Guus Bakkeren, Ph.D.
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.
CURRENT COLLABORATIONS
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
POST-SECONDARY EDUCATION
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,
POSITIONS HELD
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
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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
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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
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Wang, X., McCallum, B.D., Fetch Jr., T.G., Bakkeren, G., and Saville, B.J. (2015). The involvement of reactive oxygen species during the germination and infection of wheat leaf rust fungus. Puccinia triticina. Botany 2015, July 25-29, Edmonton, Alberta, Canada (poster).
2015 - View publication details
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Wang, X., McCallum, B.D., Fetch, T., Bakkeren, G., Saville, B.J. (2015). Sr36- and Sr5-mediated resistance response to Puccinia graminis f. sp. tritici is associated with callose deposition in wheat guard cells. Phytopathology, [online] 105(6), 728-737. http://dx.doi.org/10.1094/PHYTO-08-14-0213-R
2015 - View publication details
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Ali, S. and Bakkeren, G. (2015). "Conversion of BAC clones into binary BAC (BIBAC) vectors and their delivery into basidiomycete fungal cells using Agrobacterium tumefaciens.", Methods in Molecular Biology (Clifton, N.J.), 1227, pp. 199-215. doi : 10.1007/978-1-4939-1652-8_9
2015 - View publication details
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Panwar, V., Jordan, M.C., McCallum, B.D., Fobert, P., and Bakkeren, G. (2014). "Host-induced gene silencing of Puccinia triticina genes shows enhanced resistance to leaf rust disease in transgenic wheat plants.", XVI 2014 APS-CPS Joint Meeting, Minneapolis, Minnesota, USA, August 9-13, 2014. (Abstract)
2014 - View publication details
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Bakkeren, G. (2014). "RNA Interference Technology: Applications for Agriculture.", 56th Annual Horticulture Growers’ Short Course, Abbotsford, BC, Canada, January 30, 2014, Invited lecture & chapter in on-line proceeding. Lower Mainland Horticultural Improvement Association.
2014 - View publication details
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Bakkeren, G., Fellers, J.P., Panwar, V., Joly, D.L., Szabo, L.J., Kolmer, J.A., Hulbert, S., Wang, M., Yin, C., Chen, X., Rampitsch, C., McCallum, B.D., Wang, X., Goldberg, J., Young, S., Hamelin, R.C., Saville, B.J., and Cuomo, C.A. (2014). "Comparative genomics of rust fungi drives research and innovations for crop protection.", 16th conference of the International Society for Molecular Plant-Microbe Interactions, Rhodes, Greece, July 6-10, 2014.
2014 - View publication details
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Panwar, V., Kassa, M.T., Bakkeren, G., Fobert, P., Jordan, M.C., McCallum, B.D., and McCartney, C.A. (2014). "VIGS as a powerful genomics resource for identifying host or pathogen gene targets for the control of cereal rust diseases.", 2nd Canadian Wheat Symposium, Saskatoon, SK, Canada, June 8-11, 2014.
2014 - View publication details
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Rampitsch, C., Beimcik, E., Bakkeren, G., Linning, R., Joly, D.L., and McCallum, B.D. (2014). "Quantitative proteomics with custom database searching to reveal differences in the haustorial proteomes of three races of wheat leaf rust, Puccinia triticina.", 12th European Conference on Fungal Genetics, Sevilla, Spain, March 2014.
2014 - View publication details
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Rampitsch, C., Bakkeren, G., and McCallum, B.D. (2014). "Custom database searching to reveal differences in the haustoria proteomes of three races of wheat leaf rust, Puccinia triticina.", 1st Meeting of the International Plant Proteomics Organization, Hamburg, Germany, August 31- September 4, 2014. (Presentation)
2014 - View publication details
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Bakkeren, G., Fellers, J.P., Panwar, V., Joly, D.L., Szabo, L.J., Kolmer, J.A., Hulbert, S., Wang, M., Yin, C., Chen, X., Rampitsch, C., McCallum, B.D., Wang, X., Goldberg, J., Young, S., Hamelin, R.C., Saville, B.J., and Cuomo, C.A. (2014). "Comparative genomics of rust fungi drives research and innovations.", XXII Plant & Animal Genome Conference, Town & Country Convention Center, San Diego, CA, USA, January 10-15, 2014.
2014 - View publication details
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Rampitsch, C., Beimcik, E., Günel, A., Bakkeren, G., Linning, R., Joly, D.L., McCallum, B.D., and Fan, T. (2014). "Custom database searching to reveal differences in the haustorial proteomes of three races of wheat leaf rust, Puccinia triticina.", Canadian Society of Mass Spectrometry, Montreal, QC, Canada, April 13-16, 2014.
2014 - View publication details
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Duplessis, S., Bakkeren, G., and Hamelin, R.C. (2014). "Advancing knowledge on biology of rust fungi through genomics.", in Martin, F.M. (ed.) - Advances in Botanical Research Vol. 70, Academic Press, Chapter 6, pp. 173-209.
2014 - View publication details
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Bélanger, R.R., Lefebvre, F., Joly, D.L., and Bakkeren, G. (2014). "From bad to good fungus: new insights into genetic factors leading to biocontrol lifestyle in fungi.", XVIth International Congress of Virology - International Union of Microbiological Societies (IUMS 2014), July 27 - August 1, 2014, Montréal, Québec, Canada, July 27-August 1, 2014.
2014 - View publication details
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Bakkeren, G. and Valent, B. (2014). "Do pathogen effectors play peek-a-boo?", Frontiers in Plant Science, 5(DEC: Article number 731), pp. 2 pages. doi : 10.3389/fpls.2014.00731
2014 - View publication details
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Bruce, M., Neugebauer, K.A., Joly, D.L., Migeon, P., Cuomo, C.A., Wang, S., Akhunov, E., Bakkeren, G., Kolmer, J.A., Fellers, J.P. (2014). Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat. Frontiers in Plant Science, [online] 4(JAN), http://dx.doi.org/10.3389/fpls.2013.00520
2014 - View publication details
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Ali, S., Laurie, J.D., Linning, R., Cervantes-Chávez, J.A., Gaudet, D., 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 Evolution. PLoS Pathogens, [online] 10(7), http://dx.doi.org/10.1371/journal.ppat.1004223
2014 - View publication details
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Rampitsch, C., Beimcik, E., Bakkeren, G., and Fan, T. (2013). "Comparative proteomics in Puccinia triticina using race-specific database searches.", 26th CSMS conference, Lake Louise AB, Canada. (Poster)
2013 - View publication details
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Rampitsch, C., Beimcik, E., Günel, A., Bakkeren, G., McCallum, B.D., and Fan, T. (2013). "Comparative proteomics of monoclonal-antibody enriched haustoria from three races of Puccinia triticina.", 27th American Genetics Society meeting on Fungal Genetics, Asilomar, CA, USA. (Poster)
2013 - View publication details
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Contact
Research facility
Expertise
Affiliations
Adjunct Professor at the Department of Botany, University of British Columbia, Vancouver.
https://www.botany.ubc.ca/people/guus-bakkeren