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.
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 effectors that elicit defense and resistance responses (avirulence effectors).
Research Program: Genomics on major agricultural fungal pathogens: the basidiomycete wheat leaf rust fungus, Puccinia triticina, and the barley covered smut fungus, Ustilago hordei. Generation of whole genome sequences and annotation efforts, bioinformatic database mining and comparative analyses among rusts. Wheat rust fungus population studies. P. triticina pan-genome analysis and its potential for diagnostics. Analysis of fungal and host transcriptomes (gene expression patterns) and proteomes during P. triticina - wheat and U. hordei – barley interactions and infection. Special interest in (secreted) virulence and avirulence factors triggering defence and resistance in the host. Support breeding efforts for resistance, and to develop alternative rust disease management strategies.
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 and sustainable production of crops. Consumers will benefit directly from the availability 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).
Faculty at the Michael Smith Laboratories (Kronstad and Li), and Dept. of Botany (Li, Zhang), and the Georg August University in Goettingen (dr. Ivo Feussner), supported by NSERC-CREATE (“PRoTECT – Plant Responses To Eliminate Critical Threats”) and DFG-IRTG grants to jointly train the next generation of molecular plant pathologists
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, Simon Fraser university, Burnaby, BC, Michael Smith Genome Sciences Centre in Vancouver, Dr. Barry Saville, Trent University, ON, Canada, Dr. Curtis Pozniak and Dr. Andrew Sharpe, University of Saskatchewan, and Genome BC on a joint project Digital Technology Supercluster Project “Precision Agriculture to Improve Crop Health”
USDA laboratories in St. Paul, MN (Dr. Les Szabo) and Manhattan, KS (Dr. Jun P. Fellers); Broad Institute for genome research, Cambridge, MA (Dr. Christina A. Cuomo); John Innes Centre, Norwich, UK (Dr. Diane Saunders), and the University in Cologne, Germany (Drs. B. Őkmen and G. Doehlemann)
Summerland Research & Development Centre (Okanagan Valley)
Ökmen, B., Schwammbach, D., Bakkeren, G., Neumann, U. and Doehlemann, G. 2021. The Ustilago hordei-barley interaction is a versatile system to characterize fungal effectors. J. Fungi 7(2):86. https://doi.org/10.3390/jof7020086
Fellers, J. P., Sakthikumar, S., He, F., McRell, K., Bakkeren, G., Cuomo, C. A. and Kolmer, J. A. 2020. Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations. bioRxiv: 2020.2007.2022.212464. under revision
Bakkeren, G. and Szabo, L. 2020. Progress on molecular genetics and manipulation of rust fungi. Phytopathology. 110(3), 532-543. https://doi.org/10.1094/PHYTO-07-19-0228-IA
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
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
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 Pathogens 10: e1004223. DOI:10.1371/journal.ppat.1004223