Guus Bakkeren, Ph.D.

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 the wheat leaf rust fungus (Puccinia triticina) and the covered smut fungus of barley and oats (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.



Scientists at AAFC-Cereal Research Centre, Morden, MB, and AAFC research centres in Lethbridge, AB, and Ottawa, ON;

Faculty at the Michael Smith Laboratories (Dr. X. Li), and Dept. of Botany (Dr. Y. Zhang), and Dr. G. Brar, Faculty of Land and Food Systems, at UBC, Vancouver, BC, Canada; Dr. R. Kutcher, University of Saskatchewan, SK, Canada.


Vancouver-based company Terramera in a joint project funded by the Digital Technology Supercluster Project “Precision Agriculture to Improve Crop Health” , which includes Dr. B. Saville, Trent University, ON, and Drs. C. Pozniak and A. Sharpe, U. od Saskatchewan, SK, Canada.


Internationally: Dr. J. Fellers, USDA-ARS, Manhattan, KS, USA; Dr. L. Szabo, USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, USA; Dr. C. Cuomo, Broad Institute, MIT, Cambridge, MA, USA; Dr. D Saunders, John Innes Centre, Norwich, UK.


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. Dinushika Thambugala, Colin Hiebert, Brent McCallum, Mallorie Lewarne, Andriy Bilichak, Curtis Pozniak, Guus Bakkeren, Harmeet Singh Chawla, Curt McCartney (2023) Fine mapping of the wheat leaf rust resistance gene Lr2a. International Plant and Animal Genome Conference, January 13-18, 2023, San Diego

    2023 - View publication details

  2. Bykova NV, Rampitsch C, McCallum B, Bakkeren G, Wang X, Huang M, Fernando U, Radovanovic N, Rampitsch M, Linning R (2021) Profiling the total and nuclear proteomes of host-pathogen interactions of the wheat Thatcher near-isogenic line for Lr2a resistance gene with virulent and avirulent races of Puccinia triticina. 4th International Plant Proteomics Organization (INPPO) Conference. Virtual Conference hosted from Winnipeg, Canada, March 9-11, 2021. Poster

    2021 - View publication details

  3. Ökmen, B., Schwammbach, D., Bakkeren, G., Neumann, U., Doehlemann, G. (2021). The ustilago hordei-barley interaction is a versatile system for characterization of fungal effectors. Journal of Fungi, [online] 7(2), 1-17.

    2021 - View publication details

  4. Montenegro Alonso, A.P., Ali, S., Song, X., Linning, R., Bakkeren, G. (2020). UhAVR1, an HR-Triggering Avirulence Effector of Ustilago hordei, Is Secreted via the ER�Golgi Pathway, Localizes to the Cytosol of Barley Cells during in Planta-Expression, and Contributes to Virulence Early in Infection. Journal of Fungi, [online] 6(3), 1-32.

    2020 - View publication details

  5. Parcey, M., Gayder, S., Morley-Senkler, V., Bakkeren, G., Úrbez-Torres, J.R., Ali, S., Castle, A.J., Svircev, A.M. (2020). Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance. Genomics, [online] 112(5), 3762-3772.

    2020 - View publication details

  6. Wang, X., Che, M.Z., Khalil, H.B., McCallum, B.D., Bakkeren, G., Rampitsch, C., Saville, B.J. (2020). The role of reactive oxygen species in the virulence of wheat leaf rust fungus Puccinia triticina. Environmental Microbiology, [online] 22(7), 2956-2967.

    2020 - View publication details

  7. 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

  8. 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. Plant Biotechnology Journal, [online] 16(5), 1013-1023.

    2018 - View publication details

  9. 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. Proceedings of the National Academy of Sciences of the United States of America, [online] 115(12), 3108-3113.

    2018 - View publication details

  10. Coelho, M.A., Bakkeren, G., Sun, S., Hood, M.E., Giraud, T. (2017). Fungal sex: The basidiomycota. Microbiology Spectrum, [online] 5(3),

    2017 - View publication details

  11. 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

  12. 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. G3: Genes, Genomes, Genetics, [online] 7(2), 361-376.

    2017 - View publication details

  13. 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

  14. 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

  15. 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. Canadian Journal of Plant Pathology, [online] 38(1), 91-102.

    2016 - View publication details

  16. 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. Canadian Journal of Plant Pathology, [online] 38(1), 1-18.

    2016 - View publication details

  17. Khalil, H.B., Wang, X., Linning, R., Joly, D.L., Cram, D., Thiessen, N., Taylor, G.P., McCallum, B.D., Saville, B.J., and Bakkeren, G. (2015). "Comparative analysis of transcriptome profiles during infection of near-isogenic susceptible or resistant wheat lines by various Puccinia triticina races; time courses reveal race-specific pathogenicity factors and corresponding host reactions.", Botany 2015, Shaw Convention Center, Edmonton, Alberta, Canada, July 25-29, 2015. (Abstract)

    2015 - View publication details

  18. Panwar, V., McCallum, B.D., and Bakkeren, G. (2015). "A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by Agroinfiltration.", in Mysore, K.S. and Senthil-Kumar, M. (eds.) - Methods in Molecular Biology Series, Springer New York, Chapter 13, pp. 179-189.

    2015 - View publication details

  19. Montenegro-Alonso, A.P., Ali, S., Linning, R., Grewal, T.S., and Bakkeren, G. (2015). "Functional characterization of barley smut fungus, Ustilago hordei, avirulence effector UhAvr1.", Botany 2015, Shaw Convention Center, Edmonton, Alberta, Canada, July 25-29, 2015. (Abstract)

    2015 - View publication details

  20. Bakkeren, G., Linning, R., Joly, D.L., Khalil, H.B., Wang, X., Panwar, V., Mullock, B., Goldberg, J., Young, S., Fellers, J.P., Szabo, L.J., Hulbert, S., Chen, X., Hamelin, R.C., McCallum, B.D., Cuomo, C.A., and Saville, B.J. (2015). "Comparative genomics of rust fungi to probe wheat interactions; the road to crop protection.", Botany 2015, Shaw Convention Center, Edmonton, Alberta, Canada, July 25-29, 2015, Invited oral presentation. (Abstract)

    2015 - View publication details

Research facility

4200 Highway #97
Summerland, BC V0H 1Z0


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