Plant Defence Genetics

The displacement of nature by global plant production needs to be minimized to counteract the climate and biodiversity crises. It is essential to ensure high crop yields, for instance by efficient disease control. The research group aims to combat plant pathogens through insight in the exceedingly complex molecular mechanisms of plant-pathogen interactions.

Our primary focus is on the powdery mildew, stripe rust and speckled leaf blotch fungal pathogens of barley and wheat. However, we also use for instance bacteria and Arabidopsis as model instruments in our studies. We are interested in how defence is activated in plants after pathogen attack, how it is regulated and manifested. We study how pathogens suppress these plant defence mechanisms by employing effectors, and how induction of defence can be exploited for disease control.











Powdery mildew fungal effectors and effector targets

Fungal pathogens secrete hundreds of effector proteins to promote disease. Effectors are highly interesting, as they are unique to each pathogen clade and thus represent an immense source of novel proteins. Effectors can be seen as tools used by pathogens to manipulate host proteins that are important for the interaction with the pathogens. Therefore, effectors provide us access to identify these vital plant components.

In coordination with other research groups, we study how effectors influence plant immunity and membrane traffic. We evaluate the importance of selected effectors for disease using RNAi-mediated silencing and bacterial type-3 secretion-based protein introduction into host cells. We also over-express effectors to see how they influence sub-cellular localization of marker proteins important for immunity. Yeast 2-hybrid is used to identify host protein targets, the importance of which are evaluated using RNAi-mediated silencing as well as mutations. From this, we learn how pathogens attack and how plant immunity functions in concert with general plant cellular processes.

Membrane trafficking in plant immunity

Membrane trafficking is a prerequisite for eukaryotic life. It sustains cell growth and division, establishes and maintains intracellular compartmentalization, and promotes cell-to-cell communication. In short, general membrane trafficking consists of 1) a budding process, where vesicles containing cargo molecules from the donor compartment are made, 2) transport, where the vesicles are delivered to their right destination, and 3) membrane fusion, where vesicles fuse with the acceptor compartment.

Our interest in membrane trafficking comes from studying immunity in plants, where we have identified several components involved. Our main focus is to determine how plants use membrane trafficking to defend themselves against potentially infectious pathogens. Special interest is taken in multivesicular bodies (MVBs) and their fusion to the plasma membrane (PM), which is essential for the build-up of defence structures between the plant cell wall and the PM. Interestingly, MVB/PM fusion results in release of extracellular vesicles, which is a phenomenon of significant interest. Our findings include importance of the GTPase, ARFA1b/1c, and the ARF-GEF, GNOM, in pre-invasive immunity, as well as the Rab GTPase, ARA7, and the Rab GEF, VPS9a, in post-invasive immunity. Recently, we found the two syntaxins, PEN1 and SYP122, to be essential for membrane fusions mediating both pre- and post-invasive immunity. Furthermore, we study how barley powdery mildew effectors influence these pathways.

Plant susceptibility to the powdery mildew, incl. the extrahaustorial membrane

Pathogens exploit plant mechanisms to their own benefit. Such mechanisms can include nutrient transfer to the pathogens and establishment of a membrane niche for the pathogen.

However, unlike immunity, susceptibility is poorly understood despite its potential basis for alternative forms of disease resistance. We are interested in the fact that some pathogens develop haustorial structures inside the plant cells. Here the pathogens stimulate the plant cell to generate extrahaustorial membranes (EHMs) as an essential susceptibility component. We previously demonstrated that the barley powdery mildew EHM shares features with the endoplasmic reticulum (ER) membrane, suggesting that this plant compartment is involved in the EHM formation. More recently, we showed that the EHM allows translocation of proteins from the plant cytosol, in particular when these have neutral pI. We currently aim to uncover more details of how the EHM is generated by the plant cell. In parallel, a mutant approach is taken to uncover powdery mildew susceptibility components in Arabidopsis.

Biopesticides for control of plant diseases

Biopesticides cover a long range of agents of biological origin used e.g. for control of plant diseases. When living microorganisms are used for disease control, the protection is termed “biological control”. Societal interest in biopesticides is increasing, as this may significantly reduce the use of chemical fungicides and increase sustainable plant production.

The mode of action of biological control biopesticides can for instance be antibiosis, competition and parasitism. Yet, another important mode of action is “induced resistance”, where the immunity in the plant is either induced directly or alerted in what is referred to as “defence priming”. Our studies of biopesticides/inducers of resistance include screening for agents effective under controlled conditions as well as in greenhouse and field tests. To optimise the use of these biopesticides, we aim to uncover their mode of action. Screens for agents functioning according to novel principles are ongoing.

A main focus is on control of Septoria tritici blotch in wheat, but studies also include a range of biotrophic, hemibiotrophic and necrotrophic pathogens causing problems in both monocots and dicots under temperate, tropical and greenhouse conditions. Many types of control agents have been tested, ranging from microorganisms like fungi and bacteria (including endophytes), plant extracts (botanicals) as well as chemicals.

