Research on trees is one of our main focus at UPSC. We often use genetically modified trees as tool to understand tree growth and development. Take a look on how we make and work with genetically modified trees!
Ove Nilsson (Photo: Anne Honsel)
On their meeting on the 12th of December 2019, the Royal Swedish Academy of Agriculture and Forestry (KSLA) elected 30 new fellows. Ove Nilsson, director of UPSC and professor at the Swedish University of Agricultural Science, will be one of eight new fellows that will join the Forestry section of the academy. The fellows are chosen because of their outstanding knowledge and experience in their respective field of work. They are expected to actively participate in the activities of the Academy.
The Forestry section of the Academy works with questions regarding forest management and usage of the forest as natural resource including industrial and market aspects. It takes up specific education and counselling questions and questions related to hunting as well as environmental issues that are associated with the liability of the industry sector. Among the eight new Forestry sector fellows are six Swedish citizens and two foreign fellows.
The Royal Swedish Academy of Agriculture and Forestry (KSLA) was founded in 1811. Apart from the Forestry section, it comprises two other sections, a General section and an Agricultural section. The Academy is a free and independent network organization working with issues related to agriculture, food, forestry, fishing and hunting. Its independent position shall create a unique opportunity for meetings and constructive discussions, which can be used as starting point for taking initiatives on measures or activities that stimulate development in the respective focus areas.
Link to the announcement of the Royal Swedish Academy of Agriculture and Forestry (in Swedish)
https://www.ksla.se/senaste-nytt/nyheter/nya-ledamoter-skogsavd-2019/
The newly printed version of the special issue. (Photo: Carolin Rebernig)
The Scandinavian Journal of Forest Research recently published a special issue on the usage of vegetatively propagated Norway spruce clones in Swedish forestry. The UPSC Centre for Forest Biotechnology, a Vinnova Competence Centre, initiated this publication to disseminate research findings widely within the forest sector. Lately, the large-scale usage of genomically selected, vegetatively propagated plants became technically possible and the researchers want to launch a discussion about the pros and cons of the usage of clones. During 2020, the results of the issue will also be presented and discussed in an open seminar.
The need of an educated discussion about gains and possible risks advanced the idea of publishing a special issue about the usage of clones in Swedish forestry. “We initiated an extensive literature search on the current knowledge related to the use of clones in forestry and its implications for Swedish forestry. This involves knowledge about the effects from a breeding, silviculture, population genetics and ecology standpoint” explains Ove Nilsson, the Director of the Vinnova Competence Centre and guest editor of the special issue.
All together the reviews show that not only from an economical viewpoint considerable gains can be made by the use of clonal mixtures, but also that the effect on the genetic diversity in Swedish forests will be very minor during the foreseeable future. Ove Nilsson emphasizes that due to the rapidly changing climate quick selection methods to deploy better adapted plants are needed. “We show that these techniques can be key to be able to meet future rapid changes reacting on for example pathogens and droughts caused by the climate change. This adaptation process is currently very slow.” He also pointed out that it is important for UPSC to discuss this topic. “We have knowledge in this area and we have a goal to make sure that our basic research findings can be used to breed for future generations of tree seedlings with better properties and better adaptation to new climate.”
Norway spruce is one of the economically most important forest trees in Sweden. Efforts to optimize productivity, resistance to diseases and to get more resilient plants adapted to a changing climate are constantly made. One way to get rapid access to the very best material from the operational tree breeding programs is vegetative propagation – especially when this method is used in combination with applications of genomic information through a process called genomic selection. The discussion about gains and possible risks of such applications, especially about the effects of a reduced genetic diversity when using clones, is ongoing.
Full reference of the publication and link to the online edition:
Special Issue: Using Norway Spruce Clones in Swedish Forestry. Scandinavian Journal of Forest Research, vol. 34, 2019, Issue 5.
https://www.tandfonline.com/toc/sfor20/34/5?nav=tocList
For more information please contact:
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
From left to right: Joanna Porankiewicz-Asplund (Agrisera), Catherine Bellini (Chair of the UPSC board), Jan Karlsson; photo: Anne Honsel
[2019-12-04] This year’s UPSC Agrisera Prize is awarded to Jan Karlsson to acknowledge his ceaseless technical support for everyone working at UPSC. Jan Karlsson works as IT-coordinator at the Department of Plant Physiology, Umeå University, but carries out many additional tasks that are important to keep the research infrastructure at UPSC running. The prize was awarded during today’s traditional UPSC Christmas lunch.
