News Article | May 8, 2017
Overviews of the use of cleanerfish in Scotland, Norway, Iceland, the Faroes and Ireland made for a fascinating first afternoon of the inaugural International Cleaner Fish Summit, which kicked off in Glasgow today (May 8th). The first day consisted of a national overview of the developments in cleanerfish deployment by a key player from each of the five countries represented. While each representative gave their own unique perspective – based on their own experiences and the factors governing their relevant nations – a number of common themes emerged. One was the importance of ensuring that those working at sites containing cleanerfish were supportive of the idea. Cleanerfish can cause a great deal of extra work for site staff, but “as soon as they see the cleanerfish are working the site managers are hooked,” reflected Chris Hempleman from Scottish Sea Farms, who spoke about how the industry was evolving in Scotland. Another was the need to only use farmed cleanerfish in the long run. In Ireland, where cleanerfish have only been deployed since late 2015, all the wrasse used by the country’s largest producer are still wild-caught, but 100% of the lumpsuckers are now farmed. Elsewhere, the trend also seems to be moving in the right direction – in Scotland companies such as Scottish Sea Farms “now have the confidence and the capacity to stock purely farmed wrasse at some sites,” Chris Hempleman reflected. Meanwhile, in Norway, 57% of the 26.4 million cleanerfish (wrasse and lumpsuckers) deployed in 2015 were farmed, up from 16% of the 16.2 million cleanerfish deployed in 2013, according to Olav Breck, from Marine Harvest Norway. “We need to move towards using entirely farmed, vaccinated cleanerfish,” he argued. A third theme was the need for more cleanerfish to be produced. Every year Norway alone requires over 40 million cleanerfish to cope with the 400 million smolts stocked annually, according to Olav Breck. “It’s all about numbers, no company has enough cleanerfish at the moment,” added Chris Hempleman. Looking ahead, the need to improve survival rates of cleanerfish was seen as a further goal – not only by improving husbandry techniques, feeds and vaccines for cleanerfish species but also, in the longer run, by the development of selective breeding programmes. “Give us 15 years – ie five generations of cleanerfish – to bring down the mortality rate. It’s a new species and will take time,” argued Dr Jonas Jonasson, CEO of StofnFiskur, who spoke about cleanerfish production in Iceland. "But the key is to have a plan in place to demonstrate that they’re improving,” he added. Other challenges discussed were unique to individual countries – Ireland hasn’t had access to any licenced cleanerfish vaccines since 2015 revealed Sandra Schlittenhardt of Marine Harvest; while legislation in the Faroes means that they have no domestic cleanerfish farms in operation, but instead need to import all their lumpfish from producers in Iceland, such as StofnFiskur, explained Kirstin Eliasen of Fiskaaling. The event is taking place at the Technology & Innovation Centre, and is co-hosted by the Scottish Aquaculture Innovation Centre (SAIC) in partnership with the Norwegian Seafood Research Fund (FHF). Reflecting on the event, Heather Jones, CEO of SAIC, said: “Greater sea lice control has been one of our priorities since day one, as has sharing the insights gleaned from SAIC-supported projects with the wider Scottish aquaculture sector. So to see our industry and academic partners exchange the knowledge being gained with their industry and international peers is a truly landmark moment.” A range of partners from participating countries – including gold partners Scottish Sea Farms; silver partners BioMar and StofnFiskur; and bronze partners AquaGen, EWOS, HiddenFjord, Patogen and Skretting – helped to make the not-for-profit event possible. Meanwhile, exhibitors include Aquality, JETE Innovation, OK Marine, Pacific Trading and Skjerneset fisk AS.
Aquagen As | Date: 2015-06-10
A method of predicting the ability of a salmon to utilise dietary pigment, the method comprising determining the alleles present at one or more DNA polymorphism in the salmon and predicting the ability of the salmon to utilise dietary pigment based on the determination of the alleles. The method may be used for selecting a salmon for use as broodstock. Also contemplated is a method of improving the ability of a salmon to utilise dietary pigment, the method including the step of administering an agent that inhibits the expression of the genes bcmo1-like and/or bcmo1 and/or an agent that inhibits the activities of the proteins Bcmo1-like and/or Bcmo1.
Palti Y.,U.S. Department of Agriculture |
Gao G.,U.S. Department of Agriculture |
Liu S.,U.S. Department of Agriculture |
Kent M.P.,Norwegian University of Life Sciences |
And 4 more authors.
