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HAVBRUK2-Stort program for havbruksforskning

Genome-based improvement of salmon sea lice resistance

Awarded: NOK 11.2 mill.

An important objective of the project has been to implement genome-based selection methods to improve sea lice resistance in farmed salmon. Challenge tests on family material from AquaGen were conducted in 2014 and 2015 to evaluate the effect of one generation of genomic selection for lice resistance. The results showed 15-20% less lice in resistant compared to susceptible families. The same data was used in a GWAS detecting a QTL for sea lice resistance in the AquaGen population. Follow up studies on this QTL showed that fish with one or two copies of the susceptible allele of the most significant marker have 11% and 28% more lice than fish being homozygous for the alternative allele of the marker. The QTL was implemented in the breeding program of AquaGen in 2015 and is expected to make an important contribution to reduce sea lice in salmon aquaculture. Another main activity of the project was to study salmon-louse interactions in a controlled challenge experiments with lice (common garden experiments), to detect genes and pathways involved in resistance to sea lice, and equally important, to identify differences in gene expression when lice are exposed to a susceptible versus a resistant host. To ensure largest possible genetic contrasts in the experiment, we selected salmon from AquaGen families based on genomic breeding values. The trial was carried out in two stages where the salmon in Experiment 2 was deloused and re-infected before lice counting and collection of tissue samples. For both experiments, tissue samples were collected at day 0 and after 1, 3, 5, 10 and 18 days after lice infection. Lice were counted in both experiments and tissue samples were collected from skin (behind the dorsal fin), kidney and spleen. The statistical analysis of lice counts in the experiment showed significant differences between the genetic groups of salmon. RNA from 376 samples were isolated and sequenced using RNA-Seq. Differentially expressed genes (DEGs) were identified by contrasting the two lines (HR vs LR) at each sampling point, which identifyed 72 DEGs in head kidney and 136 DEGs in skin. Many overlapping DEGs, related to innate immune functions, most notably NOD-like receptors that can recognize cell damage and activate the immune system were identified in the two tissues. In parallel with the collection of salmon tissues, sea lice were collected and classified in various stages of development. Transcriptome analysis was done on samples of salmon lice pooled by fish and developmental stage. Overall, analyses showed that the samples differed mainly due to stage and instar age and that samples from the HR/LR were not significantly different. Moreover, co-expression network analysis, including RNA-Seq data from both salmon and lice, identified some chitin pathway-involved genes as potential candidate genes for follow up studies like gene knock-down experiments. Expression differences in Experiment 1 and Experiment 2 may suggest that lice infections effects gene expression through epigenetic modifications in the genome. To investigate this, we have examined the methylome of 200 samples from the two experiments. Analyses are still ongoing, but preliminary data show a profound effect of infection on salmon methylome and identify a significant portion of genes in inflammatory pathways affected by these changes. Additionally, we are now investigating to what extend methylation patterns effects gene expression in the same samples and how this may relate to HR\LR phenotypes. This is particularly relevant for the material obtained in the project in which we have repeatedly controlled infection experiments with lice which provides documented differences in gene expression in salmon. Another important analysis in the final phase of the project is to investigate if expression differences in susceptible versus resistant salmon is caused by structural variation or familial differences in Transposable Elements (TE). This is done using Nanopore sequencing (MinION), which is a new and pioneering sequencing technology with extremely long read lengths.

With this proposal we will bring together researchers from the Atlantic salmon and sea lice communities with the clear objective of developing new approaches for combating the sea lice threat, and building upon understanding of the biology underlying the host-pathogen interaction. Several key resources (including challenge test material, reference genomes to both pathogen and host, and high resolution genotyping and expression tools) are now becoming available making this the appropriate time to begin suc h an investigation. Our strategy is to use extensive sea lice challenge-test data together with state-of-the-art genomics tools to implement genome-based selection methods not previously used in aquaculture. Subsequently, genetically resistant and suscept ible salmon will be constructed for use in controlled common garden experiments targeting natural resistance against the salmon lice L. salmonis, as well as functional genomics studies of salmon-louse interaction. This integrative approach will reveal gen es and pathways involved in resistance to sea lice in the salmon, but it will also identify differential gene expression responses in the sea lice when exposed to a susceptible versus a resistant host. The project will make an important contribution to th e understanding of both the salmon and lice genomes, enabling the discovery of novel approaches for genetic, immunological and nutritional parasite control. Improved parasite control will benefit the salmon industry operationally and financially, and also reduce the negative impact of farming on wild salmonid populations.

Funding scheme:

HAVBRUK2-Stort program for havbruksforskning