Article Science Technology

How the latest platforms are scaling-up our impact in aquaculture

Millions of people around the world rely on farmed fish as a critical source of nutrition - and, as our global population grows, so does the need to improve the productivity of aquaculture.

16 February 2024

But the climate crisis threatens both water quality and availability. Humans don’t just need to produce more fish, we need fish able to cope with - or thrive in - the likely changes in their environment.

Earlham Institute researchers are investigating existing genetic diversity in the Nile tilapia, Oreochromis niloticus, a fish widely farmed in freshwater aquaculture due to its adaptability to environmental conditions and its ease of feeding.

This popularity means there is a huge demand for techniques that can better inform breeders, such as genomics - an area where the Institute’s blend of scientific expertise and the latest technology can offer help.

Genomic selection offers significant advantages over traditional aquatic breeding programmes by identifying genes associated with advantageous traits, such as tolerance to salinity, temperature, or fluctuating oxygen levels, as well as increased size and faster growth.

It can also be used to accurately predict the genetic basis of complex polygenic traits, such as disease resistance.

The Institute has a strong track record of aquaculture research. This includes our work on the Genetically Improved Farmed Tilapia (GIFT) strain, which grows twice as fast as unimproved tilapia.

The Nile Tilapia is a key component of a nutritious diet for millions of people
A farmer holds a freshly caught Nile Tilapia

The scale of the work

Dr Tarang Mehta is a postdoctoral research scientist working in the Haerty Group. He will be using data generated on the Illumina NovaSeq X Plus - the Earlham Institute was the first site in the UK to acquire the platform - to look at the tilapia genome in a whole new way.  

There are approximately 2,000 species of cichlid fish - the group tilapia belong to - and around 40 described species of tilapia.

Dr Mehta describes tilapia as a highly adaptable organism - able to develop adaptive traits and resilience to survive and multiply in a range of environmental conditions.

“Fascinatingly, despite the large amount of observable (phenotypic) differences between cichlid species,” he says, "only 0.1 to 0.25 percent of the genome is different. This therefore means that subtle genetic differences control how, when, and where genes function to manage these adaptive traits.”

Dr Mehta previously used the NovaSeq 6000 to sequence the transcriptome – the various products of actively expressed genes – and the epigenome – chemical compounds and proteins which attach to DNA, modifying the way genes behave. 

“Using the epigenome, we can finely pinpoint the non-coding portion of the genome, and any genetic differences between species, to determine where [in tissues] and when [in an organism's development], a gene is switched on or off,” he explains.

“This is very useful for mapping out networks of genes and their regulators controlling the function of adaptive traits.”

He says new platforms will allow the Institute to refine these previously developed techniques for understanding wider aquaculture-relevant traits such as disease resistance.  

“We will be able to scale up our research and generate larger datasets at a lower cost. Working with data from this platform will allow quicker and higher-resolution mapping of genetic loci.

“The findings will be more precise, more accurate, and offer greater insights for breeding programmes.”

Fish-friendly pipelines

Dr Wilfried Haerty, Group Leader at the Earlham Institute and leader on our tilapia projects, says the fish are very versatile in the levels of salinity they can cope with. Habitats range from fresh water, brackish water, and estuaries through to hyper-saline lakes with pH levels of 9 or 10. 

The fish also feed on easily available phytoplankton and algae - making them much easier for farmers to feed and maintain than predators, such as salmon, which must be fed on fish meal.

“As the impact of climate change unfolds, fresh water is sadly likely to become a scarce resource,” he says. 

“Increased salinity tolerance will alleviate the pressures associated with climate change.”

Dr Haerty says hybridisation is an ongoing problem as the fish can be invasive, absorbing native species of tilapia when introduced to lakes, and the quality of hybrids is also unpredictable. 

“However, in terms of controlled introduction through breeding programmes and genetic investigation, hybridisation is useful. It allows the characterisation of genes which may not otherwise have been available.

“Our next steps will be to contribute to a deeper understanding of the genetic bases associated with traits of relevance such as pathogen resistance and environmental resilience. 

“This will involve the functional annotation of the non-coding genomic sequences that control gene expression, enabling the prediction of the impact of genetic variation, prioritisation of genetic variants and validation in cell systems.”

Transformative technologies like the NovaSeq X Plus help us reduce the cost, increase speed, and up the scale of what we can do. This changes the questions we are able to ask - and the subsequent impact we can potentially make.

Dr Karim Gharbi, Head of Technical Genomics

Local access to low-cost, ultra high-throughput sequencing capability and associated expertise is essential for the success of this work.

Dr Karim Gharbi, Head of Technical Genomics, oversaw the acquisition of the NovaSeq X Plus and explains the work undertaken by his group.

“A small clip is taken from one of the fins," he says, "which is non-lethal and allows the fish to survive after the sample is taken.”

Samples are shipped to the Earlham Institute by our collaborators at WorldFish - a research institute and CGIAR centre who have spearheaded the Genetically Improved Farmed Tilapia (GIFT) programme.

“We can isolate genetic material from this sample to analyse the whole genome or probe specific areas that are linked to traits that we might be interested in” adds Dr Gharbi.

“We are always looking to improve our workflows, our scientists are continually using their expertise to find new and better ways to explore the genome. 

“Transformative technologies like the NovaSeq X Plus help us reduce the cost, increase speed, and up the scale of what we can do. 

“This changes the questions we are able to ask - and the subsequent impact we can potentially make.”


The Earlham Institute’s platforms and expertise support the wider UK bioscience community, not just our own research groups.

To explore the range of ways you can work with the Institute, please contact us.

Profile of Amy Lyall
Article author

Amy Lyall

Scientific Communications and Outreach Officer