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Improving European aquaculture by advancing selective breeding to the next level for the six main finfish species

Periodic Report Summary 1 - FISHBOOST (Improving European aquaculture by advancing selective breeding to the next level for the six main finfish species)

Project Context and Objectives:
Only about 10% of today’s global aquaculture production use genetically improved stocks. In Europe, some breeding programmes consist of only the basic components of a breeding scheme. Hence, there is large potential to increase efficiency and profit by domestication and genetic improvement of farmed finfish. The main challenge of FISHBOOST is to realise this potential into economic and social acceptable breeding schemes, and advance these for each of the six target species. Acknowledging the different capacities of the species, the aim of FISHBOOST is: ‘To improve the efficiency and profitability of European aquaculture by advancing selective breeding to the next level for each of the six main finfish species through collaborative research with industry’. FISHBOOST considers the main components of breeding programmes for Atlantic salmon, common carp, European seabass, gilthead seabream, rainbow trout and turbot. 14 well-recognised RTD participants in Europe on aquaculture breeding will collaborate from February 2014 until January 2019 in this comprehensive research project with 7 SMEs, 4 large industries and 1 NGO throughout Europe that are in the lead of the development of their species’ breeding programmes or are vectors between industry and RTD. A mixture of low- and high-technological advances depending on current capacities of the species will be developed to move each species’ breeding program to the next level.
Project Results:
During the first year of FISHBOOST, activities have started in all WPs. Deliverables have been submitted in WP4, WP5, WP7 and WP8, and many tasks have started up.
WP1 studies the genetics behind the resistance of these species to specific diseases. During the first period, six successful challenge tests of breeding stocks to different diseases have begun, of which four have been successfully completed and two are still ongoing. In addition, families of fish have been produced for validation of two of the diseases under production conditions. These data sets make up the basis for phenotypic, genetic and genomic analysis during subsequent periods of the project. The researchers responsible for the challenge experiments form the expert veterinary committee, which reviews the challenge experiments, discusses best practices, pathology, animal welfare and trait definitions.
WP2 examines traits related to production efficiency in the six species. In the first period, families of fish for experiments to be performed in periods 1 and 2 have been produced. Work has been initiated to define indicator traits for feed efficiency and fillet%, i.e. traits which traditionally have been difficult to improve genetically. Experiments have been initialized to study the genetic adaptation to new diets, in particular feed with several new plant-based components simultaneously.
The experiments of WP1 and WP2 are performed together with the industry partners, facilitating continuous knowledge transfer by co-doing.
WP3 develops genomics tools for use in aquaculture breeding. DNA extraction of fish from the challenge tests of WP1 has started for later genotyping by sequencing activities of RAD, 2bRAD or ddRAD methods that are now being optimized to obtain single nucleotides polymorphisms (SNP) in a cost efficient way. An Expert Genomics Committee has met to discuss and advise on the RAD sequencing techniques. Further, three tasks on tools for increased accuracy of selection using genomics information have started and are thus still ongoing.
In WP4, software has been developed to set up a base population for breeding, BASEPOP. It uses genotypes and phenotypes to select individuals in an optimum way for a base population, based on the genomic relationships of individual fish within and between different strains. The software will now be tested within the consortium, thereafter it will be freely available for everybody who wants to set up a new breeding population.
In WP5, interviews have been performed with representatives’ organizations on the perception of aquaculture breeding. A report summarizing these results has been written. Preparation of a survey on the producers’ perception of aquaculture breeding has started.
In WP6, FISHBOOST has initiated work on economic assessments of breeding programs in aquaculture. In collaboration with the AQUATRACE project, a survey was conducted to obtain an overview on e.g. traits under selection, selection method and productivity in European aquaculture breeding programs for the six species of FISHBOOST. This data is still being analysed. For all six species, an economic assessment of breeding programs has been initiated.
In WP7, dissemination from the project is coordinated. One scientific article, the website and production of a newsletter, a folder, news articles and brochures about aquaculture breeding and FISHBOOST are directed to towards end-users and consumers.
Management of FISHBOOST is organised in WP8. The consortium has been successfully established and progress is monitored through monthly WP meetings and monthly reports and a fully functional intranet site. Two general assemblies and two board meetings have been organised. Overall, FISHBOOST has delivered as planned and achieved its sub goals for the first period. At the end of period 1, none of its deliverables are outstanding and/or delayed.

Potential Impact:
The most important impacts of FISHBOOST will arise when commercial fish breeders integrate new breeding technologies and software, and adopt accurate measurements of new traits to attain genetic gain, thereby taking the development of the species’ breeding programs to the next level. Optimised breeding designs, including economic assessment of these, and genomics tools for improving accuracy of selection for the six species will be developed. FISHBOOST addresses two economically and sustainably important groups of traits that traditionally have been difficult to improve genetically: disease resistance and production efficiency. Improved accuracy of selection and information about the genomic architecture will assure the genetic gain for these groups of traits. FISHBOOST investigates the societal views on acceptable systems and methods of aquaculture breeding. Higher productivity, through more efficient fish, may lead to reduced prices of aquaculture products for the consumers. Reduced mortality in aquaculture production through selection for disease resistance reduces impact on wild fish in addition to increased health and welfare of the aquaculture fish, and thus alleviates societal concerns.
Based on submitted deliverables, FISHBOOST has the following impact for the European aquaculture industry, society and FISHBOOST partners:
• BASEPOP is a useful tool to select individual fish or strains for new aquaculture breeding programs in an optimal way. Information from the scientific publication on the design of a base population is useful for choosing numbers of markers and identifying which fish should constitute the base population (WP4).
• Knowledge on which perceptions European representative organisations have on aquaculture breeding will make the European aquaculture breeding industry better able to decide on acceptable traits and methods in the future (WP5).
• Brochures and the site give information about aquaculture breeding and FISHBOOST to society (WP7).
The seven European SMEs and large industries have been highly active in period 1 of FISHBOOST through planning and running of experiments, and they interact continuously with RTD in this project. This interaction has generated valuable new knowledge about aquaculture breeding and resulted in mutual benefit for these partners.

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