Molecular Ecology Resources | Year: 2015
In this study, we describe the development and characterization of the first high-density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor (Affymetrix). The SNP genotyping quality was high, and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes are evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40 900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size, the number of polymorphic markers was between 10 577 and 24 330. Comparison between genotypes from individual populations suggests good potential for identifying candidate markers for populations' traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly that has not been previously anchored to chromosomes. © 2014 John Wiley & Sons Ltd.
Odegard J.,AquaGen AS |
Meuwissen T.H.E.,Norwegian University of Life Sciences
Genetics Selection Evolution | Year: 2015
Background: Genomic selection (GS) allows estimation of the breeding value of individuals, even for non-phenotyped animals. The aim of the study was to examine the potential of identity-by-descent genomic selection (IBD-GS) in genomic selection for a binary, sib-evaluated trait, using different strategies of selective genotyping. This low-cost GS approach is based on linkage analysis of sparse genome-wide marker loci. Findings: Lowly to highly heritable (h2 = 0.15, 0.30 or 0.60) binary traits with varying incidences (10 to 90%) were simulated for an aquaculture-like population. Genotyping was restricted to the 30% best families according to phenotype, using three genotyping strategies for training sibs. IBD-GS increased genetic gain compared to classical pedigree-based selection; the differences were largest at incidences of 10 to 50% of the desired category (i.e. a relative increase in genetic gain greater than 20%). Furthermore, the relative advantage of IBD-GS increased as the heritability of the trait increased. Differences were small between genotyping strategies, and most of the improvement was achieved by restricting genotyping to sibs with the least common binary phenotype. Genetic gains of IBD-GS relative to pedigree-based models were highest at low to moderate (10 to 50%) incidences of the category selected for, but decreased substantially at higher incidences (80 to 90%). Conclusions: The IBD-GS approach, combined with sparse and selective genotyping, is well suited for genetic evaluation of binary traits. Genetic gain increased considerably compared with classical pedigree-based selection. Most of the improvement was achieved by selective genotyping of the sibs with the least common (minor) binary category phenotype. Furthermore, IBD-GS had greater advantage over classical pedigree-based models at low to moderate incidences of the category selected for. © 2015 ødegård and Meuwissen; licensee BioMed Central.
Holm H.,Norwegian University of Life Sciences |
Santi N.,Aquagen AS |
Kjoglum S.,Aquagen AS |
Perisic N.,Weifa AS |
And 2 more authors.
Fish and Shellfish Immunology | Year: 2015
Atlantic salmon is susceptible to the salmon louse (. Lepeophtheirus salmonis) and the variation in susceptibility within the species can be exploited in selective breeding programs for louse resistant fish. In this study, lice counts were completed on 3000 siblings from 150 families of Atlantic salmon identified as high resistant (HR) and low resistant (LR) families in two independent challenge trials. Skin samples behind the dorsal fin (nearby lice attachment) were collected from ten extreme families (HR or LR) and analyzed by qPCR for the expression of 32 selected genes, including a number of genes involved in T helper cell (Th) mediated immune responses, which have been previously implied to play important roles during salmon louse infections.Most genes showed lower expression patterns in the LR than in HR fish, suggesting an immunosuppressed state in LR families. The average number of lice (chalimi) was 9 in HR and 15 in LR fish. Large variation in lice counts was seen both within resistant and susceptible families, which enabled us to subdivide the groups into HR<10 and HR>10, and LR<10 and LR>10 to better understand the effect of lice burden per se. As expected, expression patterns were influenced both by genetic background and the number of attached parasites. Higher number of lice (>10) negatively affected gene expression in both HR and LR families. In general, strongest down-regulation was seen in LR>10 and lesser down-regulation in HR<10. HR in general and especially HR<10 fish were better at resisting suppression of expression of both Th1 and Th2 genes. However, the best inverse correlation with infection level was seen for the prototypical Th1 genes, including several members from the interferon pathways. In addition, skin histomorphometry suggests that infected LR salmon had thicker epidermis in the area behind the dorsal fin and larger mucous cell size compared to infected HR fish, however marginally significant (. p=0.08). This histomorphometric finding was in line with the immune response being skewed in LR towards the Th2 rather than a Th1 profile. Our findings suggest that the ability to resist lice infection depends on the ability to avoid immunosuppression and not as much on the physical tissue barrier functions. © 2014 Elsevier Ltd.
Odegard J.,AquaGen AS |
Moen T.,AquaGen AS |
Santi N.,AquaGen AS |
Korsvoll S.A.,AquaGen AS |
And 2 more authors.
