MGSA Science & Research Working Group - Aquaculture Science & Research Strategy

MGSA S&RWG was tasked to produce a comprehensive research strategy prioritised on respective contribution to informing the sustainable growth of the Scottish aquaculture industry and potential impacts of the 2020 sustainable production targets as detailed

02 Table Stock Improvement

General Topic
Priority Ranking (1-8)


Relevance to 2020 target

Potential deficiencies in Infrastructure/Resource Requirements

1) Selective breeding

Increase the resistance of salmon to parasite infections from sealice and Amoebic Gill Disease ( AGD).

Use selective breeding enhanced with the application of the latest genomic tools to increase the resistance of farmed salmon strains. Research indicates there is a genetic basis for sealice resistance in Atlantic salmon. Lice challenges, both controlled and natural of pedigreed salmon strains will identify individuals with greater resistance as future breeding candidates and strains with greater resistance.

Use selective breeding enhanced with genomic tools to estimate levels of innate resistance to this new parasite in salmon strains.

Sealice are an immediate and major concern for the Scottish and global salmon farming industry. Salmon strains with increased resistance to lice will reduce the frequency of treatments and add to a multifaceted approach to controlling this parasite.

AGD is an emerging problem that requires frequent costly, time-consuming and stressful treatment. The cost of managing and treating this parasite is restricting the growth and the long-term sustainability of the salmon sector in Scotland.

Resources for the production of lice for experimental work are presently inadequate either for producing lice for challenges or different strains of lice e.g. naïve and resistant to different therapeutics. The development of experimental lice breeding facility should have a HIGH PRIORITY.

Experimental facilities that enable large numbers of fish from pedigreed or newly selected strains to be assessed under commercial conditions are not available. Such facilities would also benefit research into nutrition and fish health. The genetic improvement research should be done in collaboration with these other priority areas.


2) Production of more robust disease resistant salmon

To increase resistance to viral and bacterial diseases. Breeding programs have increased the robustness of salmon strains to a number of viral ( IPNV, ISA, PD, HSMI) and bacterial diseases (Furunculosis). New and emerging diseases needed. Increased disease resistance particularly benefits early development stages prior to any possible vaccination. Cumulative effect of increasing resistance will result in more robust farmed strains.

There are new/emerging viral and bacterial diseases appearing on a regular basis. New genomic technologies can result in the rapid identification of markers or genes associated with resistance that can speed up the rate of selection. Emerging viral pathogens often have chronic subclinical but result in major losses in production.

The new genomic tools to sequence, assemble and analyse the function and structure of fish genomes and potentially also those of shellfish and crustacean are still not available or are at an early stage of development compared to terrestrial farmed animals. Next Generation Sequencing ( NGS) technologies now mean that whole genome assembly of the main farmed species can be achieved rapidly and cost effectively and should be undertaken as a priority. This will speed up the rate of genetic improvement. This work will also have major benefits for those involved in fish nutrition and fish health This research should be done collaboratively with these groups.


3) Production of fish and shellfish with traits for higher production value.

To identify the genes underpinning important production and value traits e.g. growth, foodstuff utilisation, body conformation, flesh quality and fillet yield.; in the context of the industry using new more sustainable feed ingredients (new sources of fats and protein).

Classical selection of fish stock is critical to the long-term sustainability of any farmed species. Today most breeding programs utilize genomic technologies to define the traits and speed up the rate of selection. Simple growth performance is no longer a priority: priorities will be traits that improve the survival and quality and value of the farmed stock and that can make optimal use of new feeds or which are better at retaining polyunsaturated fatty acids ( PUFAs) in their muscle tissue and have improved efficiency of protein deposition. Particularly if these can be assessed directly and non-destructively in breeding candidates, as this will speed up the rate of genetic improvement.

The transcriptomes of farmed species have still to be studied in detail under a range of normal and different challenge conditions. NGS technologies offer a rapid methodology to better understand the functional genomics of farmed fish. Functional genomic studies of fish reared under various feeding regimes need to be undertaken. This research and development should be closely linked to the Nutrition Research.


There is a need to develop new non-destructive methods to assess post harvest quality traits in aquatic organisms application of new technologies such as CT scanning and Near Infra Red need to be assessed.


4) Genetic management and improvement of new fish and shellfish species.

To improve the genetic management, particularly in the early stages of the domestication process to avoid the genetic degradation that can occur if the broodstock replacement process is not closely monitored.

New fish species include various wrasse species and lumpsucker as biological controls of sealice. New shellfish hatchery for Scottish production of disease-free oyster, sea urchin and mussel spat.

New species need appropriate broodstock management and replacement strategies at an early stage in the domestication process to avoid genetic degradation of the newly acquired wild or farmed animals. That will hinder the future management and improvement of these stocks.

Development of pedigree assignment and broodstock replacement strategies. Molecular markers need to be developed for the above.


5) Stock management strategies to help productivity

Many production traits can be manipulated without changing the genetics of the organism.

Single sex stocks increase the productivity of existing strains of farmed fish. Sexual maturation reduces performance and increases the risk of disease and mortality in most species.

Our understanding of sex-determination and its manipulation in most species of fish and shellfish is still at an early stage. NGS/genomics techniques are starting to change this and offer the potential for rapid progress in this area.


6) Gender control and sterility

To develop single sex or sterile production fish and shellfish to reduce the impact of sexual maturation on the performance and quality of fish and shellfish in the grow-out phase in farmed Scottish species, e.g.: Single sex female trout and halibut Sterile Salmon, trout, oysters

Sterile fish also reduce the risk of interaction between farmed and wild strains and can reduce the costs of environmental manipulation to avoid maturation in normal stocks. Single sex/sterile production systems enable year round production of high quality fish and shellfish.

Single sex/sterile fish will become the norm for farmed and recreational fish species.

Response to pathogens will be impacted by both state of maturation and ploidy needs to be addressed in relation to health and welfare.


7) Epigenetic and maternal programming

To understand the environmental factors that can cause heritable but non-genetic effects on the phenotypes of young animals that can have either long-term positive or negative effects on the performance of these animals and their offspring.

It is already known that the environmental conditions under which fish are reared can impact on their subsequent performance and that of their offspring.

Optimising rearing environments and husbandry will ensure higher quality offspring, manipulating these environments may result in fish that are better adapted to rearing conditions resulting in better performance.

We need to develop an epigenomic toolbox including novel sequencing technologies and bioinformatics. Due to rapid changes in molecular tools these techniques will allow for large scale screening of epigenetic changes in gametes and embryos. So we better understand the regulation of genome expression under different environments.

8) Environmental manipulation

To develop appropriate reproductive controls technologies. There is a need to increase our basic understanding of reproductive physiology and environmental perception in existing and new farmed species.

Ontogeny during embryogenesis key for sensor organs smolts.

Light manipulation is critical in the timely and consistent production of gametes. Control of smoltification, puberty and therefore productivity as well as ensuring better welfare through more even dispersion of fish in rearing pens. Ontogenetic development is better synchronized and is critical to the development of sensory receptors in young fish and their subsequent development and performance.

This work requires the availability of experimental facilities with precise control of lighting and water. Research is needed to develop biomarkers that accurately define seed quality traits in farmed fish and shellfish.



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