Bakkeren Lab web page

(last updated: July 2018)

Facilities & Location

Research Interests:

Towards the broader goal of contributing to the efforts to combat biotic stresses in cereal crops, we want to understand plant-pathogen interactions in the leaf rust/wheat & Ustilago hordei/barley pathosystems on a molecular level. We focus on finding fungal factors essential for pathogenic development on or in the host that could be targets for highly specific inhibitors. Such sophisticated “pesticides” can be produced in antagonistic microbes, applied as crop dressings or produced in crop plants modified through biotechnology. We are interested in why only certain microbes are pathogenic on certain plants. We want to study genes that therefore can be defined as pathogenicity factors and contribute to host range. Pathogens can be more or less virulent or aggressive upon infection, a phenomenon that is often controlled by the additive effect of many "virulence" or "fitness" genes, more recently identified as coding for effectors. Genetically superimposed on this "basic compatibility" of a pathogen to cause disease, we can sometimes identify single dominant genes that render it non-virulent. These genes have therefore been dubbed "avirulence" genes and are prime targets of research in many laboratories because they are (genetically) interacting with cognate plant host resistance genes and determine whether compatible or incompatible interactions will ensue.

Conversely, we can learn which host components are important during the pathogenic interaction, be it as targets of pathogen subversion through the action of their effectors, or involved in active host defense and resistance responses triggered by the recognition of pathogen components. These host factors can potentially be modified. Although initial recognition might be specific for a given pathogen-host combination, it is becoming clear that subsequent signaling and defense pathways converge and have common molecular components among different (related) plant species. That is, isolated plant genes involved in defence and resistance in one pathosystem can be used to clone, understand and manipulate those of related hosts. As a consequence, the introduction of these (engineered) components may allow improved, more durable host resistance, potentially against related pathogens.

Fungal mating systems are also of interest because, at least in the smuts, the mating-type gene complexes regulate mating which is a prerequisite for pathogenic development. In rusts, sex increases the virulence potential, for example by resorting avirulence effectors which can result in progeny overcoming resistance in cultivars.

Current projects:

Rust fungi

Ř  Structural Genomics of the wheat leaf rust fungus, Puccinia triticina. Collaborations with C. Cuomo, the Broad Institute of Harvard and MIT, Cambridge, MA, J. Fellers, USDA-ARS, Manhattan, KS, L. Szabo, USDA-ARS, St. Paul, MN (funded through a NSF-USDA Microbial Genome Sequencing Program grant & the AAFC Canadian Crop Genomics Initiative), and scientists at the Michael Smith Genome Sciences Centre in Vancouver, BC, and Genome Quebec, Montreal, QUE. After having generated a reference genome sequence for P. triticina (Cuomo et al., 2017), next-generation, large fragment sequencing and assembly technologies are being used to improve the assembly.

Ř  Comparative genomics over 95 P. triticina genome sequences have been generated from Canadian isolates with known virulence profiles on 20 differential cultivars; collaboration with Dr. B. McCallum (AAFC -  Morden Research and Development Centre, MB). GWAS analysis is employed to identify potential avirulence effectors. Variation in other virulence factors among these isolates may identify novel targets for crop protection.

Ř  Functional Genomics of rust genes involved in pathogenicity, virulence and avirulence, including predicted secreted proteins, using heterologous Ustilago systems and Host-Induced Gene Silencing (HIGS) technologies (Hu et al., 2007; Panwar et al., 2013a,b; 2014; 2015;m 2016; 2018) and P. triticina. Rusts are difficult to genetically transform; initial attempts have been encouraging for P. triticina (Webb et al., 2006) and optimization is in progress. The use of a heterologous expression system to allow functional analysis of rust genes was explored. The corn smut fungus, Ustilago maydis, was found to allow the expression of a P. triticina MAP kinase gene and to complement a non-pathogenic U. maydis MAPK deletion mutant to restore full pathogenicity (Hu et al., 2007).

Ř  Proteomic analysis of P. triticina infection structures (collaboration with Dr. C. Rampitsch, (AAFC -  Morden Research and Development Centre, MB; see Song et al., 2011).



Ř  Functional analysis of Ustilago hordei effectors, including the cloning and functional analysis of avirulence genes (Linning et al, 2004; Ali et al, 2014). Isolation and study of genes representing effector targets during the interaction of U. hordei with barley and P. triticina and wheat.

Ř  U. hordei structural and smut fungi comparative genomics.



Ř  Study of host responses during compatible, incompatible and nonhost interactions through (confocal and EM) microscopy and gene expression patterns (RNAseq transcriptome profiling) in wheat and barley.