Scientists map aspen tree genes across seasons, creating a detailed genetic roadmap

As days grow shorter and nights colder, the first yellow leaves begin to appear. Deciduous trees like aspen have evolved to adjust their growth cycle to such seasonal changes. Guided by temperature, light and day length, they form buds in autumn, pause growth during winter and burst into life again in spring, leading into their most active growth phase in summer. To study this cycle in the lab, scientists simulate seasonal changes by adjusting day length and temperature. But how well do these artificial conditions reflect what happens in nature?

“We wanted to understand which genes are active in wild aspen trees throughout the year, and how this compares to trees grown under controlled conditions in the greenhouse”, explains Ove Nilsson, who led the study. “By comparing controlled indoor conditions and more varying outdoor environments, we identified which genes are switched on at different times of the year, and which environmental signals might control these genes.” 

A detailed map of seasonal gene activity 

Over the course of a year, the team collected monthly samples from aspen trees growing on Umeå University’s campus. Alongside samples from various lab experiments, they analysed gene activities in more than 200 samples, resulting in a very large dataset. With the help of the bioinformatician Torgeir R. Hvidsten from the Norwegian University of Life Sciences, they prepared a detailed map of active genes throughout the year and identified differences between indoor and outdoor grown trees. 

“We were very happy to see that we can largely mimic many of the important changes that occur over the seasons with our indoor data from controlled experiments,” says Ove Nilsson. “There is, however, a large set of genes that are specifically expressed under the outdoor conditions that we miss in our controlled experiments. We speculate that these genes can, for instance, be associated with responses to pathogens or adverse growth conditions, such as drought.”

An app that allows scientists to identify similarly behaving genes

Encouraged by these results, Ove Nilsson’s team went a step further and developed a database and an app to make their data accessible. Other plant scientists can now easily explore when specific genes are active throughout the year and under different conditions. The app also shows which genes behave in similar ways, helping researchers understand how they might be connected or influence each other. Ove Nilsson’s team also plans to continue working with the dataset, focusing on some of their favourite genes that control the timing of bud set and bud break in aspen trees.  

“This study highlights the relevance of the findings made in controlled indoor experiments, but also its limitations when translating it to what is happening out in nature,” concludes Ove Nilsson. “It took several years until we had all data together and the driving forces behind the analysis were my former PhD student Alice Marcon, who recently defended her thesis, and my current PhD student Laura García Romañach, who has developed the app.”