AquaLeap: Innovation in Genetics and Breeding to Advance UK Aquaculture Production

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Sustainable and profitable aquaculture in the UK relies on high quality stock. In contrast to terrestrial agriculture, the sources of stock for aquaculture species range from use of wild stock for several species, to pedigree-based breeding programmes incorporating genomic tools in salmon. Well managed programmes of domestication and breeding have huge potential for cumulative gains in production, including by preventing infectious disease outbreaks. Barriers to applying such approaches in commercial aquaculture include knowledge gaps in the genetic basis of economically important traits, and a lack of genetic tools and expertise applied to aquaculture. 'AquaLeap' establishes a leading interdisciplinary hub focused on innovation in aquaculture genetics to enable each sector to take a 'step' or 'leap' forward in stock enhancement.We will target advances for four species of economic importance or potential for UK aquaculture; European lobster (Homarus gammarus), European flat oyster (Ostrea edulis), lumpfish (Cyclopterus lumpus) and Atlantic salmon (Salmo salar). For each of these species, we will develop genomic tools and methods which will then be used to tackle industry-defined barriers to progress in stock enhancement.The genomic tools include high quality reference genome sequences using cutting-edge sequencing technology for the species for which they are currently lacking (lobster, oyster, lumpfish). These genome sequences will be used to exploit standard (e.g. single nucleotide polymorphism, SNP) and novel [e.g. copy number variation (CNV) and epigenetic modifications] sources of variation. Gene editing techniques will be developed, as this technology is likely to lead to breakthroughs in addressing aquaculture problems in the near future. Lobsters are a high value species with potential for diversifying UK aquaculture. Building on previous studies into the on-growing of hatchery-reared lobsters in aquaculture systems, and using the aforementioned genomic tools, we will assess the contribution of genetic and epigenetic variation to growth and survival traits. These results will inform selective breeding, hatchery conditions and choice of juveniles for on-growing, and has potential to improve the performance of lobsters at sea. Native oysters have declined dramatically in recent years, and there is significant interest in restocking from both an aquaculture and ecological perspective. A major barrier to hatchery-based restocking and production is the parasitic disease Bonamia. We will build on previous genomic tool development to identify SNP markers that can be used to predict breeding animals with innate resistance to Bonamia, informing selection of native oysters for stocking and tackling a major production issue.Lumpfish are used extensively as cleaner fish for biological control of sea lice in salmon farming. Hatchery reproduction is now possible, and the next step is selective breeding for traits to enhance their robustness and performance. To help facilitate this, we will assess wild stock diversity to inform base populations for breeding, to estimate genetic parameters for production traits, and develop SNP marker panels for stock management.Breeding of salmon is advanced, and uses genomic tools to enhance trait improvement and inbreeding control via genomic selection (GS). We will apply innovative approaches to improve the cost-efficiency of GS, and test these approaches for the emerging aquaculture species. We will assess the role of potential novel sources of genetic variation (CNVs) in gill health traits. Finally, we will use gene editing to modify a specific gene causing resistance to a viral disease in salmon, with a view to future editing of salmon genes to improve resistance to infectious diseases. The scientific programme is complemented by a series of training, dissemination and public engagement activities, including addressing skills gaps identified by the ARCH-UK network.