Frontiers in Genetics | Year: 2014
Reliability of genomic selection (GS) models was tested in an admixed population of Atlantic salmon, originating from crossing of several wild subpopulations. The models included ordinary genomic BLUP models (GBLUP), using genome-wide SNP markers of varying densities (1-220 k), a genomic identity-by-descent model (IBD-GS), using linkage analysis of sparse genome-wide markers, as well as a classical pedigree-based model. Reliabilities of the models were compared through 5-fold cross-validation. The traits studied were salmon lice (Lepeophtheirus salmonis) resistance (LR), measured as (log) density on the skin and fillet color (FC), with respective estimated heritabilities of 0.14 and 0.43. All genomic models outperformed the classical pedigree-based model, for both traits and at all marker densities. However, the relative improvement differed considerably between traits, models and marker densities. For the highly heritable FC, the IBD-GS had similar reliability as GBLUP at high marker densities (>22 k). In contrast, for the lowly heritable LR, IBD-GS was clearly inferior to GBLUP, irrespective of marker density. Hence, GBLUP was robust to marker density for the lowly heritable LR, but sensitive to marker density for the highly heritable FC. We hypothesize that this phenomenon may be explained by historical admixture of different founder populations, expected to reduce short-range lice density (LD) and induce long-range LD. The relative importance of LD/relationship information is expected to decrease/increase with increasing heritability of the trait. Still, using the ordinary GBLUP, the typical long-range LD of an admixed population may be effectively captured by sparse markers, while efficient utilization of relationship information may require denser markers (e.g., 22 k or more). © 2014 Ødegård, Moen, Santi, Korsvoll, Kjøglum and Meuwissen.
Odegard J.,AquaGen AS |
Meuwissen T.H.E.,Norwegian University of Life Sciences
Genetics Selection Evolution | Year: 2014
Background: Genomic selection methods require dense and widespread genotyping data, posing a particular challenge if both sexes are subject to intense selection (e.g., aquaculture species). This study focuses on alternative low-cost genomic selection methods (IBD-GS) that use selective genotyping with sparse marker panels to estimate identity-by-descent relationships through linkage analysis. Our aim was to evaluate the potential of these methods in selection programs for continuous traits measured on sibs of selection candidates in a typical aquaculture breeding population. Methods. Phenotypic and genomic data were generated by stochastic simulation, assuming low to moderate heritabilities (0.10 to 0.30) for a Gaussian trait measured on sibs of the selection candidates in a typical aquaculture breeding population that consisted of 100 families (100 training animals and 20 selection candidates per family). Low-density marker genotype data (∼ 40 markers per Morgan) were used to trace genomic identity-by-descent relationships. Genotyping was restricted to selection candidates from 30 phenotypically top-ranking families and varying fractions of their phenotypically extreme training sibs. All phenotypes were included in the genetic analyses. Classical pedigree-based and IBD-GS models were compared based on realized genetic gain over one generation of selection. Results: Genetic gain increased substantially (13 to 32%) with IBD-GS compared to classical selection and was greatest with higher heritability. Most of the extra gain from IBD-GS was obtained already by genotyping the 5% phenotypically most extreme sibs within the pre-selected families. Additional genotyping further increased genetic gains, but these were small when going from genotyping 20% of the extremes to all phenotyped sibs. The success of IBD-GS with sparse and selective genotyping can be explained by the fact that within-family haplotype blocks are accurately traced even with low-marker densities and that most of the within-family variance for normally distributed traits is captured by a small proportion of the phenotypically extreme sibs. Conclusions: IBD-GS was substantially more effective than classical selection, even when based on very few markers and combined with selective genotyping of small fractions of the population. The study shows that low-cost GS programs can be successful by combining sparse and selective genotyping with pedigree and linkage information. © 2014Ødegård and Meuwissen; licensee BioMed Central Ltd.