Genetic resources for research and pre-breeding

The department host the Danish apple collection at the Pometum, which we use for genome wide association studies aimed at identifying genetic components influencing aroma and other fruit and tree traits. This project is performed in collaboration with researchers from Section for Crop Science, Section for Organismal Biology and Department of Food Science, all at KU, partners at SLU (Sweden), LUKE (Finland) and Graminor (Norway) as well as Dalhousie University (Canada).

In the apple-project we are mainly interested in identifying genes influencing aroma-characters and other fruit traits and in applying germplasm for pre-breeding for future challenges under Nordic conditions. 

The department also has a collection of wild crocus species, which may be utilized as a genetic resource for improving saffron crocus. Saffron is the most expensive food spice. It is highly appreciated and obtained from the stigmas of Crocus sativus, an ancient species only known from cultivation and with very little genetic variation. Crocus sativus originates from the wild species, C. cartwrightiana. It arose from an unreduced gamete and it is therefore triploid and sterile. In collaboration with researchers from Iran, we aim at recreating new types of C. sativus by chromosome doubling of accessions of C. cartwrightiana followed by crosses of 2x and 4x types. This work is based on our collection of wild accessions from Greece and it will be completed in collaboration with Marian Ørgaard and Niels Jacobsen, Section for Organismal Biology and researchers from University of Tehran. 

Genetics of biological nitrification inhibition (BNI) in wheat

Nitrous oxide (N2O) is a serious greenhouse gas, 300x more potent than CO2. Nitrous oxide is emitted for agricultural soils when nitrogen fertilizers are converted by microbial processes in the soil. This occurs when ammonium (NH4+) is nitrified to nitrite (NO2-) and nitrate (NO3-), and when these products in turn are denitrified to the gasses, free nitrogen (N2), nitric oxide (NO) and nitrous oxide. While the three gasses are lost to the atmosphere, nitrate binds poorly to soil particles and may leach to the surrounding environment.

Some species and genotypes of plants can exude compound from their roots to inhibit the first nitrification step in this microbial turn-over of soil nitrogen. This biological nitrification inhibition (BNI) capacity improves the plant uptake of nitrogen and minimize nitrous oxide release.

This is also the case for wheat, and we are interested in the genetic background for wheat’s BNI capacity. For this we use crosses of high BNI wheat and genome-wide association studies (GWAS).





















Powdery mildew fungal effectors and effector targets
Membrane trafficking in plant immunity
Biopesticides for control of plant diseases
  • Aarhus University
  • Danish Technological Institute
  • SEGES Innovation
  • University of Mysore, India
  • Can Tho University, Vietnam
  • Makerere University, Uganda
  • Private companies (Knud jepsen a/s; Chr. Hansen A/S; Bioomix APS; Novozymes; FMC)

Genetics of biological nitrification inhibition (BNI) in wheat


  • Ahmed AA, Pedersen C, Schultz-Larsen T, Kwaaitaal M, Jørgensen HJL, Thordal-Christensen H (2015) Barley powdery mildew effector candidate CSEP0105 inhibits chaperone activity of a small heat shock protein. Plant Physiology 168, 321-322.
  • Aguilar GB, Pedersen C, Thordal-Christensen H (2016) Identification of eight effector candidate genes involved in early aggressiveness of the barley powdery mildew fungus. Plant Pathology 10.1111/ppa.12476
  • Ahmed AA, Pedersen C, Thordal-Christensen H (2016) The barley powdery mildew effector candidates CSEP0081 and CSEP0254 promote fungal infection success. PLOS ONE 10.1371/journal.pone.0157586
  • Thordal-Christensen H, Birch PRJ, Spanu PD, Panstruga R (2018) Why did filamentous plant pathogens evolve the potential to secrete hundreds of effectors to enable disease? Molecular Plant Pathology 19, 781-785.
  • Thordal-Christensen H (2020) A holistic view on plant effector-triggered immunity presented as an iceberg model. Cellular and Molecular Life Sciences 77, 3963-3976.
  • Liao W, Nielsen MW, Pedersen C, Xie WJ, Thordal-Christensen H (2022) Barley powdery mildew effector CSEP0162 targets endosomal MON1 important for immunity. J. Exp. Bot. erac403.

Nielsen ME, Jürgens G, Thordal-Christensen H (2017) VPS9a activates the Rab5 GTPase ARA7 to confer distinct pre- and postinvasive plant innate immunity. Plant Cell 29, 1927–1937.

