Santi N.,Aqua Gen AS
PLoS ONE | Year: 2013
We have studied stress-induced reversion to virulence of infectious pancreatic necrosis virus (IPNV) in persistently infected Atlantic salmon (Salmo salar L.) fry. Naïve fry were persistently infected with a virulent strain (T217A221 of major structural virus protein 2, VP2) or a low virulent (T217T221) variant of IPNV. The fry were infected prior to immunocompetence as documented by lack of recombination activating gene-1, T-cell receptor and B-cell receptor mRNA expression at time of challenge. The fish were followed over 6 months and monitored monthly for presence of virus and viral genome mutations. No mutation was identified in the TA or TT group over the 6 months period post infection. Six months post infection TA and TT infected groups were subject to daily stress for 7 days and then sampled weekly for an additional period of 28 days post stress. Stress-responses were documented by down-regulation of mRNA expression of IFN-α1 and concomitant increase of replication levels of T217T221 infected fish at day 1 post stress. By 28 days post stress a T221A reversion was found in 3 of 6 fish in the T217T221 infected group. Sequencing of reverted isolates showed single nucleotide peaks on chromatograms for residue 221 for all three isolates and no mix of TA and TT strains. Replication fitness of reverted (TA) and non-reverted (TT) variants was studied in vitro under an antiviral state induced by recombinant IFN-α1. The T217A221 reverted variant replicated to levels 23-fold higher than the T217T221 strain in IFN-α1 treated cells. Finally, reverted TA strains were virulent when tested in an in vivo trial in susceptible salmon fry. In conclusion, these results indicate that stress plays a key role in viral replication in vivo and can facilitate conditions that will allow reversion from attenuated virus variants of IPNV. © 2013 Gadan et al.
Zhang Z.,Beijing Normal University |
Zhang Z.,University of Tromsø |
Niu C.,Beijing Normal University |
Storset A.,Aqua Gen AS |
And 2 more authors.
Fish and Shellfish Immunology | Year: 2011
Selective breeding has been employed to improve resistance to infectious diseases in aquaculture and it is of importance to investigate the expression profiles of immune genes together with complement activity of Atlantic salmon with different genetic background in response to pathogens, in particular against Aeromonas salmonicida. This study examined acute phase products, and several central T cell cytokines and a transcription factor in different tissues, namely head kidney, spleen and liver, in two families of Atlantic salmon with high and low mortalities, after challenge by A. salmonicida. The results showed that the expression pattern of target genes differed in lymphoid and non-lymphoid organs in the two families. Generally, in lymphoid organs, higher expression of pro-inflammatory genes, such as TLR5M, TLR5S, GATA3, IFN-γ, IL-17D, as well as the pleiotropic cytokine gene IL-10 in the resistant family was observed at the same time point. One may speculate that a relatively high immune response is a pre-requisite for increased survival in a A. salmonicida challenge test. In addition, the resistant fish possessed higher complement activity pre-challenge compared to susceptible fish. Complement activity may be applied as an indicator in selective breeding for enhanced disease resistance. © 2011 Elsevier Ltd.
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.
Lien S.,Norwegian University of Life Sciences |
Gidskehaug L.,Norwegian University of Life Sciences |
Moen T.,Norwegian University of Life Sciences |
Moen T.,Aqua Gen AS |
And 6 more authors.
BMC Genomics | Year: 2011
Background: The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD) event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs), multisite variants (MSVs) and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species.Results: A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs) was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus). The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1) which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres.Conclusion: The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization), aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence. © 2011 Lien et al; licensee BioMed Central Ltd.
Karlsson S.,Nofima Marine |
Moen T.,Aqua Gen AS |
Moen T.,Norwegian University of Life Sciences |
Lien S.,Norwegian University of Life Sciences |
And 2 more authors.
Molecular Ecology Resources | Year: 2011
Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species. © 2011 Blackwell Publishing Ltd.
