-Velasco J.,Landcatch Natural Selection Ltd | Guy D.R.,Landcatch Natural Selection Ltd | And 4 more authors.
Aquaculture | Year: 2013

This study examined performance traits between diploid and triploid siblings within 44 full-sib families (produced by 15 sires and 44 dams) under commercial rearing conditions from first feeding to harvest. Survival did not differ between ploidy levels throughout the production cycle. Triploids grew faster (+30%) in freshwater, but slower during the seawater phase (-7.5%), although overall growth was comparable between ploidy levels (SGR 1.17 vs. 1.18%day-1). Triploids showed no visual deformity in freshwater but a significantly increased prevalence in seawater, mainly evident as jaw malformations and radiological deformed vertebrae. However, severity of deformities was considerably lower than in previous studies, as was the occurrence of cataracts. Using fixed effect linear models the combined effect of deformity and cataract only explained 50% of reduced growth performance, suggesting that other factors were also contributing to reduced performance in triploids. These differences could be due to different nutritional requirements and environmental tolerances in triploids. Family differences were obtained for growth traits (weight and length). Family ranking for production traits was also consistent between diploid and triploid siblings. Harvest quality grading was high (>99% superior) and flesh quality was comparable between ploidy levels, although triploids did have significantly higher PUFA levels at harvest. The study indicates the potential for superior triploid growth, and in conjunction with development of triploid specific diets may be sufficient in order to establish viable triploid salmon aquaculture. © 2013 Elsevier B.V.


Bell J.G.,University of Stirling | Dick J.R.,University of Stirling | Strachan F.,University of Stirling | Guy D.R.,Landcatch Natural Selection Ltd | And 2 more authors.
Aquaculture | Year: 2012

The benefits of consuming a diet rich in seafood are now well respected and are based not only on the high levels of long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFA) but also due to the range of beneficial macro and micronutrients present in fish. Atlantic salmon culture is now established globally and is a major source of high-quality oil rich in LC n-3 PUFA. However, salmon flesh can accumulate persistent organic pollutants (POPs), including dioxins and furans (PCDD/Fs), dioxin-like polychlorinated biphenyls (DL-PCBs) and polybrominated diphenyl ethers (PBDEs) that are derived from marine feed components, especially fish oil (FO). The aim of this study was to grow salmon smolts on alternative diets with a reduced FM level, that contained either 100% of added oil as FO or a blend of vegetable oils (VO), over a full production cycle and to assess the effects of these diets on POP deposition. Three families of salmon were used with two being chosen as being either "Lean" or "Fat", based on flesh adiposity derived from a breeding programme, while the third (CAL) was a mix of non-pedigreed commercial families. Fish were ongrown for 55 weeks when they reached 3 kg followed by a switch to a decontaminated FO for a further 24 weeks to restore LC n-3 PUFA levels in the VO-fed fish. The average sum flesh PCDD/Fs, across the 3 salmon strains, were reduced from 1.94 ± 0.01 ng. TEQ/kg in the fish fed FO to 0.46 ± 0.02 ng. TEQ/kg in the fish fed VO. The sum PBDEs were reduced from 2.82 ± 0.24 ng/g in the FO fish to 0.52 ng/g in the VO fish. Average reduction in sum PCDD/Fs, DL-PCBs and PBDEs was 52, 79 and 82%, respectively, in the VO fed salmon. There was evidence of higher PBDE retention in the Fat fish but this was not significant. This study shows that salmon can be produced with very low levels of POPs and that concentrations can be reduced significantly by the careful selection of raw materials. The use of decontaminated fish oils has an important role in this process although care should be taken to use oils that are treated with protocols that reduce PCCD/Fs, DL-PCBs and PBDEs to ensure very low levels of POPs in commercial salmon. © 2011 Elsevier B.V.


Grant
Agency: European Commission | Branch: FP7 | Program: BSG-SME | Phase: SME-1 | Award Amount: 1.34M | Year: 2008

With the rapid growth of aquaculture seen in recent years, one major fundamental problem has arisen being the environmental pollution due to increased numbers of escapee fish interacting with wild populations. A greater public awareness, the need to protect natural resources and increase the food safety requires the development and implementation of new environmental regulations. There is therefore an urgent need to address this negative environmental impact of salmon farming. To date, two means are available 1) preventing fish escaping by improving cage design and containment or 2) produce sterile fish. Although considerable technological advances have been made in the design of cage systems, no system will be fully reliable as escapees through natural disasters are inevitable. Therefore, there is a clear need to revive the previously abandoned triploid concept as the only means, known to date, to address the environmental impact of escapees contributing to genetic pollution. Furthermore, the production of sterile fish would be very beneficial to salmon breeders as a way to protect their domesticated stocks which are the result of long and costly selection processes aiming to improve important traits such as disease resistance, growth performance and flesh quality. Triploidy would also alleviate early maturation problems and subsequent welfare associated infringements and decreased quality standards. However, prior to discussing the potential implementation of such a radical change within the salmon farming industry, previously based on equivocal results, a sounder understanding of triploid requirements and performances is needed at a commercial scale given the significant advancement in rearing protocols made throughout the production cycle over the last decades. It is only through the establishment of a strong trans-national collaboration supported by key players of the salmon industry that such a project can be undertaken.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2011.1.2-11 | Award Amount: 8.00M | Year: 2012

