The Roslin Institute
Roslin Logo

Research supports sustainable growth in fish farming

Developments in genetics are helping to meet the challenge of producing farmed fish and shellfish, to provide nourishment to many.

Atlantic Salmon
Atlantic salmon accounts for almost 5 per cent of the global fish and seafood market.

Farmed fish and shellfish have become a vital source of healthy protein around the world as human populations grow and become wealthier.

To increase production sustainably and meet demand, relying on wild fisheries alone will be insufficient.

Aquaculture – farmed production of fish and shellfish – accounts for just over half of the seafood market and is set to reach 109 million tonnes in 2030. This represents an increase of almost one-third compared with 2018, according to the United Nations’ Food and Agriculture Organisation.

Fish and shellfish farming can enable a good return on investment, making it accessible to producers in low and middle-income countries as well as larger and more advanced economies.

It is among the most sustainable forms of food production, needing little land and fresh water and with relatively low greenhouse gas emissions.

However, it does not come without challenges, with disease in farmed fish and shellfish populations costing £6bn each year to farmers worldwide, in addition to major animal welfare and environmental concerns.

Disease challenges

“The species and systems used for aquaculture production vary substantially with geography, but a common theme is the challenge of infectious disease across all species,” says Professor Ross Houston, an aquaculture genetics expert at the Roslin Institute.

Farmed fish are susceptible to disease from existing and emerging bacteria, viruses and parasites. In some cases, this risk can be increased by high population density and exposure to the open water environment, which creates a challenge to prevent the spread of harmful organisms.

The diversity of farmed fish and shellfish – more than 500 species – presents a significant challenge for scientists and farmers to understand how each responds to a broad range of harmful organisms, and to then develop effective solutions to control disease.

In addition, antibiotics are heavily used for some species in certain regions, raising the risk of long-term ineffectiveness from increased antimicrobial resistance.

Healthy production

Controlling infectious disease requires a holistic approach. Good management practices, including disease testing, managing the spread of harmful organisms, high standards of hygiene, and maintaining diversity within farm stocks, are key to managing the risks of disease.

“Aquatic diseases are hard to control,” said Professor Dan Macqueen. “Prevention is better than cure, and gets round the issue of use of blanket treatments. Genomic tools can help us diagnose relevant pathogens in a rapid and accurate way to help inform decision making.”

Investigating genetic resistance to disease – identifying naturally occurring genetic variations in fish or shellfish that give them a higher level of resistance – is a useful approach that can help improve the health of farmed populations.

Fish and shellfish breeders can select individuals with beneficial genetic variants for breeding, in the likelihood that their offspring will inherit higher resistance to disease.

Selective breeding combined with genomic tools can complement the use of vaccination, while also reducing reliance on vaccines, which are challenging to administer to fish, and impossible for shellfish owing to their lack of an adaptive immune system.

“Fish and shellfish are recently domesticated and highly fecund, both characteristics that offer huge potential for making rapid progress in breeding for disease resistance in farmed stocks,” says Professor Houston. “However, this must be done via well-managed breeding programmes to maintain the genetic diversity and concurrent improvement in other target traits.”

Species research

Atlantic salmon is among the most popular fish, with almost 5 per cent of the global market. It has been well studied from the perspective of managing disease. In every location where it is farmed, however, the species is susceptible to infection by parasites – particularly sea lice and amoebic gill disease. In addition, viruses and bacteria can cause outbreaks with high levels of disease and death.

These diseases not only present a stress and welfare concern for the farmed fish, but can impact on the environment and on wild populations of fish. This can happen via direct transmission of diseases, but also owing to the use of chemical treatments for certain parasites.

The Roslin Institute’s research has a major focus on developing an understanding of the genome of Atlantic salmon, including how variation in the genome can contribute to traits of importance to farming.

“Our understanding of the salmon genome is expanding rapidly thanks to new genomic tools,” says Professor Macqueen. “For example, we are currently learning much about how gene expression is being controlled in this species, which will help us uncover gene variants responsible for biological characteristics relevant to production and fish welfare.”

Research into farmed fish, including their response to disease, is undertaken at the newly opened freshwater Aquaculture Genetics Research Facility at the Roslin Institute. The facility supports research into disease resistance and genome editing of farmed fish, in particular salmon and related species.

Applying technology

The Roslin Institute team are also focusing on using genome editing approaches to understand the genes affecting variation in resistance to disease. Genome editing technology such as CRISPR can enable very targeted changes to the genome of fish and shellfish, which could also be potentially useful for improving production, while making farming more sustainable and less impactful to the environment.

Salmon was the first approved genetically modified (GM) food, and has been made available in the US and Canada. Production of the AquAdvantage fish, which has been modified to overexpress growth hormone, enabling year-round growth, is produced in indoor facilities to prevent fish from mixing with or impacting on wild populations.

GM foods are modified to express genes from another organism, and regulatory approaches to the use of GM products vary around the world. Genome editing, however, is a precise technology that can result in changes to gene variants that already exist within a species, which may not be considered GM under regulations in some nations.

“Genome editing is a really useful research tool at the moment, as it allows us to assess the function of genes involved in traits like disease resistance,” says Professor Houston. “Ultimately its application in fish and shellfish farming will be best placed where there are benefits for production, environment, and animal welfare. Disease resistance is a good candidate trait.”

Research into genetics and health could help make these technologies more precise and contribute to aquaculture sustainability, food security, and animal welfare.

Related links

UN The State of World Fisheries and Aquaculture 2020

Aquaculture research at the Roslin Institute

Image credit: CSIRO