PubMed | Norwegian University of Life Sciences, Norwegian Veterinary Institute and AquaGen AS
Type: Journal Article | Journal: Preventive veterinary medicine | Year: 2015
Pancreas disease (PD) is an important viral disease in Norwegian, Scottish and Irish aquaculture causing biological losses in terms of reduced growth, mortality, increased feed conversion ratio, and carcass downgrading. We developed a bio-economic model to investigate the economic benefits of a disease triggered early harvesting strategy to control PD losses. In this strategy, the salmon farm adopts a PCR (Polymerase Chain Reaction) diagnostic screening program to monitor the virus levels in stocks. Virus levels are used to forecast a clinical outbreak of pancreas disease, which then initiates a prescheduled harvest of the stock to avoid disease losses. The model is based on data inputs from national statistics, literature, company data, and an expert panel, and use stochastic simulations to account for the variation and/or uncertainty associated with disease effects and selected production expenditures. With the model, we compared the impacts of a salmon farm undergoing prescheduled harvest versus the salmon farm going through a PD outbreak. We also estimated the direct costs of a PD outbreak as the sum of biological losses, treatment costs, prevention costs, and other additional costs, less the costs of insurance pay-outs. Simulation results suggests that the economic benefit from a prescheduled harvest is positive once the average salmon weight at the farm has reached 3.2kg or more for an average Norwegian salmon farm stocked with 1,000,000smolts and using average salmon sales prices for 2013. The direct costs from a PD outbreak occurring nine months (average salmon weight 1.91kg) after sea transfer and using 2013 sales prices was on average estimated at NOK 55.4 million (5%, 50% and 90% percentile: 38.0, 55.8 and 72.4) (NOK=0.128 in 2013). Sensitivity analyses revealed that the losses from a PD outbreak are sensitive to feed- and salmon sales prices, and that high 2013 sales prices contributed to substantial losses associated with a PD outbreak.
PubMed | Norwegian University of Life Sciences and AquaGen AS
Type: | Journal: Genetics, selection, evolution : GSE | Year: 2015
Genomic selection (GS) allows estimation of the breeding value of individuals, even for non-phenotyped animals. The aim of the study was to examine the potential of identity-by-descent genomic selection (IBD-GS) in genomic selection for a binary, sib-evaluated trait, using different strategies of selective genotyping. This low-cost GS approach is based on linkage analysis of sparse genome-wide marker loci.Lowly to highly heritable (h(2) = 0.15, 0.30 or 0.60) binary traits with varying incidences (10 to 90%) were simulated for an aquaculture-like population. Genotyping was restricted to the 30% best families according to phenotype, using three genotyping strategies for training sibs. IBD-GS increased genetic gain compared to classical pedigree-based selection; the differences were largest at incidences of 10 to 50% of the desired category (i.e. a relative increase in genetic gain greater than 20%). Furthermore, the relative advantage of IBD-GS increased as the heritability of the trait increased. Differences were small between genotyping strategies, and most of the improvement was achieved by restricting genotyping to sibs with the least common binary phenotype. Genetic gains of IBD-GS relative to pedigree-based models were highest at low to moderate (10 to 50%) incidences of the category selected for, but decreased substantially at higher incidences (80 to 90%).The IBD-GS approach, combined with sparse and selective genotyping, is well suited for genetic evaluation of binary traits. Genetic gain increased considerably compared with classical pedigree-based selection. Most of the improvement was achieved by selective genotyping of the sibs with the least common (minor) binary category phenotype. Furthermore, IBD-GS had greater advantage over classical pedigree-based models at low to moderate incidences of the category selected for.
PubMed | Norwegian University of Life Sciences, Norwegian Computing Center, Lincoln University at Christchurch, Norwegian Veterinary Institute and 2 more.
Type: | Journal: Preventive veterinary medicine | Year: 2016
Pancreas disease (PD) is a viral disease associated with significant economic losses in Scottish, Irish, and Norwegian marine salmon aquaculture. In this paper, we investigate how disease-triggered harvest strategies (systematic depopulation of infected marine salmon farms) towards PD can affect disease dynamics and salmon producer profits in an endemic area in the southwestern part of Norway. Four different types of disease-triggered harvest strategies were evaluated over a four-year period (2011-2014), each scenario with different disease-screening procedures, timing for initiating the harvest interventions on infected cohorts, and levels of farmer compliance to the strategy. Our approach applies a spatio-temporal stochastic model for simulating the spread of PD in the separate scenarios. Results from these simulations were then used in cost-benefit analyses to estimate the net benefits of different harvest strategies over time. We find that the most aggressive strategy, in which infected farms are harvested without delay, was most efficient in terms of reducing infection pressure in the area and providing economic benefits for the studied group of salmon producers. On the other hand, lower farm compliance leads to higher infection pressure and less economic benefits. Model results further highlight trade-offs in strategies between those that primarily benefit individual producers and those that have collective benefits, suggesting a need for institutional mechanisms that address these potential tensions.