Skip to main content

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

Periodic Report Summary 2 - 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 collaborate from February 2014 until January 2019 in this comprehensive research project with 7 SMEs, 4 large industries and 1 NGO throughout Europe. These partners 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 is being developed to move each species’ breeding program to the next level.

Project Results:
During the first half of FISHBOOST, all WPs are well underway, and WP5 was completed. WP1 studies the genetics behind the resistance of the six finfish species to specific diseases. WP3 is about genomics tools and has in period 2 to a large extent been collaborating with WP1. Large-scale and powerful disease challenge experiments have been performed for rainbow trout, seabass, seabream (x2), carp and turbot. All of these experiments resulted in informative disease resistance measures. This data was used in one of the largest co-ordinated genotyping-by-sequencing efforts (RAD Sequencing) of aquaculture species in the world to date to successfully generate genome-wide genetic marker data for disease challenged fish. Individual fish samples were genotyped using various RAD sequencing approaches (RAD-Seq, ddRAD-Seq, 2bRAD-Seq). In all cases, the genotyping resulted in population-level, genome-wide SNP marker data for the samples. These results have highlighted the utility of RAD techniques for cost-effective genotyping-by sequencing in aquaculture species, and may lead to wider scale implementation of genomics into aquaculture breeding programmes. Data and samples from the disease challenge and RAD-sequencing experiments are used to estimate genetic parameters for resistance, detect and validate genetic markers affecting resistance, calculate genomic predictions and, ultimately, apply the results in selective breeding for resistance to disease in each of these species. WP2 is about production efficiency traits. In FISHBOOST a lot of effort is put on getting indicator traits for production efficiency traits that are difficult to measure and to get ways to measure production efficiency traits on live fish. When traits can be measured on live fish, it means that traits that normally can only be recorded on sibs of the candidates can be measured on the selection candidates themselves. That makes the selection more efficient. WP6 performs economic assessment of breeding programs. A survey among producers showed how many breeding programs exist per species and revealed the main characteristics of these breeding programs. Market shares of breeding companies per species were: 65-68% for trout, 93-95% for salmon, 43-56% for seabass, 60-66% for seabream, and 100% for turbot, showing that selective breeding plays an important role in European aquaculture. Bioeconomic models for the derivation of economic values for growth, feed intake, mortality and uniformity have been developed to quantify the importance of these traits for the European aquaculture breeding industry. WP5 is about producer perceptions of aquaculture breeding. This WP completed all its tasks, deliverables and milestones in period 2. Using interviews and a survey among producers and representative organisations, we were able to determine positive points, concerns and expected sensitive areas of aquaculture breeding for producers, advantages and challenges for the aquaculture producers regarding implementation of breeding practises, existing and novel breeding methods and in the importance of different traits. These results together with results from all other WPs will be used as input to optimise the breeding programmes in WP4 for the six species. Biological and technological specificities and constraints of each species are taken account of for this optimisation.

Potential Impact:
The most important impacts of FISHBOOST will arise when commercial fish breeders integrate new breeding technologies and adopt accurate measurements of new traits to attain genetic gain. Thereby, they take the development of the species’ breeding programs to the next level. Optimised breeding designs, including economic assessment of these, and genomics tools for e.g. improving accuracy of selection for the six species are developed. FISHBOOST addresses two economically and sustainably important groups of traits that are difficult to improve genetically: disease resistance and production efficiency. 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 and increases health and welfare of the farmed fish, thus alleviates societal concerns.

Scientific, technological, commercial, social and environmental impact of FISHBOOST:
• The use of different RAD sequencing library techniques sequenced on the new NextSeq500 machine will make it possible to compare the different efficiency of these genotyping-by sequencing techniques, for future applications in aquaculture and other species. (WP3)
• Putative QTL for resistance to VNN in European seabass have been mapped. Genomic prediction of breeding values increased accuracy of selection by 50% compared to traditional methods. These results can be taken up by the breeding industry. (WP1)
• A new method to pool DNA from individuals with extreme phenotypes (dead/alive) from a disease challenge test and use this data for genomic prediction of individually genotyped fish can reduce costs for genomic selection in aquaculture species, while maintaining high accuracy of selection. (WP3)
• A genetic epidemiology study on turbot, using the parasite Philasterides, showed significant genetic variation in different components of the disease resistance phenotypes, including resistance, tolerance, resilience and infectivity. Results have broad implications for understanding genetic epidemiology in aquaculture. (WP1)
• For gilthead seabream, a method has been validated to predict fillet yield from non-destructive morphometric records, without a need for sacrificing the fish. Selection for non-destructive fillet yield predictors is expected to effectively improve the true fillet yield. This method addresses the 3R issue. (WP2)
• In rainbow trout, feed efficiency can be improved via simultaneous selection for rapid growth while holding the lipid percentage constant. This makes it possible to breed for improved feed efficiency, which is a difficult trait to select for, because it cannot be measured individually in fish. Improved feed efficiency reduces environmental impact of the aquaculture production (WP2)
• In common carp, studies have been done on lipid reserves during the winter. Results show medium to high heritability for growth, muscle fat content and visceral index. This is the first practical step forward for building a breeding program for common carp in Europe. (WP2)
• BASEPOP is a software tool to select individual fish or strains for new aquaculture breeding programs in an optimal way. FISHBOOSTSEL is a software tool that maximises genetic gain with restriction on inbreeding and assigns matings to different tanks, which is a common constraint in aquaculture breeding. These software tools are freely available to the aquaculture industry. (WP4)
• Knowledge on which perceptions European aquaculture producers and 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)

List of Websites: