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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:
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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:
www.upsc.se/ove_nilsson
Peter Robert Kindgren
Section for Molecular Plant Biology
Department of Plant and Environmental Sciences
University of Copenhagen
e-mail:
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:
www.upsc.se/ewa_mellerowicz
Annika Nordin
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email:
www.upsc.se/annika_nordin
Stéphane Verger
Umeå Plant Science Centre
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Science
Email:
www.upsc.se/stephane_verger
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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/
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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:
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:
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:
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
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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:
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:
- 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:
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:
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:
www.upsc.se/nathaniel_street
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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
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
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Stéphanie Robert at the Umeå Plant Science Centre (photo: Anne Honsel)
Every other year, the Sven and Ebba-Christina Hagberg foundation awards two young recognized scientists from the medical or biochemical field. This year, the prize goes to Stéphanie Robert, group leader at UPSC, and Ville Kaila from Stockholm University. They are both awarded with a personal prize and a research grant.
Stéphanie Robert, Associate Professor at the Swedish University of Agricultural Sciences, receives the prize for her studies of the regulation of plant cell growth and plant morphogenesis. Professor Ville Kaila is awarded for his theoretical studies in the bioenergetics field, especially on proton and electron transport in the respiratory chain enzymes.
Stéphanie Robert started her group at the Umeå Plant Science Centre in 2010. She combines in her research chemical biology and cell biology to dissect on the cellular level different signalling pathways involved in plant growth. “I am really honoured to receive this prize, it feels really special. This is mainly a recognition of the hard work from present and past members of my research group.”, says Stéphanie Robert.
The Sven and Ebba-Christina Hagberg foundation aims to encourage and promote scientific research within the medical and biochemical field. Every time, the prize is awarded to one female and one male young, outstanding researcher located in Sweden. In questions regarding nominations, the foundation collaborates with the Royal Swedish Academy of Sciences and Karolinska Institutet.
Sven Hagberg (1894-1961) was a civil engineer and grain chemist. He developed a new method for measuring baking properties of flour. The method, "Hagberg Falling Number", is used worldwide today. Ebba-Christina Hagberg (1900-1972) was involved in association work and shared her husband's interest in foreign cultures. The spouses had no children but bequeathed their inheritance to the foundation, which annually awards a prize to two promising researchers.
For further information regarding the Sven and Ebba-Christina Hagberg Prize, please contact:
Dr. Gunnar Hagberg, chairman of the foundation (
Prof. Gunnar von Heijne, Board Member (
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When a herbivore attacks a host plant, a defence response is initiated, triggered either by the herbivore or by the plant itself. Knowledge about the mechanism behind such responses are used to develop pest management strategies that align with UN-sustainability goals for crop protection. In a new article published in the journal Plant Physiology, a UPSC-team led by Karen Kloth and Benedicte Albrectsen questioned the role of a cell wall modifying enzyme for defence responses to aphid attacks.
In their experiments, the researchers investigated the feeding behaviour of an insect, the so-called green peach aphid, on plant cell walls of thale cress (Arabidopsis thaliana). The aphid manoeuvres its needle-like mouth through the cell wall matrix to reach the phloem, a transport tissue in plants transporting sugars from the leaves to the roots. It feeds on the sugar-rich phloem sap. This penetration through the cell wall damages the cell wall to a certain extent. The researchers wanted to test the hypothesis that plant defence responses are the result of certain cell wall components that break of cell wall carbohydrate pectin, in response to the aphid penetration.
Their study focused on the effect of a special pectin modifying enzyme, called Pectin Acetylesterase 9 (PAE9), which has not been studied in this context up to now. They investigated mutants of the model plant thale cress, which have been modified to shut off PAE9. Their experiments showed that PAE9 is important for general defence reactions. The mutants that did not contain the PAE9 enzyme initially produced less defence hormones and metabolites. These defence compounds seem to make the plant more resistant to aphids. In the mutants, the aphids started phloem feeding earlier than in control plants with normal levels of defence compounds. However, with time, levels of defence compounds recovered to control levels also in the mutants. The researchers concluded therefore that PAE9 act as a front door guard that delays and initially fends off intruding aphid pests.