Meuwissen T.H.E.,Norwegian University of Life Sciences |
Odegard J.,Aqua Gen AS |
Andersen-Ranberg I.,NORSVIN |
Genetics Selection Evolution | Year: 2014
Background: With the advent of genomic selection, alternative relationship matrices are used in animal breeding, which vary in their coverage of distant relationships due to old common ancestors. Relationships based on pedigree (A) and linkage analysis (GLA) cover only recent relationships because of the limited depth of the known pedigree. Relationships based on identity-by-state (G) include relationships up to the age of the SNP (single nucleotide polymorphism) mutations. We hypothesised that the latter relationships were too old, since QTL (quantitative trait locus) mutations for traits under selection were probably more recent than the SNPs on a chip, which are typically selected for high minor allele frequency. In addition, A and GLA relationships are too recent to cover genetic differences accurately. Thus, we devised a relationship matrix that considered intermediate-aged relationships and compared all these relationship matrices for their accuracy of genomic prediction in a pig breeding situation. Methods: Haplotypes were constructed and used to build a haplotype-based relationship matrix (GH), which considers more intermediate-aged relationships, since haplotypes recombine more quickly than SNPs mutate. Dense genotypes (38 453 SNPs) on 3250 elite breeding pigs were combined with phenotypes for growth rate (2668 records), lean meat percentage (2618), weight at three weeks of age (7387) and number of teats (5851) to estimate breeding values for all animals in the pedigree (8187 animals) using the aforementioned relationship matrices. Phenotypes on the youngest 424 to 486 animals were masked and predicted in order to assess the accuracy of the alternative genomic predictions. Results: Correlations between the relationships and regressions of older on younger relationships revealed that the age of the relationships increased in the order A, GLA, GH and G. Use of genomic relationship matrices yielded significantly higher prediction accuracies than A. GH and G, differed not significantly, but were significantly more accurate than GLA. Conclusions: Our hypothesis that intermediate-aged relationships yield more accurate genomic predictions than G was confirmed for two of four traits, but these results were not statistically significant. Use of estimated genotype probabilities for ungenotyped animals proved to be an efficient method to include the phenotypes of ungenotyped animals. © 2014 Meuwissen et al.; licensee BioMed Central Ltd.
Karlsson S.,NOFIMA Marine |
Moen T.,Aqua Gen AS
BMC Research Notes | Year: 2010
Background. An increasing number of aquaculture species are subjected to artificial selection in systematic breeding programs. Rapid improvements of important commercial traits are reported, but little is known about the effects of the strong directional selection applied, on gene level variation. Large numbers of genetic markers are becoming available, making it feasible to detect and estimate these effects. Here a simulation tool was developed in order to explore the power by which single genetic loci subjected to uni-directional selection in parallel breeding populations may be detected. Findings. Two simulation models were pursued: 1) screening for loci displaying higher genetic differentiation than expected (high-FSToutliers), from neutral evolution between a pool of domesticated populations and a pool of wild populations; 2) screening for loci displaying lower genetic differentiation (low-FSToutliers) between domesticated strains than expected from neutral evolution. The premise for both approaches was that the isolated domesticated strains are subjected to the same breeding goals. The power to detect outlier loci was calculated under the following parameter values: number of populations, effective population size per population, number of generations since onset of selection, initial FST, and the selection coefficient acting on the locus. Among the parameters investigated, selection coefficient, the number of generation since onset of selection, and number of populations, had the largest impact on power. The power to detect loci subjected to directional in breeding programmes was high when applying the between farmed and wild population approach, and low for the between farmed populations approach. Conclusions. A simulation tool was developed for estimating the power to detect artificial selection acting directly on single loci. The simulation tool should be applicable to most species subject to domestication, as long as a reasonable high accuracy in input parameters such as effective population size, number of generations since the initiation of selection, and initial differentiation (FST) can be obtained. Identification of genetic loci under artificial selection would be highly valuable, since such loci could be used to monitor maintenance of genetic variation in the breeding populations and monitoring possible genetic changes in wild populations from genetic interaction between escapees and their wild counterpart. © 2010 Karlsson et al; licensee BioMed Central Ltd.
Aqua Gen AS | Date: 2010-09-07
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Aqua Gen AS | Date: 2015-01-08
The present invention relates to a method of predicting resistance to a viral infection in a subject, the method comprising determining in the subject the variant present at one or more amino acid position in a cadherin protein, and/or the alleles present at one or more DNA polymorphism in the gene for cadherin, and predicting whether or not the subject is resistant to viral infection based on the determination of the variant and/or the alleles.
Aqua Gen AS | Date: 2013-07-08
The Invention relates to a method of predicting resistance to infectious pancreatic necrosis in salmon, the method comprising determining the alleles present at a DNA polymorphism in the salmon and predicting whether or not the salmon is resistant to infectious pancreatic necrosis based on the determination of the alleles. The invention also relates to a method of selecting a salmon for use as broodstock, wherein the salmon is selected based on the prediction by the first method that the salmon will have resistance to infectious pancreatic necrosis.