  • Hansen LL, Nielsen ME (2017) Plant exosomes: using an unconventional exit to prevent pathogen entry? Exp. Bot. 69, 59-68.
  • Schultz-Larsen T, Lenk A, Kalinowska K, Vestergaard LK, Pedersen C, Isono E, Thordal-Christensen H (2018) The AMSH3 ESCRT-III-associated deubiquitinase is essential for plant immunity. Cell Reports 25, 2329–2338.
  • Rubiato HM, Liu MQ, O'Connell RJ, Nielsen ME (2022) Plant SYP12 syntaxins mediate an evolutionarily conserved general immunity to filamentous pathogens. Elife 11, e73487.
  • Kwaaitaal M, Nielsen ME, Böhlenius H, Thordal-Christensen H (2017) The plant membrane surrounding powdery mildew haustoria shares properties with the endoplasmic reticulum membrane. Exp. Bot. 68, 5731–5743.
  • Smigielski L, Aguilar GB, Kwaaitaal M, Zhang W-J, Thordal-Christensen (2019) The isoelectric point of proteins influences their translocation to the extrahaustorial matrix of the barley powdery mildew fungus. Microbiol. 21, e13091
  • Shetty R, Jensen B, Shelton D, Jørgensen K, Pedas P, Jørgensen HJL (2021). Site-specific, silicon-induced structural and molecular defence responses against powdery mildew infection in roses. Pest Management Science. 77: 4545-4554.
  • Collinge DB, Jensen B, Jørgensen HJL (2022). Fungal endophytes in plants and their relationship to plant disease. Current Opinion in Microbiology 69: Article 102177.
  • Høyer AK, Jørgensen HJL, Hodkinson TR, Jensen B (2022). Fungal endophytes isolated from Elymus repens, a wild relative of barley, have potential for biological control of Fusarium culmorum and Pyrenophora teres in barley. Pathogens. 11: Article 1097.
  • Kumakech A, Jørgensen HJL, Collinge DB, Edema R, Okori P (2022). Plant extracts as potential control agents of Black Sigatoka in banana. Journal of Plant Pathology.
  • Madriz-Ordeñana K, Pazarlar S, Jørgensen HJL, Nielsen TK, Zhang Y, Nielsen KL, Hansen LH, Thordal-Christensen H (2022) The Bacillus cereus strain EC9 primes the plant immune system for superior biocontrol of Fusarium oxysporum. Plants 11: 687.
  • Musaqaf N, Jørgensen HJL, Sigsgaard L (2022). Plant resistance induced by hemipterans - effects on insect herbivores and pathogens. Crop Protection. Article 106122.
  • Rojas EC, Jensen B, Jørgensen HJL, Latz MAC, Esteban P, Collinge DB (2022). The fungal endophyte Penicillium olsonii ML37 reduces Fusarium head blight by local induced resistance in wheat spikes. Journal of Fungi. 8: 345.
  • Pazarlar S, Madriz-Ordeñana K, Thordal-Christensen H (2022). Bacillus cereus EC9 protects tomato against Fusarium wilt through JA/ET-activated immunity. Frontiers in Plant Science https://doi: 10.3389/fpls.2022.1090947


  • Larsen B, Zigicovsky Z, Jeppesen A A, Gardner K M, Toldam-Andersen TB, Myles S, Ørgaard M, Petersen MA, Pedersen C (2019) Genome-wide association studies in apple reveal loci for aroma volatiles, sugar composition and harvest date. Plant Genome 12,3835
  • Larsen, B, Gardner K, Pedersen C, Ørgaard M, Migicovsky Z, Myles S, Toldam-Andersen TB (2018) Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing. PLoS ONE 13, e0201889
  • Larsen B, Toldam-Andersen TB, Pedersen C, Ørgaard M (2017) Unravelling genetic diversity and cultivar parentage in the Danish apple gene bank collection. Tree Genetics and Genomes 13, 14
  • Larsen B, Ørgaard M, Toldam-Andersen TB, Pedersen C (2016) A high-throughput method for genotyping S-alleles in apple. Molecular Breeding 36,
  • Larsen B, Orabi J, Pedersen C, Ørgaard M (2015) Large intraspecific genetic variation within the Saffron-Crocus group (Crocus L., Series Crocus; Iridaceae). Plant Syst Evol 301, 425-437.






Group members

Name Title Phone E-mail
Carsten Pedersen Associate Professor +4535333450 E-mail
Erhan Ar PhD Fellow +4535325822 E-mail
Hans Jørgen Lyngs Jørgensen Associate Professor +4535333775 E-mail
Hans Thordal-Christensen Professor +4535333443 E-mail
Jelco Mensch PhD Fellow +4535321746 E-mail
João Paulo Alves Plácido PhD Fellow +4535331420 E-mail
Kenneth Madriz Ordenana Special Consultant +4535325070 E-mail
Mads Eggert Nielsen Special Consultant +4535320270 E-mail
Mette Sylvan Laboratory Coordinator +4535333146 E-mail
Ole Reppien Christensen PhD Fellow +4535332035 E-mail
Shakhina Khanam Industrial PhD   E-mail
Sixuan Zhao PhD Student   E-mail
Sohini Deb Postdoc +4535324794 E-mail
Sudip Paul PhD Fellow +4535329346 E-mail
Sílvia A Godinho Barquinha Tavares Guest Researcher   E-mail
Wenjun Xie Guest Researcher +4535333858 E-mail
Xuan Li Postdoc +4535333810 E-mail

Research group leader

Hans Thordal-Christensen
+45 35 33 34 43