The UPSC board received two independent nomination letters for Jan Karlsson for the UPSC Agrisera Prize 2019. Both letters highlighted his ambition to solve all upcoming technical problems as soon as they appear even if it is challenging and demands to work outside the normal working hours. “He is the one, who we hope to find in his office when we need a solution for a challenging technical issue”, is stated in one of the letters. “His everyday work contributes to the successful research of many of us at UPSC.”
Jan Karlsson is IT-coordinator at one of the two UPSC departments. He is responsible for the growth chambers and cabinets, is technically supporting the new phenotyping platform, helps to fix things that are broken and much else. During the recent renovations at the Department of Plant Physiology, he was one of those who helped to make the moving and the setting up of the new lab as smooth as possible without neglecting his normal responsibilities. “We would like to thank Janne for being so available and make our work doable in this institute. This Agrisera prize is the opportunity for us to do so”, is written in the second nomination that was supported by more than 30 people.
The UPSC Agrisera Prize is awarded every year to a PhD student, a postdoc or a technician for excellent scientific achievement and positive contributions to improve the UPSC work environment. It is sponsored by Agrisera but the members of the UPSC board select the winner of the prize. The name of the winner is traditionally announced during the UPSC Christmas lunch. This year, the board received in total eight nominations for six candidates. The prize was presented by Joanna Porankiewicz-Asplund from Agrisera and by the chair of the UPSC board, Catherine Bellini.
From left to right: Leszek Kleczkowski (chair of the public defence), Tom Beeckman (committee member), Maria Eriksson (commitee member), Abdellah Lakehal, Catherine Bellini (PhD supervisor), Malcolm Bennett (opponent), Alain Goossens (committee member); photo: Anne Honsel[2019-12-02] When young, dark-grown seedlings of thale cress are given light, they start to form roots from the stem-like part of the plant, called hypocotyl. Abdellah Lakehal used this system to study how the initiation of these adventitious roots is regulated at the molecular level. He identified new components of the complex regulatory network and elucidated further how the main components of the network interact with each other. Abdellah Lakehal successfully defended his PhD thesis on Thursday, 28th of November 2019 at Umeå University.
Plant hormones are growth regulators that play an important role in the regulation of adventitious root initiation. The plant hormones auxin, jasmonate and cytokinin interact with each other to control adventitious root initiation. While auxin promotes adventitious root formation, jasmonate and cytokinins inhibit this process. Abdellah Lakehal now added several new molecular pieces to this complex regulation.
He identified two so-called auxin co-receptors, proteins that fine tune the auxin response during adventitious root initiation. He also showed how jasmonate controls the degradation of auxin in a feedback manner by regulating the expression of another protein. Abdellah Lakehal concluded that this protein mediates a molecular circuit that allows to stabilize the interaction between auxin and jasmonate. In addition, he identified additional components from the jasmonate pathway that prevents the formation of adventitious roots by regulating cytokinin signalling.
Abdellah Lakehal worked with thale cress seedlings. To induce the formation of adventitious roots, he first let the seedlings grow in darkness for three days. Then, the dark-grown seedlings were exposed to light to trigger the development of adventitious roots on the hypocotyl, which is an embryonic stem.
Adventitious roots are important for the vegetative propagation of plants. Many plant species naturally form adventitious roots like for example grasses, cereals or bulb plants but also blackberries or strawberries to propagate without setting seeds. But adventitious roots can also be induced by wounding, flooding or changes in temperature. The vegetative propagation of plants is widely used in forestry and agriculture to clonally multiply elite genotypes.
About the public defence:
The public defence took place on Thursday, 28th of September Umeå. It was chaired by Prof. Leszeck Kleczkowski. The faculty opponent was Malcolm Bennett, Professor, Plant and Crop Sciences, School of Biosciences, University of Nottingham, UK. The defence committee was composed of Docent Maria Ericksson (Umeå University), Prof. Tom Beeckman (VIB, Ghent University, Belgium) and Prof. Alain Goossens (VIB, Ghent University, Belgium). Abdellah Lakehal's supervisor was Prof. Catherine Bellini.
