Predicting how plants respond to their environment

Yanjun Zan’s path towards computational plant genetics began with an experiment that did not work as expected.

During his master’s studies in China, he worked with molecular biology and poplar. His group had identified genes that could potentially be important for the cambium, the tissue responsible for producing wood. Yanjun spent about two years modifying poplar plants to study some of these candidate genes – but the experiments did not produce the clear answers they had hoped for.

“We were probably too optimistic about how much one gene could do,” Yanjun says. “The modified plants also did not grow very well, so it was difficult to tell whether an effect came from the genetic change or the growing conditions. It’s a big part of science. You learn something from the mistakes.”

The experience made him wonder whether there was a better way to identify promising genes before investing years in experiments. Bioinformatics was emerging at the time, and Yanjun decided to move in that direction.

Meanwhile, rapidly falling sequencing costs were transforming the field, opening up new possibilities to combine quantitative genetics with increasingly large genomic datasets and computational approaches. This combination of quantitative genetics and genomics became the focus of his PhD.

The same environment, a different response

Today, one question in particular drives Yanjun’s research: why do individuals of the same species respond so differently to the same environment depending on their genetic background?

He has observed such differences, for example, in studies of how plants respond to temperatures like those found around Umeå. In some of the populations Yanjun studied, colder conditions led to faster growth, earlier flowering and more seeds. For other populations of the same species, however, the same cold conditions acted as a stress and had the opposite effect.

“The same environmental change can lead to completely different responses,” he says. “I’m interested in understanding the genetic reasons behind these differences.”

If we could predict from one environment to another or reduce the amount of testing we need to do, that would be a very useful thing for breeding.

But Yanjun wants to go one step further and explore whether genetic information can help predict how a plant will perform in an environment where it has never been tested.

Being able to make such predictions could be particularly useful for plant breeding. Breeders routinely test large numbers of plants across many locations to identify which varieties perform best under particular conditions. These field trials require considerable time, land and resources.

“If we could predict from one environment to another or reduce the amount of testing we need to do, that would be a very useful thing for breeding,” he says.

Yanjun has already worked with such approaches in maize breeding in China, contributing to tools designed to help breeding companies decide where particular varieties should be tested.

At IceLab, Yanjun Zan can combine biology with mathematical and computational approaches.

ImageGabrielle Beans

Connecting biology and prediction

In Umeå, Yanjun plans to develop his research along two closely connected lines. One focuses on understanding the molecular mechanisms behind interactions between genes and the environment, initially using Arabidopsis. The other continues his work on prediction and breeding, primarily with crops. In the longer term, he hopes to expand this work towards forest trees.

Being affiliated with both UPSC and IceLab provides an ideal setting for Yanjun to connect these two sides of his research.

“I think I got lucky,” he says. “This field is not new, but it sits between several traditional disciplines, so it has not always been easy to find a community that brings all of them together.”

At UPSC, he can connect his quantitative work more closely with molecular plant biology and research on forest trees. At IceLab, where he is also part of the interdisciplinary complexity centre Stress Response Modeling, he can work across the boundaries between biology and more quantitative disciplines.

This field is not new, but it sits between several traditional disciplines.

“My background is primarily in biology, genetics and quantitative genetics,” he says. “Being part of IceLab gives me the opportunity to combine that perspective with expertise in mathematics, statistics and computational science.”

At the same time, Yanjun believes his biological background can contribute by helping to identify the questions that are worth addressing with mathematical models.

“We are really good at solving problems, but we are not equally good at identifying the problems,” he says.

For Yanjun, bringing these perspectives together is key to developing models that not only describe data well but also address meaningful biological questions and, ultimately, become useful for breeding and conservation.

Contributing to something that lasts

Yanjun is not establishing a research group for the first time. He started leading his own group in China in 2023, and the experience changed how he thinks about scientific leadership.

“At that time, I was very focused on the scientific questions I personally wanted to explore,” he says. “I wanted to try this and try that.”

After several years of leading a group, his priorities have shifted. His first priority, he says, is now to support the researchers in his group and help them develop. For Yanjun, this does not necessarily mean preparing everyone for an academic career. They might instead bring their knowledge into plant breeding, conservation or other areas where they can contribute.

Earlier I would probably have ranked my own scientific interests first. Now supporting the people in my group and contributing to the research environment come before that.

His second priority is contributing to the broader research environments at UPSC and IceLab rather than operating independently from them.

“I want to work on something that actually makes sense to the community,” he says, “either the broader scientific community or the communities here at UPSC and IceLab.”

Individual projects end and researchers eventually move on, while a strong scientific environment can continue much longer. For Yanjun, that longer perspective has changed how he weighs his different priorities as a group leader.

“Scientific curiosity is still very important to me,” he says. “But earlier I would probably have ranked my own scientific interests first. Now supporting the people in my group and contributing to the research environment come before that.”

In the longer term, Yanjun Zan hopes to expand his research to include trees.

ImageMalin Grönborg

Coming back to a second home

Moving to Umeå also means returning to a country Yanjun already knows well. He first came to Sweden in 2013 and spent around nine years here before moving to China. When he and his wife began considering where to go next, Sweden felt like a natural option.

“We know Sweden so well that it feels more like coming to my second hometown,” he says.

Outside of research, Yanjun enjoys being active outdoors. He likes running along Nydala lake, cycling and walking, and regularly plays badminton and basketball. This time, however, he is settling into life in Umeå in a new way: with a house, a garage and a garden – things he had been looking forward to for a long time.

“Now I can do something in my garden as well, and I think my son will enjoy it,” he says.