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Professor Ross Houston on aquaculture genetics

Genetic studies for improving disease resistance in aquaculture species, his experience of working with companies and running marathons

Ross Houston's group
Ross Houston’s group investigates disease resistance in fin fish and shell fish.

Professor Ross Houston is Personal Chair of Aquaculture Genetics and research group leader at the Roslin Institute. In this interview with Science Communication Intern Maggie Szymanska, he talks about his research on disease resistance in aquaculture species, the future and applications of his work, and the challenges he encounters as a scientist.

Could you briefly tell me about your work?

My work focuses in understanding and improving disease resistance in aquaculture species, including fin fish (like salmon, trout, sea bass and tilapia) and shellfish (like oysters and mussels). Our projects look at all these species, trying to understand why some individuals are more resistant and why some individuals are more susceptible to disease.

The research we do is mainly with the goal of applying that data in breeding programs. By using genetic markers to make selection decisions, we can improve the resistance of fish and shellfish.

We also do studies that investigate why some regions of the genetic makeup – what we call the genome - are associated with disease resistance. We do this by looking at the genes and coming up with hypotheses about which genes might have a function related to disease resistance.

And how do you do that?

One of the ways is to use RNA sequencing to look at the differences in gene expression between resistant and susceptible animals. After we’ve hypothesised about a specific gene that might be involved directly in disease resistance, we sometimes use genome-editing technology, trying to target that specific gene and look at the effect of target changes to that gene on the trait of interest.

How did you become interested in this field of research?

I come from a genetics background, not an aquaculture one. My undergraduate degree was actually in human biology, which had a genetics component. My first contact with aquaculture was in my first postdoctoral position which was in Atlantic salmon genetics. That started a series of projects that looked at using genetic markers to make salmon more resistant to a viral disease called infectious pancreatic necrosis. From there, I started working more and more in aquaculture.

How do you see the future of your research?

I think the area that we are working in (aquaculture genetics) is becoming more important and is beginning to be seen as an important part of sustainable food production. Acceptance of the use of genetics as a solution to disease is increasing, therefore there is more research effort being put into this direction and companies are becoming more interested in applying selective breeding for disease resistance.

This is really exciting for the future of my research because I remember when disease resistance was not thought of as something related to selective breeding at all. It has only been in the past five, ten years where it has become a major part of what selective breeding is all about, at least in aquaculture species.

Why is disease resistance such an important trait in aquaculture?

I think it is because diseases are a big problem in aquaculture, perhaps because there is less research into other potential control mechanisms like vaccinations or drug development. Another reason may be that, in aquaculture, especially seawater aquaculture, fish and shellfish are very exposed to the environment around them. This makes it very difficult to contain diseases using biosecurity, which may be possible to do in other types of farming. A benefit of working on disease resistance is the knowledge that it benefits both the economy and animal welfare.

Could you tell me about some challenges you’ve experienced working as a scientist?

I can think of two challenges that immediately come to mind. The first is a technical challenge that luckily, currently affects me much less. When you’re working on a species that not a lot of people are working on, you have to do a lot of extra work just to get to the same level of model species, with regards to resources and tools.

For example, a few years ago we wanted to research disease resistance in oysters and do a genome-wide association study, but we were unable to complete it as we didn’t have the genetic tools we needed. For other livestock species, or a more researched fish like salmon, this may have been possible. Aquaculture species also tend to have a lot of wonderful and weird genomes, which are very complicated with many repeats and duplications, making research even harder.

The second challenge is from a more applied point of view. We rely on working alongside commercial partners to conduct large disease experiments and field trials. It can be challenging to work at the interface of academia and industry, for example we can’t give away commercially sensitive information in publications but, at the same time, we want to publish to show the scientific advances we are making. We deal with this challenge by developing strong long-term mutually-beneficial relationships with companies and learning from past experiences. We are currently working with quite a few companies and we understand what they want out of the collaboration and we are sensitive to that, and vice-versa, they understand and help us with what we want to do.

Do you have a favourite project from your time here?

There are many projects I have enjoyed working with, and getting involved in working on new species, new diseases and with new collaborators is always an enjoyable challenge. However, one of the most successful projects was the first project in which we mapped a locus – the position of a gene - affecting resistance to a viral disease called infectious pancreatic necrosis in salmon. We did not know what to expect beforehand, but generally most traits of interest in selective breeding are controlled by many different genes. The unique thing we found about this disease was that it was controlled largely by one single section of the chromosome, which was very interesting but also very useful practically. It meant that, by using only a few genetic markers, salmon farmers could immediately select if their fish were resistant or susceptible.

This was very important as it was a defining moment in the relationship between us and the outside world. It helped the aquaculture industry to buy into the idea we can use genetics to predict susceptibility or resistance, and to convince people that using molecular genetic data to improve aquaculture breeding was worthwhile.

The mortality from the disease has fallen off quite sharply since this test was used for resistance. It was nice to see a practical output from research that has been going on for more than ten years. Many of the projects since then have built on these outcomes, directly or indirectly, by using different tools and techniques to understand and improve production traits in various aquaculture species.

Why did you decide to become a scientist?

Maths and science were always my strong subjects at school and I decided to do a biology degree at the undergraduate level. As time went by I became increasingly more interested as I went along. Doing my PhD I got more and more invested and much more engaged and that helped me realise that this is what I want to do. I was always thinking about the next experiment, what to test and how to organise it.

And finally, if you weren’t a scientist, what would you be?

A retired professional marathon runner!! Perhaps more realistically I would be in some sort of business-focused job. I remember looking into accountancy at one stage, as it was something numerical and involved science skills. But it’s clearly not as interesting as being a scientist!

Related links

European consortium to ensure safer and healthier fish

Scottish consortiums take giant leap forward for salmon gill health

Propensity to transmit diseases depends on genes