Title of the thesis: A molecular network mediating adventitious root initiation in Arabidopsis thaliana
Link to the thesis: http://umu.diva-portal.org/smash/record.jsf?pid=diva2%3A1368017&dswid=6231
For more information, please contact:
Abdellah Lakehal
Department of Plant Physiology
Umeå Plant Science Centre
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
The UPSC Greenhouse (Photo: Anne Honsel)
In their meeting on the 21st of November 2019, the Kempe Foundations decided to grant a package of six post-doctoral stipends and to approve four additional applications from UPSC. The stipend package is granted to UPSC and it will be used in the frame of a recently started genome sequencing project of Norway spruce and Scots pine that is coordinated by Ove Nilsson. Peter Kindgren and Ewa Mellerowicz receive funding for their research projects, Annika Nordin for doing field work and Stéphane Verger support to buy a new advanced microscope.
UPSC is currently developing a significantly improved reference version of the spruce genome and a full sequence of the Scots pine genome, together with extensive resequencing of spruce and pine genomes. This project was funded in January 2019 by the Knut and Alice Wallenberg Foundation together with a linked project at the Science for Life Laboratory in Uppsala/Stockholm coordinated by Ulf Gyllensten. The six post-doctoral fellows granted by the Kempe Foundations will allow UPSC groups to take full advantage of the new conifer genomic tools and to help to further improve the resource.
Peter Kindgren (SLU) is investigating the functional role of non-coding transcripts in plants. These transcripts originate from genome regions that do not contain protein information and were first thought to be insignificant noise but have been shown to play diverse biological roles. Peter Kindgren plans to apply a recently developed method to study these non-coding transcripts in tree species like aspen and spruce. He wants to find out how the non-coding DNA of these tree species is used to adapt them to their environment.
Ewa Mellerowicz’s project is focussing on certain lipophilic compounds of the aspen wood which often impact pulping negatively but are interesting for pharmaceutics, cosmetics and the paint industry. Ewa Mellerowicz and her group want to elucidate the nature of these compounds, their link to hemicellulose, one of the main components of wood, and see if they occur also in other tree species. They hope that their results can improve the pulping process. In a parallel approach, they plan to test if these lipids have antibacterial or anticancer properties and might serve as basis to develop new products from the wood.
Annika Nordin and her co-applicant, Jonas Öhlund from Skogforsk, are planning to study how the choice of planting spot on a forest clear-cut in combination with timing of planting and fertilization of the seedlings can improve the establishment and growth of newly planted trees. The researchers hope that their results will improve the efficiency of forest regeneration practices and contribute to more sustainable forestry. The funding from Kempe Foundations will cover the costs for the field work.
Stéphane Verger is doing research on plant cell-to-cell adhesion and plant biomechanics. The Kempe Foundations grant will, together with additional funding from SLU, allow to acquire an Atomic Force Microscope (AFM) to complement the existing high-end microscopy equipment available at UPSC. This technology provides a large array of possibilities to quantify the mechanical properties of plants. The spectrum reaches from measuring the pressure inside living cells, to measuring the stiffness of the plant cell walls in seedlings or in wood, to the nanoscale structure of components making up the plant, like cellulose. The AFM will be used by several research groups at UPSC and KBC.
Contact information of the project leaders:
Ove Nilsson
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/ove_nilsson
Peter Robert Kindgren
Section for Molecular Plant Biology
Department of Plant and Environmental Sciences
University of Copenhagen
e-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://plen.ku.dk/english/employees/?pure=en%2Fpersons%2Fpeter-robert-kindgren(525289c6-db78-4032-8942-ade2c82c3792).html
Ewa Mellerovicz
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/ewa_mellerowicz
Annika Nordin
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/annika_nordin
Stéphane Verger
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/stephane_verger
Ondřej Novák and Karin Ljung (Photo: Carolin Rebernig)
On 19th of November 2019, Clarivate Statistics published its annual list of Highly Cited Researchers. This list is based on a citation analysis of the Web of Science databases and identifies highly cited scientific publications. This year two UPSC researcher are on the list – Karin Ljung and Ondřej Novák. Both are listed as authors of highly cited papers that rank among the top one percent in the field of “Plant & Animal Science” during their year of publication.
Since 2002, the list of the world´s most highly cited scientific authors have been presented. Karin Ljung has been on the list for the sixth year in a row, for Ondřej Novák it’s the second time. In total the 2019 list comprises about 6000 Highly Cited Researchers from almost 60 Nations in 21 different categories.
