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.
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).
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 elicit defense and resistance responses.
Topics: I am currently 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, their annotation and comparative analyses among many natural isolates, analyses of pathogen-host interactive transcriptomes generated by RNA-sequencing, structural & functional genomics, proteomics and the study of avirulence and virulence effectors.
Pioneering work is performed on two apple pathogens: the bacterium Erwinia amylovora, causing fire blight, and the fungus Venturia inaequalis, causing scab. Whole genome sequencing for Canadian population structures, as well as virulence assays as a tool to assist resistance breeding and the molecular basis of pesticide resistance are among the topics studied.
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: Agriculture & Agri-Food Canada Science & Technology Branch. My group is part of a National Program on ‘Molecular strategies for the improvement of disease resistance and pathogen management in cereals’, involving more than 30 scientists, PDFs, technicians and Graduate Students in different AAFC centres across Canada such as in Morden, MB, Lethbridge, AB, and Ottawa, ON (Bakkeren lab at PARC-Summerland).
• Research project on "Genomics Approaches to Mitigate Fungal Threats to Crops" with B. Saville, Trent University, ON, an Ontario Ministry of Research and Innovation-funded project on large-scale transcriptome analyses of cereal rust and other fungi during host infections
• Sequencing of various 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
Summerland Research & Development Centre (Okanagan Valley)
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
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 (http://journal.frontiersin.org/researchtopic/1925/genomics-research-on-non-model-plant-pathogens-delivering-novel-insights-into-rust-fungus-biology), covering 14 published papers for which these 3 authors were co-editors. DOI:10.3389/fpls.2016.00216
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 evolution. PLoS Pathog 10: e1004223
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 virus. Plant 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
Bakkeren, G. Kruzel, E.K., and Hull, C.M. 2012. Sex and Virulence in Basidiomycete Pathogens. In: Evolution of Virulence in Eukaryotic Microbes. Eds. L. David Sibley, Barbara J. Howlett, and Joseph Heitman. Wiley-Blackwell, Hoboken, New Jersey. ISBN 978-1-118-03818-5. Pp. 437-460
Ali, S., and Bakkeren, G. 2012. Fungal and oomycete effectors; strategies to subdue a host. Can J Plant Pathol 33, 425-446
Bakkeren, G., Song, X., Panwar, V., Linning, R., Wang, X., Rampitsch, C., McCallum, B., Fellers, J., and Saville, B. 2012. Functional genomic approaches in cereal rusts. Can J Plant Pathol 34. 3-12
Xu, J., Linning, R., Fellers, J., Dickinson, M., Zhu, W., Antonov, I., Joly, D.L., Donaldson, M.E., Eilam, T., Anikster, Y., Banks, T., Munro, S., Mayo, M., Wynhoven, B., Ali, J., Moore, R., McCallum, B., Borodovsky, M., Saville, B. and Bakkeren, G. 2011. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi. BMC Genomics 12:161
Song, X., Rampitsch, C., Soltani, B., Mauthe, W., Linning, R., Banks, T., McCallum, B. and Bakkeren, G. 2011. Proteome analysis of wheat leaf rust fungus, Puccinia triticina, infection structures enriched for haustoria. Proteomics 11, 944-963
Cervantes-Chávez, J. A., Ali, S. and Bakkeren, G. 2011. Response to environmental stresses, cell wall integrity and virulence are orchestrated through the calcineurin pathway in Ustilago hordei. Mol Plant-Microbe Interact 24, 219-232
Gaudet, D. A., Wang, Y., Penniket, C., Frick, M., Lu, Z-X., Bakkeren, G. and Laroche, A. 2010. Morphological and molecular analyses of host and nonhost interactions involving barley and wheat and the covered smut pathogen Ustilago hordei. Mol Plant-Microbe Interact 23, 1619-1634
Laurie, J. D., Linning, R. and Bakkeren, G. 2008. Hallmarks of RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago maydis. Curr Genet 53, 49-58