New species, new traits, new opportunities

The aim of this project was to establish the tools and methods necessary to get started with marker-assisted and genomic selection for Lumpfish (Cyclopterus lumpus), Tilapia (Oreochromis niloticus) and Sea bass (Dicentrarchus labrax). In addition, we have analysed new traits relevant to the breeding of Rainbow trout. In fish breeding, one wishes to associate the fish's measurable traits with the fish's gene variants. To study gene variants one uses so-called SNP-markers, which are variable single bases scattered around the genome. In order to fully utilize this technology, we need access to the full genome sequence of the species in question. The Lumpfish reference genome did not exist before project start. Therefore, in this project, we have sequenced and assembled the entire Lumpfish genome using so-called second (Illumina) and third generation (Oxford Nanopore) sequencing technology. The reference sequence that was created is ~550 million base pairs long and appears to be of high quality. The Lumpfish draft genome was made available in November 2018 via figshare (https://doi.org/10.6084/m9.figshare.7301546). An updated version of the genome is scheduled for publishing in 2020. Using the Lumpfish assembly, Aquagen has developed a Lumpfish SNP-array. This SNP-array is used by Aquagen to look for genes that provide improved disease resistance in fish. Promising results were found for increased resistance against A. salmonicida; a disease being a major problem in the Lumpfish industry. For Tilapia, challenges tests were conducted to detect increased resistance to Streptococcus agalactiae and Francicella. These results will be used in breeding of Tilapia with increased resistance to these bacteria. In the tilapia industry, there is a great demand for male fish, as these grow faster, and male only production avoid unwanted spawning. Female Tilapia can change sex if reared in high temperature, and the ratio of how often this happen, is a heritable trait. With DNA sequence from male and female fish, Genomar hope to develop a genetic sex test that will enable them to offer fish with genetics that change sex after heat treatment. In the project, 43 individual Sea bass has been sequenced and the data have been handed over to Aquagens collaborator Culmarex. Attempts were made to carry out Sea bass disease challenge tests, but these were not successful. Results and methods from this project will nevertheless be adopted and further developed by researchers working with Sea bass. With the tools and methods developed in this project, we have conducted successful searches for gene variants that affect important characteristics of Rainbow trout such as skin colour, fillet colour, growth, and maturation. These traits will therefore be part of the future Aquagen Rainbow trout breeding program.

I dette prosjektet er det utviklet nødvendige verktøy for å etablere et kommersielt genombasert avlsprogram for rognkjeks. Dette arbeidet kan få positive effekter for den nasjonale rognkjeksnæringen, og da spesielt for Namdal rensefisk, som er leverandør av rensefisk til fire store oppdrettsselskap som opererer i hele Norge. Genomreferansen og SNP-array utviklet i prosjektet vil være nyttig for forskere i hele verden. For havabbor er det generert sekvensdata som har gjort det mulig for samarbeidspartner å forbedre sine genomiske verktøy. For sjøørret er genetiske markører identifisert for flere av de undersøkte egenskapene. Dette vil kunne bli kommersielt viktig for Aquagen og Aquagen sitt datterselskap Aquasearch i Danmark. Smittetestene for resistens mot Streptococcus og Francicella i tilapia har gitt Genomar verdifull informasjon om genetiske parametere i populasjonen og de har startet seleksjon for bedret overlevelse ved sykdomsutbrudd.

This project focuses on the application of genomics in selective breeding for key non-salmon aquaculture species, providing a vital part of the foundations for AquaGen?s upcoming involvements with the species. AquaGen has recently established a breeding programme, aiming at breeding forth healthy lumpfish with a strong appetite for lice. The project will establish vital genomics tools for the species, a genome reference sequence and a high-density SNP-chip. The project will thereafter use this tool in order to identify genes or genome regions (QTL) affecting lice grazing abilities and resistance to Aeromonas and Vibrio. In tilapia, we will scan the genome for QTL for Streptococcus- and Franciscella-resistance, as well as temperature-induced sex ratios. The research will be carried out within the framework of Aquabel, a Brazilian fry/fingerling producer which AquaGen has recently acquired. Results will be commercialized within the same framework. In sea bass, the project will add to an already established project undertaken in collaboration with Culmarex (Spain), aiming at the identification of QTL for nodavirus resistance in sea bass. The project will also produce the contents needed for the future production of a SNP-chip for sea bass, a step towards a stronger future involvement in the species. In rainbow trout, we will carry out genetics research that could help in the marketing of large, sea-reared trout as a high-value product, as compared to the portion size trout which dominates the market. We will target the traits skin colour, fillet colour, and sea-water tolerance. All activities are geared towards generating DNA-markers that can be utilised in marker-assisted selection or genomic selection, following the business model AquaGen has successfully applied on Atlantic salmon. The project is likely to contribute to more sustainable aquaculture of the species in question and to state-of-art of genomics research within the species.