The Aqua Genome project

WP 1-3 Cod: We have made a more complete reference genome assembly of Atlantic cod, gadMor3. Differentiation between populations of Atlantic cod is small (but existing) outside the inversions. Thus, the new assembly is crucial to pinpoint key regions for adaptation. Preliminary analyses show that haplotype-based analysis reveal evidence for adaptation and genetic basis of traits of interest also outside the inversions. Using gadMor3 we are now addressing adaptation to low salinity (Brieuc et al. in prep) and for a large-scale analysis of Atlantic cod populations, species divergence and demographic history and extent of local adaptation (Baalsrud & Brieuc et al. in prep). For coastal cod, resequencing data are mapped to gadMor3 for investigating the inversions (Brieuc et al. in prep). To address the Northeast Arctic cod (NEAC) populations response to temperature changes, parts of the AGP dataset have been combined with historical samples generated in another project. Results indicate that high frequencies of the cold adapted alleles have remained stable over time, despite temperature shifts. However, presence of the warm- adapted allele at low frequency, suggests that the NEAC population are able to adapt to changes in temperature, depending on the intensity of future selective pressure and standing genetic variation for other adaptive alleles (Helmerson et al. in prep.). WP1-3 Atlantic salmon: The AGP has enabled us to detect and describe genetic variation in 948 fish representing multiple European (Norwegian) and Canadian populations. Millions of SNPs (single nucleotide polymorphisms) are now being analysed by researchers in Norway, Canada and UK in an effort to relate them to fish migration, environmental factors (water-flow and temperature), as well as population structure and evolution. Patterns of variation are suggesting that genetic material from Canadian populations has introgressed into salmon in Finnmark in their separation millions of years ago. This signature is localized to a few specific chromosomal locations containing, among other things, genes related to immunity. The dataset has been mined not only for SNPs, but also for larger structural variations (SVs) which can have dramatic effects on gene-expression, this the first time any salmonid species has been analysed for SVs using genome-wide methods. A catalogue of more than 15,000 SVs has been assembled and used to define population structure, the result of which was in strong agreement with proposed structure from SNP data. SVs showing the highest differentiation between wild and farmed individuals seem to be related to domestication processes and highlight specific genes and pathways underlying this genomic transition. WP 4 Salmon: Effects of incubation temperature on survival during the seawater phase was found with higher survival in the low embryonic temperature groups until harvest. Moreover, fish raised at low temperature showed a 4-fold reduction in visible deformities. No major differences in fillet quality was shown between the groups, except for a higher firmness in fast growing groups. A large number of genes were found to be differentially expressed in muscle of larvae, and subsets were affected by incubation temperature, genetic background, and combinations. Genes involved in the immune response, response to abiotic stress and metabolic processes were detected. Both temperature and genetic background affected the differentially methylated sites. Thus, salmon bred for fast growth at relatively high temperatures are subjected to a higher level of metabolic stress likely reflected in the earlier onset of muscle hypertrophy and lower growth potential at sea. Atlantic cod: Body growth in cod was affected by early temperature, and increased temperature during early somitogenesis resulted in larger fish after 180 days and 30 months. However, their offspring seemed to grow slower, indicating the impact of incubation temperature in the previous generation. Transcription and methylation analyses are currently performed including the next generation testing transgenerational effects of temperature treatment. WP 5: Atlantic cod: Results from the transcriptome analyses of vaccinated (Vibrio) and challenged (Francisella) juveniles were published in 2019 with implications for our understanding of immune memory and regulation (Solbakken et al. 2019 a, b). Investigations in relation to adaptations of copy number variations, immune genes and simple tandem repeats in coding regions are ongoing activities. There have been limited activities in WP 5 on Atlantic salmon in the reporting period (due to the fact that the funding for activities had been spent prior to the prolongation).

The AGP project has generated important results for Atlantic cod and Atlantic salmon with respect to wild populations, fisheries management and aquaculture. New knowledge of genes of importance for growth, muscle development, muscle pigmentation, disease resistance and sex determination has been generated. For both cod and salmon, we have shown that structural variants (i.e. copy number variation, simple tandem repeats, rearrangements, inversions) are crucial for local adaptation (cod) and for domestication (salmon). Taken together, the results from the AGP project, including the genomic databases for cod and salmon, will have vast implications for future research, stock management and breeding. The project has also enhanced national and international collaborations (both with industry and research) for both species and exposed biologists and bioinformaticians to social sciences research on important aspects of fisheries and aquaculture.

Aquaculture and fisheries of Atlantic salmon and cod face considerable future challenges from factors including disease, climate change, and product quality. This proposal aims to create a foundation for sustainable production of these species through dis secting the genetic basis of observed phenotypic variation, and gaining a deep understanding of how the genomes are influenced by artificial selection and the environment. Utilizing and further developing the resources and competence of the FUGE programme through the national platforms for genotyping (CIGENE), sequencing (NSC) and the GenoFisk Consortium, we aim to exploit the vast potential that the salmon and cod reference genome sequences now offer. Specifically, this project will utilize the latest hi gh-throughput sequencing technologies to generate a comprehensive genetic database for cod and salmon by re-sequencing 1000 individuals of each species representing a broad range of aquaculture stocks, phenotypes and wild populations. The identified seque nce variation will be combined with extensive datasets from genome scans to target candidate genes underlying economically important traits. Landscape genomic approaches will utilise high-resolution environmental data to identify genomic regions and genes under selection in the natural environment. Environmental effects on phenotypic plasticity and epigenetic processes will be investigated through experimentally comparing global methylation patterns. Finally, transcriptome profiling and a range of functio nal tests will be performed in order to pinpoint the mode of action and extent of phenotypic influence of key genes identified by the connected work packages. As a whole, the project will make a dramatic contribution to bridging the genotype-phenotype gap for traits of importance for aquaculture and will significantly increase our understanding of how these species adapt to the broad spectrum of natural environmental variation and anthropogenic factors.