The article was published in Plant Physiology:
Karen J. Kloth, Ilka N Abreu, Nicolas Delhomme, Ivan Petřík, Cloé Villard, Cecilia Ström, Fariba Amini, Ondřej Novák, Thomas Moritz, Benedicte Riber Albrectsen (2019). PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding. Plant Physiology, Oct 2019: doi.org/10.1104/pp.19.00635
http://www.plantphysiol.org/content/early/2019/09/24/pp.19.00635
For more information please contact:
Benedicte Albrectsen,
Karen J. Kloth,
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Group picture of the PhD students and postdocs from UPSC in front of the greenhouses at ViPS; photo: Sonali Ranade
Last week, 34 PhD students and Postdocs from UPSC visited the Viikki Plant Science Centre (ViPS) in Helsinki. Within two days, they got an insight into the research that is performed at ViPS, presented their own research and visited the facilities. This was the second joint meeting between UPSC and ViPS.
Arriving on Wednesday afternoon, the programme started with a joint dinner at the Brewery of Suomenlinna in Helsinki. The next day focussed on research. After an introduction to the centre by its director Paula Elomaa, the group from UPSC got an insight into different research projects at ViPS and every one of them presented their own research in a two-minute-long flash talk.
The afternoon on Wednesday started with the ViPS Science Fair. PhD students and postdocs from ViPS research groups presented their projects in form of posters to master students. By joining the Science Fair, the visitors from UPSC got an overview about the broad range of research projects done at ViPS. The day finished with a UPSC/ViPS get-together and one-on-one meetings with ViSP group leaders. Several PhD students and postdocs used this opportunity and appreciated those personal meeting.
On Friday morning, the PhD students and postdocs from UPSC could visit different research facilities. They were interested to see how things are organised at ViSP and got tours to the greenhouse, the phenotyping facilities, the metabolomics unit, the sequencing service and some other labs. The group flew back to Umeå in the afternoon.
Two years ago, the PhD students from the Doctoral Programme in Plant Sciences that is associated with ViPS visited UPSC. The visit to Helsinki this year was a follow-up meeting that shall help to strengthen the collaboration between the two plant research centres.
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In case of threats plants cannot run away but they do have a defence comparable to the humane immune system. This plant immune system helps them to fight off for example microorganism attacks. By so-called defence priming the plant immune system can be trained to memorize threats and act more effective against them in future. Solid knowledge about this mechanism is still scattered. A group of UPSC researchers lead by Benedicte Albrectsen tried the first systematic approach and published a meta-analysis on defence priming in plants focusing on thale cress.
How the plant immune system memory works is not yet fully understood but it is known that different molecular mechanisms act. The whole process is triggered by external stimuli, so-called priming agents. Priming agents can be living organisms, like microorganism and arthropods or chemical compounds, like vitamins and plant hormones. These triggers can induce the priming process in all kind of plant tissues and developmental stages. During the so-called priming phase, the plant gets stimulated by a priming agent in absence of actual threats. It accumulates compounds that later play a role in the defence. The primed status is durable, does not decrease the plants fitness and can be even passed on to the next generation.
Defence priming is a known phenomenon but for applying it widely in agriculture further knowledge is needed. In the current study the researchers analysed more than 240 studies on thale cress (Arabidopsis thaliana). The group tried to find patterns in plant responses to stress and identify possible relationships between priming agents and antagonists, like pathogens or herbivores. With their analysis they clearly show that defence priming enables the plant to withstand subsequent danger better than un-primed conspecifics. It helps the plant to defend itself faster and more effective the next time the same stress occurs.
The elaborate data comparison also allowed the researchers to identify potential players in the priming challenge. “We present a list of potential priming agents that we suggest could improve plant resistance properties in the future”, explains Benedicte Albrectsen. “The list includes microorganisms and organic chemical compounds with varied effect”. They showed that several compounds, like fungi and vitamins act as strong priming agents in thale cress whereas the influence of herbivores on the priming effect seems rather week.
This publication supports the theory that defence priming has an effect. It emphasizes that on the long run it can be used to enhance thread-resilience also in crops. The current agricultural systems are facing severe challenges including increasing demands, higher costs, and a changing climate. Defence priming has the potential for raising crop productivity with little environmental risk and this could help to move towards a more sustainable agriculture.
The work was recently published in Scientific Reports:
Westman SM, Kloth KJ, Hanson J, Ohlsson AB & Albrectsen BR (2019). Defence priming in Arabidopsis – a Meta-Analysis. 9:133309 (doi.org/10.1038/s41598-019-49811-9)
For more information please contact:
Benedicte Albrectsen (