Adjunct & Associate #75

Molecular Plant-Microbe Interactions. Emphasis on cereal-infecting fungal pathogen systems: Structural & Functional Genomic and Proteomic analyses to discover the molecular basis of the wheat leaf rust fungus, Puccinia triticina, and the barley smut, Ustilago hordei, pathogenic and virulence capabilities.

Contact Information

Office Phone
Academic History

B.Sc., M.Sc, Wageningen Agricultural U., Netherlands (1984);
Ph.D., U. of Basel, Switzerland (1989); 
PDF, Friedrich Miescher Institut, Basel, Switzerland (1990); 
Research Associate, Biotechnology Laboratory, UBC (1990-1997); 
Research Scientist, Agriculture & Agri-Food Canada, PARC, Summerland, BC (1998-present).

Research Interests

Molecular genetic and cell biological understanding of plant-microbial interactions including attributes that make microbes pathogenic such as pathogenicity and virulence factors including fungal mating systems. Plant responses to infection such as recognition and accommodation of biotrophic fungi. Action of effectors that may jam host defence signalling networks, but also effectors that elicit defense and resistance responses (avirulence effectors).

Topics: 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.

Bakkeren Pic 1

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

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                                Summerland Research & Development Centre (Okanagan Valley)

Selected Publications

(for complete list with abstracts & PDFs, click here):

Yadav, V., Sun, S., Billmyre, B., Thimmappa, B.C., Bakkeren, G., Cuomo, C., Heitman, J. and Sanyal, K. 2018. RNAi-dependent centromere evolution in closely related fungal species. Proc. Natl. Acad. Sci. USA. 115(12), 3108-3113. DOI: 10.1073/pnas.1713725115


Panwar, V., Jordan, M., McCallum, B. and Bakkeren, G. 2017. Host-induced silencing of essential genes in Puccinia triticina through transgenic expression of RNAi sequences reduces severity of leaf rust infection in wheat. Plant Biotechnol. J. 16(5), 1013-1023. DOI:10.1111/pbi.12845


Cuomo, C, 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. and Fellers, J.P. 2017. Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci. G3: Genes|Genomes|Genetics. 7(2): 361-376. DOI:10.1534/g3.116.032797


Panwar, V. and Bakkeren, G. 2017..Investigating gene function in cereal rust fungi by plant-mediated virus-induced gene silencing. In: Wheat Rust Diseases: Methods and Protocols. Ed. S. Periyannan. Springer New York115-124. DOI:10.1007/978-1-4939-7249-4_10. pp. 115-124


Coelho, M., Bakkeren, G., Sun, S., Hood, M. E., and Giraud, T. 2017. FUNGAL SEX: THE BASIDIOMYCOTA. In: “The Fungal Kingdom”, Section 2: Life of Fungi. Eds. Neil Gow and Joseph Heitman. ASM Press, Microbiology spectrum, 5(3). DOI:10.1128/microbiolspec.FUNK-0046-2016


Bakkeren, G., Joly, D. L. and Duplessis, S. 2016. Genomics research on non-model plant pathogens: delivering novel insights into rust fungus biology. Front. Plant Sci. 5: 216. Editorial to Frontiers E-book ( DOI:10.3389/fpls.2016.00216


Panwar, V., McCallum, B., Jordan, M., Loewen, M., Fobert, P., McCartney, C. and Bakkeren, G. 2016. RNA silencing approaches for identifying pathogenicity and virulence elements towards engineering crop resistance to plant pathogenic fungi. In: CABI Reviews. Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources. 11(027). DOI:10.1079/PAVSNNR201611027


Panwar, V., McCallum, B. and Bakkeren, G. 2015. A functional genomics method for assaying gene function in phytopathogenic fungi through host-induced gene silencing mediated by Agroinfiltration. In: Plant Gene Silencing: Methods and Protocols. Eds. Mysore, K. S. and Muthappa, S-K. Springer New York. Chapter 13: 179-189. DOI:10.1007/978-1-4939-2453-0


Ali, S., Laurie, J.D., Linning, R., Cervantes-Chávez, J.A., Gaudet, D. and Bakkeren, G. 2014. An immunity-triggering effector from the barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolutionPLoS Pathogens 10: e1004223. DOI:10.1371/journal.ppat.1004223


Bruce, M., K. A. Neugebauer, D. L. Joly, P. Migeon, C. A. Cuomo, S. Wang, E. Akhunov, G. Bakkeren, J. A. Kolmer and J. P. Fellers. 2014. Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Front. Plant Sci. 4, 520. DOI:10.3389/fpls.2013.00520


Lefebvre, F., Joly, D.L., Labbé, C., Teichmann, B., Linning, R., Belzile, F., Bakkeren, G. and Bélanger, R.R. 2013. The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole genome analysis. Plant Cell 25, 1946-1959


Laurie, J. D., Linning, R., Wong, P. and Bakkeren G. 2013. Do TE activity and counteracting genome defenses, RNAi and methylation, shape the sex lives of smut fungi? Plant Signal. Behavior 8, e23853


Panwar, V., McCallum, B. and Bakkeren, G. 2013. Host-generated trans-specific RNAi of wheat leaf rust fungus Puccinia triticina pathogenicity genes induced by the Barley stripe mosaic virusPlant Mol Biol 81, 595-608


Fellers, J. P., Soltani, B. M., Bruce, M., Linning, R., Cuomo, C. A., Szabo, L. and Bakkeren, G. 2013. Conserved loci of leaf and stem rust share synteny interrupted by lineage-specific influx of repeat elements. BMC Genomics 14:60


Panwar, V., McCallum, B. and Bakkeren, G. 2013. Endogenous silencing of Puccinia triticina pathogenicity genes through in planta-expressed sequences leads to suppression of rust diseases on wheat. Plant J 73, 521-532


Laurie, J. D., Ali, S. Linning, R., Mannhaupt, G., Wong, P., Güldener, U., Münsterkötter, M., Moore, R., Kahmann, R., Bakkeren, G., and Schirawski, J. 2012. Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of TEs. Plant Cell 24, 1733-1745