‘I don’t create monster fish’: Her DNA quest for fast-growing snapper

In this series, people from all walks of life offer an inside – often unfiltered – take on their livelihoods and what keeps them going in their jobs. In this instalment, Dr Shubha Vij, a fish geneticist, shares the highs and lows of aquaculture research in Singapore, as told to The Straits Times.

I am 48 and a fish geneticist. A key part of my job is to collect data and identify genes that result in fish with better texture and nutritional quality, allowing local fish farmers to improve selective breeding programmes.

I’ve been researching food fish since 2012. I started with the Asian seabass, the “poster fish” of Singapore. Today, I lead the Sustainable Aquaculture Technology Centre at Republic Polytechnic School of Applied Science.

My research is critical to Singapore’s food security, as we import over 90 per cent of our food. The Government wants to strengthen local production of Asian seabass, red snapper and marine tilapia – which are found in local delicacies like fish head curry and fish soup.

Sometimes when I tell people I’m a geneticist, they think I edit genes to produce “monster” fish. If you are familiar with the Jurassic Park movie series, the lab geneticists altered and mixed the DNA of several dinosaur species to develop scarier, larger new ones for park entertainment.

But my team does not manipulate or add foreign genes. In fact, we do “detective work” to understand the biology of fishes and identify which genes can produce superior fish.

If you are a fish farmer, you want heavy, beautiful fish with a good nutritional profile so that consumers buy them. However, the most desirable qualities in fish, such as size and colour, are only visible after they grow into adults.

Importantly, we also want faster-growing fish, as shorter production cycles boost outputs and profits for farms.

It tests a small DNA sample – usually from a small clipping of the fish fin – and rapidly checks specific genetic markers for growth, nutritional quality, disease resistance and other important traits.

We do mass sampling on fingerlings to identify superior fish, and again when the fish are ready for the market, with monthly check-ins on the fish in between.

Data from this tool can then help farmers save time and resources by prioritising which baby fish to grow to harvest size and breed. Before this, breeding fish was a guessing game.

Through our data, we also found that faster-growth traits are about 30 per cent heritable in red snapper – just like how children of tall parents have a high chance of being taller. This means selective breeding can deliver steady improvements over generations.

We also made another discovery through DNA testing. Juvenile fish of different species can look very similar, so farmers thought the snappers often grown here were crimson red snappers. But our data showed they were actually Malabar red snappers, also known as Singaporean red snappers.

My team and I collaborated with James Cook University to import thousands of red snapper fish in 2021 – either fertilised eggs or one- to four-inch fingerlings – from various locations in South-east Asia, and distributed them to local farms. This was part of a research project funded by the Singapore Food Agency.

It took 18 months for the fish to reach harvest size. Farmers typically prefer to sell them when they each weigh 700g to 800g, and this takes a long time. Seabass, in comparison, takes less than a year to reach adult size.

Among the fish farms here, there are just two that I know of that continue to rear red snapper. It’s challenging to get the buy-in from farmers because they don’t have experience growing this fish.

Also, red snappers can be more aggressive, and this is a challenge for farmers: A bigger fish will bully others, and we’ve often seen fish that have lost an eye or even been eaten alive. It’s definitely not a tame fish.

Understandably, a farmer would think: Why not just grow seabass, as rearing red snapper appears to be more expensive and difficult?

So, my research aims to better understand red snapper’s biology, so that we can grow the fish faster and more profitably.

I have a degree in zoology, a master’s in biotechnology, and a PhD in rice genetics. The good thing about genetics is that if you understand plant DNA, you would understand human and fish DNA as well.

I worked with human stem cells at the National University of Singapore, before moving to A*STAR where I started working on zebrafish in 2009.

Zebrafish are widely used in biomedical research as a model for studying the human heart because their transparent embryos allow scientists to observe the beating heart directly.

I joined the world of food fish in 2012 and researched the Asian seabass extensively, from studying populations of the fish in places like South-east Asia and India, to decoding its genome. A genome is the full set of DNA that shapes how an organism grows, reproduces, responds to disease and adapts to its environment.

Because I think so much about the fish I study, I have a connection of sorts with them. I would never eat red snapper, seabass or tilapia now.

I love working with seabass the most. It’s my first love, the first food fish I started to work on, and it has such interesting biology. Most fish can either live in fresh water or salt water, but seabass can live in both, happily. Only 3 per cent of fish in the world can do this. It has a beautiful, streamlined body, and it’s also a sex-changing fish.

Many people think lab work is boring. In reality, my work takes me out to the field quite often – the job is far more hands-on and dynamic than most people imagine.

Aquaculture research is labour-intensive and requires long hours of sampling work at farms. If I were a plant researcher, my plants could be in the greenhouse. But with food fish that is farmed in the East Johor Strait, more logistics – including taking a boat – are involved.

On sampling days, my team meets around 8am and heads back to the lab at about 5pm after assessing anything from a few hundred to over a thousand fish. We record each fish’s traits such as body weight, total length, colour and overall appearance, and collect a small fin clip for DNA analysis.

I currently work with five farms more actively. Our relationship with the farmers is very important, as they trust us to come onto their farms. I have heard that farmers overseas can be very strict and won’t allow anyone to walk into the facility, to prevent their fish from getting stressed.

Thankfully, the farmers here understand. When we talk to them about research, they are not sceptical and are keen to contribute to our work.

To earn their trust and not be so “parasitic”, we ask them how we can help them.

At a farm that was growing both seabass and red snapper, the farmer came to us with a problem statement: “Could you help me compare the two fish in terms of their protein and fatty acids?” We usually eat fish for these two things, right?

We studied the fish and found that red snapper has slightly more protein than seabass. It’s also fattier and has slightly higher levels of fatty acids, which are good for heart health. This will help the farmer market it as a superior fish.

It’s a very good time to join the industry, as aquaculture has been identified as one of Singapore’s main pillars of food security. Many training opportunities are opening up in various institutes.

I lecture in RP and guest lecture in NUS. I enjoy teaching and I feel so proud to witness how much my students have grown. But I always tell them, a researcher who wants to be in this field needs to have perseverance and patience.

Got an interesting job to share? Write in to us at ssharon@sph.com.sg. Catch up on the rest of our On The Job series here.