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Trondheim, Norway

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. Source

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. Source

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. Source

Karlsson S.,Norwegian Institute for Nature Research | Diserud O.H.,Norwegian Institute for Nature Research | Moen T.,AquaGen AS | Moen T.,Norwegian University of Life Sciences | Hindar K.,Norwegian Institute for Nature Research
Ecology and Evolution | Year: 2014

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual-based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual-based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample. © 2014 The Authors. Source

Sundvold H.,Norwegian University of Life Sciences | Sundvold H.,Center for Integrative Genetics ne | Ruyter B.,Nofima Marin | Ostbye T.-K.,Nofima Marin | And 2 more authors.
Fish and Shellfish Immunology | Year: 2010

Bacterial and viral diseases are major problems in Atlantic salmon aquaculture, but may be challenged through selection of brood stock with enhanced survival to diseases. Today's selection strategy is based on controlled challenge tests using siblings of the breeding candidates, and is thus indirect. Direct trait records on breeding candidates can potentially be provided through identification of genetic variation linked to the susceptibility to the disease. Peroxisome proliferator-activated receptor gamma (PPARG) is a lipid-sensing transcription factor primarily known for inducing fat-accumulation in adipocytes, but also in lipid-accumulating macrophages, in mammalian species. Here we report a novel allele of PPARG, pparg-2, in Atlantic salmon. pparg-2 has an insertion of sixty nucleotides that encodes two additional copies of the almost perfect decapeptide motif, (F/C/Y)NHSPDR(S/N)HS, compared to the previously described pparg-1. pparg-1 contains six copies of this repeat unit whereas eight copies are present in the novel pparg-2 allele. pparg-2 mRNA was detectable in kidney and spleen of random Atlantic salmon samples. Here, we studied the effect of pparg-1 and pparg-2 on survival upon challenge to a highly virulent bacterium, Aeromonas salmonicida, causing furunculosis, and the virus causing infectious salmon anaemia (ISA), respectively, in a Norwegian aquaculture population of Atlantic salmon. ppar alleles were found to be significantly associated with survival upon challenge to A. salmonicida, but not to ISA. pparg-2 was the better allele in terms of survival in the challenge test for furunculosis, survival rates being 0.32, 0.40 and 0.42 for animals with the pparg-1,-1, pparg-1, -2 and pparg-2, -2 genotypes, respectively. We conclude that pparg-2 is in linkage disequilibrium (LD) with, or identical to, a locus contributing to different susceptibility to furunculosis in Atlantic salmon. PPARG was mapped to linkage group eight (LG8) but could only be positioned on the male linkage map since all the informative parents in the mapping families were males. This is the first report showing an association between pparg alleles and an enhanced immune response in fish. © 2009 Elsevier Ltd. All rights reserved. Source

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