The Clarivate Analytics list of Highly Cited Researchers 2019:
https://recognition.webofsciencegroup.com/awards/highly-cited/2019/
Detailed information about the analysis method Clarivate Analytics is applying can be found here:
https://recognition.webofsciencegroup.com/awards/highly-cited/2019/
From left to right: Christiane Funk (photo: Thomas Kieselbach), Henrik Hallingbäck (photo: Sven Tegelmo), Yanjun Zan (photo: Yan Ji)
[2019-11-22] On Wednesday this week, three projects affiliated with UPSC got granted by Formas, the Swedish Research Council for sustainable development. Christiane Funk, associated group leader at UPSC, and Henrik Hallingbäck, who recently started to work at the Forestry Research Institute of Sweden, Skogforsk, received a grant in the category Research and Development projects. Yanjun Zan who is working as postdoc with Harry Wu at UPSC got a mobility grant for early-career researchers.
Christiane Funk and her co-applicant Patrik Andersson, both from the Department of Chemistry at Umeå University, want to look for natural UV filters that are less harmful for the environment and human health than the current, commercially available UV filters. These filters are for example used in cosmetics to reflect or absorb UV radiation. The two researchers will analyse UV filter chemicals from microalgae and cyanobacteria from the arctic regions who are exposed to extreme sunlight under ice and protect themselves with these chemicals. Their goal is to identify the most sustainable chemicals that could substitute the currently used UV filters.
The two projects from Henrik Hallingbäck and Yanjun Zan will both focus on plant breeding strategies. Henrik Hallingbäck plans together with his two co-applicants from SLU, Harry Wu and Rodomiro Ortiz, to use a software that allows to simulate the effect of different breeding strategies on a virtual tree population. Based on these simulations, they hope to establish guidelines on how a tool called genomic selection can be best applied in conifer breeding programmes to speed up the breeding process. This tool allows to predict the breeding value of a candidate tree based on its genetic setup.
Yanjun Zan will use his mobility grant to work with Professor Harry Wu and Professor Jianbin Yan from Huazhong Agricultural University in China as international host. Based on the multi-omics data from 6000 maize individuals, he will study how local farming conditions interact with the genetic makeup of an individual that eventually affect agronomic traits. Using these results, he will develop statistical models that shall help plant breeders to stabilize plant performance by accounting for complex interactions between climate change and individual genetic makeup.
The project titles and contact information of the project leaders:
Project: Development of sustainable and bio-based UV filter chemicals
Christiane Funk
Department of Chemistry
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.umu.se/en/staff/christiane-funk/?expandaccordion=b
Project: Selection effects on the accuracy of genomic prediction in trees and other perennial plants
Henrik Hallingbäck
Skogforsk
Uppsala Science Park
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Project: Can plant breeding be improved by accounting for how genetic interactions are affected by environmental factors?
Yanjun Zan
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
More information about Formas’ annual open call:
https://www.formas.se/en/start-page/applying-for-funding/different-types-of-financing/formas-annual-open-call.html
Christiane Funk top left (photo: Thomas Kieselbach), Peter Marhavy top middle (photo: Petra Marhava), Totte Niittylä top right (photo: unknown), Markus Schmid bottom left (photo: Natuschka Lee), Nathaniel Street bottom right (photo: Mattias Pettersson)
Five projects that are affiliated with UPSC were granted by the Swedish Research Council last week. The project leaders Christiane Funk, Totte Niittylä, Markus Schmid and Nathaniel Street received a project grant and Peter Marhavy, who is planning to join UPSC in spring 2020, was awarded a starting grant to establish his research group at UPSC.
Christiane Funk, professor at the Department of Chemistry at Umeå University and associated group leader at UPSC, focuses in her research on protein degrading enzymes and on microalgae and their potential use for cleaning wastewater and biomass production. The current project aims to understand and characterize the mechanisms behind programmed cell death in single cell organisms like microalgae. The focus will be on the role of a certain group of protein degrading enzymes called metacaspases and how those have developed during evolution.
Peter Marhavy, who currently works as a postdoc in Niko Geldner’s group at the University of Lausanne, will use the funding from VR to study early defence responses in plants induced by wounding. With the help of a laser he plans to artificially induce wounding and then identify and characterize the genes and proteins that are involved in the following early defence responses. A special focus will be on the intracellular organization and the cell-wall integrity that are both affected by the wounding.
The project from Totte Niittylä who is associate professor at the Department of Forest Genetics and Plant Physiology at SLU and group leader at UPSC will concentrate on the model plant Arabidopsis thaliana. His group works on plant cell walls, and on identifying essential genes indispensable for the function of a plant cell. This project follows the groups recent discovery of an evolutionary conserved gene of unknown function that is essential for processes in the nuclear envelope and mitochondria in dividing plant cells. These processes are so far uncharacterized and the purpose of the new project is to investigate their mechanism and function.
