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

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, the best-studied model for the small grain-infecting smut fungi of the genus Ustilago. Projects feature generation of genomic resources such as EST databases, structural & functional genomics, proteomics and the study of avirulence genes. Contributions to large-scale projects involving complete fungal genome sequencing and annotation, and whole genome transcriptome analyses using microarrays and RNA-sequencing.

Long term objectives: contribute to efforts towards increasing (cereal) crop protection against biotic stresses.

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 healthier production methods.

Organization: Agriculture & Agri-Food Canada has restructured and 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 the Cereal Research Centre in Winnipeg, MB, and the Lethbridge Research Centre in Lethbridge, AB (Bakkeren lab at PARC-Summerland).

Collaborations:

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 In press 

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

Ali, S. and Bakkeren, G. 2011. Introduction of large DNA inserts into the barley pathogenic fungus, Ustilago hordei, via recombined binary BAC vectors and Agrobacterium-mediated transformation. Curr Genet 57, 63-73

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           

Wang, X., Bakkeren, G. And McCallum, B. 2010. Virulence and molecular polymorphisms of the wheat leaf rust fungus Puccinia triticina in Canada from 1997 to 2007. Botany 88, 575-589

Wang, X., Mulock, B., Bakkeren, G. and McCallum, B. 2010. Development of EST-derived simple sequence repeat markers for the wheat leaf rust fungus, Puccinia triticina Eriks. Can J Plant Pathol 32, 98-107

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

Bakkeren, G., Kämper, J. and Schirawski, J. 2008. Sex in smut fungi: structure, function and evolution of mating type complexes. A review. Fungal Genet Biol 45, S15-S21

Grewal, T. S., Rossnagel, B. G., Bakkeren, G. and Scoles, G. J. 2008. Identification of barley covered smut resistance genes and mapping of Ruh1 using Ustilago hordei strains with defined avirulence genes. Can J Plant Pathol 30, 277-284

Hu, G. G., Linning, R., McCallum, B., Banks, T., Cloutier, S., Butterfield, Y., Liu, J., Kirkpatrick, R., Stott, J., Yang, G., Smailus, D., Jones, S., Marra, M., Schein, J. and Bakkeren, G. 2007. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Mol Plant Pathol 8, 451-467

Hu, G. G., Naik., S., Kamp, A., Linning, R. and Bakkeren, G. 2007. Complementation of Ustilago maydis MAPK mutants by a wheat leaf rust, Puccinia triticina homolog; potential for functional analyses of rust genes. Mol Plant-Microbe Interact 20, 637-647

Bakkeren, G., Jiang, G., Warren, R., Butterfield, Y., Shin, H., Chiu, R., Schein, J., Lee, N., Kupfer, D., Roe, B., Jones, S., Marra, M. and Kronstad, J. W. 2006. Physical mapping of the genome of the fungal pathogen Ustilago hordei and annotation of the 500 kb MAT-1 sequence. Fungal Genet Biol 43, 655-666

Linning, R., Lin, D., Lee, N., Abdennadher, M., Gaudet, D., Thomas, P., Mills, D., Kronstad, J. W. and Bakkeren, G. 2004). Marker-based cloning of the region containing the UhAvr1 avirulence gene from the basidiomycete barley pathogen Ustilago hordei. Genetics 166, 99 - 111

Hu, G.G., Linning, R., and Bakkeren, G. 2003. Ultrastructural comparison of a compatible and incompatible interaction triggered by the presence of an avirulence gene during early infection of the smut fungus, Ustilago hordei, in barley. Physiological Mol Plant Pathol, 62, 155-166