Guus Bakkeren, PhD.

Image Guus Bakkeren
Research Scientist

My group conducts molecular genetic and cell biological research to understand plant-microbial interactions including attributes that make microbes pathogenic such as pathogenicity and virulence factors including fungal mating systems. We study plant responses to infection such as accommodation of biotrophic fungi and their recognition leading to defense and resistance responses. This includes the action of effectors that may jam host defence signalling networks, but also effectors that elicit defense and resistance responses (avirulence effectors). We use whole genome analyses and comparative approaches to exploit cereal pathogens, in particular wheat leaf rust (Puccinia triticina) and covered smut of barley (Ustilago hordei) to identify novel resistance genes and design alternate ways for crop protection.  

Current research and/or projects

I am studying two biotrophic fungal pathogens of cereals: the wheat leaf or brown rust fungus, Puccinia triticina and the barley-infecting smut fungus, Ustilago hordei, representing a model system for the small grain-infecting smut fungi of the genus Ustilago. Projects feature generation of genomic resources such as whole genome sequences and their assembly and annotation, transcriptomes, and comparative analyses among many natural isolates. We exploit these resources for functional genomics, proteomics and the study of avirulence and virulence effectors employing molecular genetic and molecular biological methods. This leads to insight into the disease strategies of the pathogens, and the identification of resistance and susceptibility genes which can be exploited to develop strategies for crop protection.

Pioneering work is performed on two apple pathogens: the bacterium Erwinia amylovora, causing fire blight, and the ascomycete fungus Venturia inaequalis, causing scab. Topics include the generation of whole genome sequencing to reveal Canadian population structures and identify virulence factors and the molecular basis of pesticide resistance, and we develop virulence assays as a tool to assist resistance breeding.

Research and/or project statements

Long term objectives: to understand the mechanisms by which pathogenic fungi cause diseases on Canadian cereal crops, and vice versa, by which host plants mount defenses, in order to design novel methods to introduce more durable disease resistance into Canadian crops.

Impact: Our efforts will contribute to the development of germplasm harboring broad-spectrum disease resistance and to more environmentally friendly production of crops. Consumers will benefit directly from the availability of cheaper and healthier products which contain reduced or no pesticide residues, and indirectly from a less polluted environment. Producers will benefit from decreasing dependence on toxic pesticides and more economical and environmentally-sustainable production methods.

Organization: The Agriculture & Agri-Food Canada Science & Technology Branch conducts research in 20 federal AAFC centres across Canada.. My group is located at the SuRDC (Summerland Research & Development Centre; Bakkeren lab at Summerland, BC).

Research program: Contributes to National Programs on the improvement of disease resistance and pathogen management in cereals and in apple, involving collaborations with several centres, universities and internationally.



• Research project on "Genomics Approaches to Mitigate Fungal Threats to Crops" with B. Saville, Trent University, ON, a project on large-scale transcriptome analyses of cereal rust and other fungi during host infections 
• Sequencing of many P. triticina genomes and comparative analyses (C. Cuomo, Broad Institute, Cambridge, MA), J. Fellers (USDA, Manhattan, KS) and L. Szabo, J. Kolmer (USDA, St. Paul, MN); Michael Smith Genome Sciences Centre in Vancouver, BC


Education and awards


Ph.D.  Microbiology                             1989     University of Basel, Switzerland

M.Sc.  Molecular Sciences*                  1984     Wageningen Agricultural University, The Netherlands

B.Sc.  Molecular Sciences*                   1981     Wageningen Agricultural University,



Research Scientist           5.98 - present                    Agriculture & Agri-Food Canada, Summerland Research & Development Centre, BC

Adjunct Professor (honorary)      11/99 - present          Department of Botany, University of British Columbia,, Vancouver, BC, Canada

Research Associate                    4/93 - 12/97           Michael Smith Laboratories, University of British Columbia, Vancouver, B.C., Canada 

