Genetic Variation for climate change resilience in growth of Atlantic salmon

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Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon

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Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon

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Impact of vaccination and selective breeding on the transmission of Infectious salmon anemia virus

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Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.)

Amoebic gill disease (AGD) is one of the most important parasitic diseases of farmed Atlantic salmon. It is a source of major economic loss to the industry and poses significant threats to animal welfare. Previous studies have shown that resistance against this disease has a moderate, heritable genetic component, although the genes and the genetic pathways that contribute to this process have yet to be elucidated. In this study, to identify the genetic mechanisms of AGD resistance, we first investigated the molecular signatures of AGD infection in Atlantic salmon through a challenge model, where we compared the transcriptome profiles of the naïve and infected animals. We then conducted a genome-wide association analysis with 1,333 challenged tested fish to map the AGD resistance genomic regions, supported by the results from the transcriptomic data. Further, we investigated the potential of incorporating gene expression analysis results in genomic prediction to improve prediction accuracy. Our data suggest thousands of genes have modified their expression following infection, with a significant increase in the transcription of genes with functional properties in cell adhesion and a sharp decline in the abundance of various components of the immune system genes. From the genome-wide association analysis, QTL regions on chromosomes ssa04, ssa09, and ssa13 were detected to be linked with AGD resistance. In particular, we found that QTL region on ssa04 harbors members of the cadherin gene family. These genes play a critical role in target recognition and cell adhesion. The QTL region on ssa09 also is associated with another member of the cadherin gene family, protocadherin Fat 4. The associated genetic markers on ssa13 span a large genomic region that includes interleukin-18-binding protein, a gene with function essential in inhibiting the proinflammatory effect of cytokine IL18. Incorporating gene expression information through a weighted genomic relationship matrix approach decreased genomic prediction accuracy and increased bias of prediction. Together, these findings help to improve our breeding programs and animal welfare against AGD and advance our knowledge of the genetic basis of host-pathogen interactions

Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

Abstract Background Infectious Salmon Anaemia virus (ISAV) is an orthomyxovirus responsible for large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus. Results Three different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post challenge) and RNA sequenced. The transcriptomes of infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes, our results suggest that other processes such as ubiquitination and ribosomal processing are important during early infection with ISAV. Moreover, the comparison between resistant and susceptible fish has also highlighted some interesting genes related to ubiquitination, intracellular transport and the inflammasome. Conclusions Atlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An immune response was observed in the head kidney in these early timepoints, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome

A workflow used to design low density SNP panels for parentage assignment and traceability in aquaculture species and its validation in Atlantic salmon

This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 654008.Accurate parentage assignment is key for the development of a successful breeding program, allowing pedigree reconstruction from mixed families and control of inbreeding. In the present study we developed a workflow for the design of an efficient single nucleotide polymorphism (SNP) panel for paternity assignment and validated it in Atlantic salmon (Salmo salar L.). A total of 86,468 SNPs were identified from Restriction Site Associated DNA Sequencing (RAD-seq) libraries, and reduced to 1517 following the application of quality control filters and stringent selection criteria. A subsample of SNPs were chosen for the design of high-throughput SNP assays and a training set of known parents and offspring was then used to achieve further filtering. A panel comprising 94 SNPs balanced across the salmon genome were identified, providing 100% assignment accuracy in known pedigrees. Additionally, the panel was able to assign individuals to one of three farmed salmon populations used in this study with 100% accuracy. We conclude that the workflow described is suitable for the design of cost effective parentage assignment and traceability tools for aquaculture species.PostprintPeer reviewe

Raman and near Infrared Spectroscopy for Quantification of Fatty Acids in Muscle Tissue—A Salmon Case Study

The aim of the present study was to critically evaluate the potential of using NIR and Raman spectroscopy for prediction of fatty acid features and single fatty acids in salmon muscle. The study was based on 618 homogenized salmon muscle samples acquired from Atlantic salmon representing a one year-class nucleus, fed the same high fish oil feed. NIR and Raman spectra were used to make regression models for fatty acid features and single fatty acids measured by gas chromatography. The predictive performance of both NIR and Raman was good for most fatty acids, with R2 above 0.6. Overall, Raman performed marginally better than NIR, and since the Raman models generally required fewer components than respective NIR models to reach high and optimal performance, Raman is likely more robust for measuring fatty acids compared to NIR. The fatty acids of the salmon samples co-varied to a large extent, a feature that was exacerbated by the overlapping peaks in NIR and Raman spectra. Thus, the fatty acid related variation of the spectroscopic data of the present study can be explained by only a few independent principal components. For the Raman spectra, this variation was dominated by functional groups originating from long-chain polyunsaturated FAs like EPA and DHA. By exploring the independent EPA and DHA Raman models, spectral signatures similar to the respective pure fatty acids could be seen. This proves the potential of Raman spectroscopy for single fatty acid prediction in muscle tissue.Raman and near Infrared Spectroscopy for Quantification of Fatty Acids in Muscle Tissue—A Salmon Case StudypublishedVersio

EX-spot: Mørke flekker i laksefilet. Årsak til dannelse og tiltak som hemmer utvikling

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Innavl bestemt av mengden homozygoti i genomet

The main aim of this PhD was to study long homozygote segments present in the genome in Norwegian Red, and find genomic options to measure inbreeding more accurately than from a pedigree database. Prior to the study, runs of homozygosity (ROH) was indicated to be a measure utilizing chromosomal regions identical by descent, thus a good genomic substitute to pedigree. Two dataset were exploited: (1) 384 bulls genotyped with the Illumina HD-panel containing 777K SNP-markers, and (2) 3,289 bulls genotyped with a 54K Illumina BeadChip and/or 25K Affymetrix, with imputations both ways if needed. The pedigree of these two datasets extended as far back as 1875.Hovedformålet med denne doktorgraden var å studere lange homozygote segmenter i genomet hos NRF, og å finne genomiske metoder som kan måle innavl mer nøyaktig enn ved bruk av slektskapsdatabase. I utgangspunktet var «runs of homozygosity» (ROH) valgt som en egnet og interessant metode for denne studien, fordi den var antatt å oppnå nøyaktige anslag. ROH ble angitt for å være et mål som på lik linje med slektskapsdatabaser utnyttet homosygositet nedarvet fra samme opphav, og dermed en god genomisk erstatning for slektskapsdatabasen. To datasett ble gransket: (1) 384 okser genotypet med Illumina HD-panelet som inneholder 777K SNP-markører, og (2) 3,289 okser genotypet med en 54K Illumina BeadChip og/eller en 25K Affymetrix, med imputering begge veier ved behov. Slektskapsdatabasen til disse to datasettene strakk seg så langt tilbake som til 1875