Sustainable development of European fish farming is dependent on the availability, environmental sustainability of feeds relying less and less on capture fisheries derived fishmeal and fish oil. The European aquaculture industry has made a determined shift towards the use of feeds based on alternative ingredients which continue to ensure the health and welfare of fish and the nutritional value of farmed seafood. However, the long term effects of such interventions and over the full life cycle of the major species farmed in Europe need to be determined. To answer this challenge, ARRAINA will define and provide complete data on the quantitative nutrient requirements of the five major fish species and develop sustainable alternative aquaculture feeds tailored to the requirements of these species with reduced levels of fish meal and fish oil. By developing innovative vectors to deliver specific nutrients, ARRAINA will increase significantly the performance at all physiological stages thus improving overall efficiency of fish production. ARRAINA will apply targeted predictive tools to assess the long-term physiological and environmental consequences of these changes in the different species. This will provide flexibility in the use of various ingredients in the formulation of feeds which are cost-efficient, environmentally friendly and which ensure production of seafood of high nutritional value and quality. ARRAINA will design and deliver new pioneering training courses in fish nutrition to increase research capacities and expertise, particularly in countries of the enlarged EU. By developing applied tools and solutions of technological interest in collaborations with SMEs, ARRAINA will further strengthen the links between the scientific community and the EU feed industry and will contribute to increase the productivity and performance of the aquaculture sector leading to competitive advantage to the whole sector at a global level.


Grant
Agency: GTR | Branch: Innovate UK | Program: | Phase: Collaborative Research & Development | Award Amount: 133.35K | Year: 2015

Salmon are a source of high-quality protein and long chain fatty acids for human nutrition and health. Salmon farming is economically important in the UK and a large source of employment in rural and coastal communities. Outbreaks of Amoebic gill disease (AGD) can cause widespread illness and losses to salmon farms. As such, this disease is one of the most serious threats to UK salmon farming and has a negative effect on salmon health and welfare . Our previous work funded by the Technology Strategy Board has led to the development of a chip containing hundreds of thousands of genetic markers for Atlantic salmon. This chip allowed us to predict how resistant a salmon is to sea lice from a sample of its DNA. In this project, we aim to apply this chip and knowledge to improve the resistance of farmed salmon stocks to AGD . By performing a controlled AGD challenge experiment and utilising measures of gill damage collected in the farm environment, we aim to identify and verify accurate measures of resistance. The data collected will be combined with genetic marker data to identify and select more resistant fish and thus help tackle the disease problem.


Grant
Agency: GTR | Branch: Innovate UK | Program: | Phase: Collaborative Research & Development | Award Amount: 325.05K | Year: 2011

Salmon farming is a key economic contributor to the UK (£0.5bn p.a.) and provides healthy, high quality food. The competitiveness and sustainability of this rural industry depend upon selective breeding. While cutting-edge genomics tools such as high density (HD) SNP chips are now routinely employed for livestock breeding decisions, salmon aquaculture has no access to such tools. This project addresses this technology gap by developing an HD salmon SNP chip for selective breeding. The project will; 1) use high-throughput sequencing to detect genome-wide SNP variation; 2) develop an HD SNP chip; 3) use the chip to perform association mapping of loci affecting resistance to sea lice; 4) verify trait-associated SNPs in a commercial context; 5) implement strategies for SNP use in breeding programmes to improve resistance to sea lice, a paradigm for other key economic traits. Sea louse infestation is the most serious disease affecting salmon farming worldwide. In the northern hemisphere, the salmon louse Lepeophtheirus salmonis is particularly problematic. L. salmonis infection of salmon can cause surface lesions, osmotic imbalance, and susceptibility to other pathogens because of host immunomodulation and lesions. Almost all salmon farms require sea lice control strategies, usually involving frequent chemotherapeutant treatment. Sea lice treatment costs vary from 0.10 Euros to 0.25 Euro per kg of fish, amounting to losses of 34M Euros per annum in the UK and 305M Euros per annum worldwide. However, without such treatment the existing salmon aquaculture industry would not be viable. Through a pilot sea louse infection trial in collaboration with the University of Glasgow and the Institute of Aquaculture at the University of Stirling, LNS have demonstrated there is widespread genetic variation for resistance to sea lice across their broodstock and that heritability for resistance to sea lice in LNS families is c30 percent. However sea lice challenge trials are an expensive and laborious means of identifying the best selection candidate fish in each generation. The approach of direct selection based on genomic information that has been applied in several agricultural sectors has been shown to be a more cost-effective and accurate means of selection, particularly for difficult/expensive to measure traits. Association of genetic markers with disease resistance requires identification of markers in population-wide linkage disequilibrium. Although a proprietary salmon SNP chip is currently available through CIGENE (Norway), its marker density (3K) is insufficient for genomic association mapping. This project aims to overcome this limitation through development of high-throughput genotyping tools for the identification of genetic markers associated with sea lice resistance and other economically important traits in farmed salmon. Key steps are firstly identifying genome-wide SNP variation across the LNS breeding stock by utilising massively parallel sequencing platforms (Illumina GAIIx and HiSeq2000) and bioinformatic analyses of reduced representation (RR) and restriction site-associated DNA (RAD) libraries. Secondly the design and manufacture of a custom HD (~200K) SNP genotyping tool for LNS fish using Affymetrix high-throughput array technology. Thirdly use of this tool for identification of SNP variants associated with resistance to sea lice by HD SNP chip genotyping and association mapping of accurate phenotypes in LNS families infected under controlled conditions. Subsequently the identified subset of informative and trait-associated markers markers will be incorporated into a lower cost genotyping platform which will be used for verification of SNPs associated with reduced levels of lice infestation in fish exposed to aquaculture conditions. Breeding strategies will be developed to apply these SNPs in selection for sea lice resistance, which will permit genetic improvement without the need for further disease challenge. Further, through use of the High Density chip for identification of markers in linkage disequilibrium with other economically important traits, these strategies will be extended to introduce genotypic selection for other traits, significantly accelerating genetic progress achieved via the LNS breeding programme.

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