Postdoctoral Scientist              10/90 - 3/93            Michael Smith Laboratories, University of British Columbia, Vancouver, B.C., Canada

Postdoctoral Scientist             1/90 - 8/90             Friedrich Miescher Institut, Basel, Switzerland


Key publications

  1. Huang M, Fernando U, Djuric-Ciganovic S, Wang X, Bakkeren G, Linning R, Bykova NV, Rampitsch C (2018) Quantitative proteomic approaches to characterize the dynamic and comprehensive defence responses of wheat to leaf rust. 66th ASMS Conference on Mass Spectrometry and Allied Topics, San Diego, CA, USA, June 3-7, 2018. Poster

    2018 - View publication details

  2. Panwar, V., Jordan, M., McCallum, B., Bakkeren, G. (2018). Host-induced silencing of essential genes in Puccinia triticina through transgenic expression of RNAi sequences reduces severity of leaf rust infection in wheat, 16(5), 1013-1023.

    2018 - View publication details

  3. Yadav, V., Sun, S., Billmyre, R.B., Thimmappa, B.C., Shea, T., Lintner, R., Bakkeren, G., Cuomo, C.A., Heitman, J., Sanyal, K. (2018). RNAi is a critical determinant of centromere evolution in closely related fungi, 115(12), 3108-3113.

    2018 - View publication details

  4. Coelho, M.A., Bakkeren, G., Sun, S., Hood, M.E., Giraud, T. (2017). Fungal sex: The basidiomycota, 5(3),

    2017 - View publication details

  5. Panwar, V. and Bakkeren, G. (2017). Investigating Gene Function in Cereal Rust Fungi by Plant-Mediated Virus-Induced Gene Silencing. Wheat Rust Diseases: Methods and Protocols. S. Periyannan. New York, NY, Springer New York: 115-124. DOI:10.1007/978-1-4939-7249-4_10

    2017 - View publication details

  6. Cuomo, C.A., Bakkeren, G., Khalil, H.B., Panwar, V., Joly, D., Linning, R., Sakthikumar, S., Song, X., Adiconis, X., Fan, L., Goldberg, J.M., Levin, J.Z., Young, S., Zeng, Q., Anikster, Y., Bruce, M., Wang, M., Yin, C., McCallum, B., Szabo, L.J., Hulbert, S., Chen, X., Fellers, J.P. (2017). Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci, 7(2), 361-376.

    2017 - View publication details

  7. Panwar, V., B. McCallum, M. Jordan, M. Loewen, P. Fobert, C. McCartney and G. Bakkeren (2016). RNA silencing approaches for identifying pathogenicity and virulence elements towards engineering crop resistance to plant pathogenic fungi. CABI Reviews. Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. Wallingford, UK, CABI. DOI:10.1079/PAVSNNR201611027

    2016 - View publication details

  8. Bakkeren, G., Joly, D.L., and Duplessis, S. (2016). "Editorial: Genomics research on non-model plant pathogens: delivering novel insights into rust fungus biology.", Frontiers in Plant Science. doi : 10.3389/fpls.2016.00216

    2016 - View publication details

  9. McCallum, B.D., Hiebert, C.W., Cloutier, S., Bakkeren, G., Rosa, S.B., Humphreys, D.G., Marais, G.F., McCartney, C.A., Panwar, V., Rampitsch, C., Saville, B.J., Wang, X. (2016). A review of wheat leaf rust research and the development of resistant cultivars in Canada, 38(1), 1-18.

    2016 - View publication details

  10. Segovia, V., Bruce, M., Shoup Rupp, J.L., Huang, L., Bakkeren, G., Trick, H.N., Fellers, J.P. (2016). Two small secreted proteins from Puccinia triticina induce reduction of ß-glucoronidase transient expression in wheat isolines containing Lr9, Lr24 and Lr26, 38(1), 91-102.

    2016 - View publication details

Research facility

4200 Highway #97
Summerland, BC V0H 1Z0


Adjunct Professor at the Department of Botany, University of British Columbia, Vancouver.