New paper published – Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Text by Lauri Laanisto /EMÜ Press

With the help of Ülo Niinemets and Leila Pazouki from our work group, researchers led by Finnish plant scientists have described the whole genome of silver birch – one of the most distinct and widespread woody species in boreal forest ecosystems of Eurasia. Here is the press release from our university:

Researchers of the Estonian University of Life Sciences involved in publishing silver birch (Betula pendula) genome


A research team led by Professors Jarkko Salojärvi and Jaakko Kangasjärvi (Dept. Biosciences, University of Helsinki, Finland), involving multiple partners from research institutions in Finland, Estonia, UK, and USA published the birch genome. Two researchers from the Estonian University of Life Sciences, Dr. Leila Pazouki and Prof. Ülo Niinemets, were involved in this pioneering research.

Silver birch is an extremely wide-spread Eurasian tree, often dominating temperate and boreal forests. Due to high growth rates and high-quality timber, it is the main tree species for commercial forestry in northern countries. Despite its high commercial value, the genome of silver birch had not been sequenced yet.

Due to its wide geographic dispersal, populations of this plant species are and have been strongly affected by environmental changes. Particularly, temperature is the main factor affecting its growth and development. At present, temperature has increased more than 1.5 °C in several birch habitats, and a warming of 4–11 °C is predicted to be reached by the end of current century. To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes.

In this study, 80 individuals of B. pendula were sequenced. Sampling was done through Finland, Germany, Norway, Ireland, and Siberia. These 80 sequenced genomes allowed the team to identify several key mutations important for understanding the environmental adaptation of birch and also serve as relevant targets for tree breeding. Such primary mutations may affect growth and development of birth trees and the way they respond to light at different latitudes and longitudes and under varies environmental conditions.

As very few tree genomes have been fully sequenced, this study provides particularly valuable information for genome structure and evolution of long-living plants such as trees. Furthermore, this research is expected to serve as a springboard for more efficient breeding of birch towards achieving higher yield and timber quality in different environments. As birch trees have local adaptations to site climates, understanding these natural adaptations will provide a major means for genetic engineering and forest biotechnology studies.

The study was published in the journal Nature Genetics.

Citation: Salojärvi, J., Smolander, O. P., Nieminen, K., Rajaraman, S., Safronov, O., Safdari, P., … & Rastas, P. (2017). Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics, doi:10.1038/ng.3862. (link to full text)



Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

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