Markus Schmid, professor at the Department of Plant Physiology at Umeå University and group leader at UPSC, wants to understand the mechanisms that control flowering time in plants. The current project will focus on a specific DNA-binding protein that regulates the activation of genes, the transcription factor FD. The aim is to find proteins that guide this transcription factor to the right DNA sequence and activate the target gene and to get a better insight in how this mechanism has evolved.
The aim of Nathaniel Street’s project is to explore how the giant genome of Norway spruce is organised and changes during development. The genomes of conifer species are almost entirely made up of regions that do not encode genes, with genes existing in a vast ocean of non-coding DNA. Nathanial Street, who is associate professor at the Department of Plant Physiology at Umeå University and group leader at UPSC, wants to understand the function of these non-coding DNA regions and how genes are physically organised by analysing the three-dimensional structure of the DNA and how these changes during development. This will be done with the help of advanced sequencing methods.
The projects and contact information of the project leaders:
- Project: Live and let die! - The involvement of metacaspase-homologues in programmed cell death of photosynthetic microorganisms
Christiane Funk
Department of Chemistry
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
https://www.umu.se/en/staff/christiane-funk/?expandaccordion=b
- Project: Electrical signal – The secret way of cell-to-cell communication
Peter Marharvy
Department of Plant Molecular Biology (DBMV)
University of Lausanne
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
- Project: The unknown unknowns of plant cell biology
Totte Niittylä
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/totte_niittyla
- Project: Binding of Arabidopsis FD to an Unusual cis-Regulatory Element – A new Role for the Master Floral Regulator LEAFY?
Markus Schmid
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/markus_schmid
- Project: Chromatin dynamics in the gigantic genome of Norway spruce
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www.upsc.se/nathaniel_street
SLU's Vice-Chancellor Maria Knutson Wedel inaugurates the new phenotyping platform at UPSC
[2019-10-30] Maria Knutson Wedel, since summer vice-chancellor at SLU, inaugurated yesterday the new tree phenotyping platform at UPSC in the course of her first official visit. This new platform allows to measure automatically and in a highly standardized way tree growth and development parameters and is a very valuable new research tool. It is not just a novelty among UPSC’s research facilities but also unique in Sweden.
The inauguration of the phenotyping platform was the highlight during the first official visit of the new SLU vice-chancellor Maria Knutson Wedel to UPSC. She got first a tour to the metabolomics facility and was then introduced by Ove Nilsson, director of UPSC, to the main research topics and the most important research plants at UPSC. After this, she officially inaugurated the new phenotyping platform.
The building of the phenotyping platform started in autumn 2017. The first test experiments begun in November 2018 and since October 2019, the first official experiment with 364 trees is running on the platform. Up to 728 trees can be monitored in total at the same time. The trees are moving on a conveyer belt and are automatically watered, fertilized, weighed and photographed once a day. This allows to characterize very precisely the tree growth of e.g. genetically modified trees in comparison with unmodified trees or of different natural variants.
The funding for the phenotyping platform came from the project “UPSC Forest Biology and Biotechnology”, that was granted in 2016 with SEK 48 million by the Knut and Alice Wallenberg Foundation and is led by UPSC’s director Ove Nilsson. This large-scale project aims to identify genes that are key players in the regulation of tree growth and wood development. It is based on data that has already been collected at UPSC over the last 20 years. The long-run goal is to increase wood production while ensuring high wood quality and lowering the need of resources to help forestry to be sustainable.
After a first characterization on the phenotyping platform, trees with interesting characteristics are going to be selected and undergo closer studies including also field trials. Currently the main tree genera characterized with the help of the platform are hybrid aspen and poplar but this might be expanded in the future to eucalyptus, spruce and pine. The services from the phenotyping platform are open to all researchers working at UPSC. A steering committee will review and prioritize suggested projects.
For questions regarding the phenotyping platform, please contact:
Ove Nilsson
Director of the Umeå Plant Science Center (UPSC) and
Professor at the Department of Forest Genetics and Plant Physiology at SLU
This email address is being protected from spambots. You need JavaScript enabled to view it.
Impressions from the visit of SLU's Vice Chancellor Maria Knutson Wedel:
Ove Nilsson (left) presents aspen as research plant 
At the tree phenotyping platform
Photos: Anne Honsel