Currently the lab has three main research themes:

Phaseolus Genomics
Phaseolus Genomics for Improved Bio-Product Development:

Relatively few genome sequences are available for Phaseolus vulgaris (dry beans) in public databases like GenBank. The lack of genomic information for the dry bean is a major anomaly for such important crop species in the world and it represents an important opportunity for a Ontario genomics effort to have a major international impact. The long-term objectives of the work are to accelerate the rate of genetic improvement in dry beans by developing genomics resources and tools for genomics-assisted improvement of Phaseolus for bio-product development. In the current study we are to focusing the genomics research in bean around five themes, namely:
  • Development of a draft genomic sequence for P. vulgaris
  • Identification of genes involved in resistance to a bacterial pathogen that causes      bacterial blight, a major disease of bean throughout the world
  • Characterization of genes that code for the phenylpropanoid pathway that results in an      enormous variety of compounds with significant disease resistance, seed quality and      nutraceutical importance
  • Characterization of the genes that code for protein composition in bean, which is the      major reason it is grown throughout the world
  • Determination of the economic consequences of bio-product demand for dry beans
Read More
Elucidation and characterization of introgression mechanisms via the OAC-Rex P. vulgaris model:
OAC-Rex has a unique pedigree, that of a P. vulgaris cultivar (G-19833) introgressed with a distant relative P. acutifolius (PI440795). This known crossing event, called an introgression, provides a unique chance for insight into the mechanisms by which plants cope with the inherent associated genomic reorganizations. By assembling and analyzing the genomes of OAC-Rex, G-19833, and PI4401795, some light may be shed on this little understood, though widely used, process.

Previous lab research themes:

Castor Genomics
Castor as a Next-Generation Crop for the Biorenewable Chemical and Energy Sectors:

A combination of market pressures have resulted in significant increases in consumption and associated cost of petroleum-based energy. These forces have co-emerged with improvements in fuel production technology, such that fuels derived from biorenewable plant-based chemical feedstocks are now a viable opportunity within the global energy sector. The global biorenewable fuels industry, while expanding rapidly in both size and value, is nevertheless confronted with significant obstacles to future growth. Chief among these is the limited availability and cost of input agricultural feedstocks - particularly those based on food crops (e.g. corn starch, Canola oil and soybean oil). For ethanol or biodiesel production, Castor meets all these criteria, and is particularly attractive as a novel source of biorenewable oil feedstocks for the liquid fuel transportation sector. In this project we propose to develop and use advanced genomics tools to develop the Castor plant (Ricinus communis L.) as a non-food source of biorenewable energy. The specific project objectives include completion of the Castor genome sequence to a high quality, developing expression arrays, whole genome tiling arrays, and reverse-genetic resources, that will accelerate development of the crop into the Ontario regional and national sectors.

Global Protein Profiling
High-throughput methods for identifying ubiquitinated proteins in Arabidopsis:

SCF ligase Regualtion
Functional Analysis of SKP1 orthologs in Arabidopsis thaliana:

Protein degradation is an important post-transcriptional gene regulatory process that allows cells to respond rapidly to changing environmental conditions by adjusting the steady state abundance of key proteins that regulate environmental responses, patterning, and development. One major process for targeted proteolysis in eukaryotes involves the Ubiquitin (Ub)/26S proteasome pathway. In which, proteins destined for degradation become modified by the covalent attachment of multiple Ub molecules under the action of E3 ligase complexes, followed by degradation via the 26S proteosome. SCF ligase, a well charcterized subclass of E3 Ligases, exhibits a quaternary structure that includes Cullin1/Cdc53, Rbx1/Roc1/Hrt1, Skp1, and F-box protein subunits. Structural analysis of a human SCF complex has shown that the Skp1 component acts as an adapter that associates Cullin to the F-box protein in the functional complex. The Arabidopsis genome contains 21 known or predicted Skp1-like (ASK) genes compared to only a single gene in both Baker's Yeast (S. cerevisiae) and Humans. The large number of ASK genes may reflect the unique adaptive strategy of plants versus animals, where plants are well-adapted to rapidly adjust their metabolic and developmental profiles in response to changing environmental conditions. All known or predicted products of the ASK gene family are believed to be part of SCF complexes (E3 ligases) but this has been directly demonstrated for only two of the genes in Arabidopsis - ASK1 and ASK2. Functional studies of a subset of the predicted ASK family of genes are being carried out initially using a reverse genetic approach. Artificial miRNA (amiRNA) constructs will be used to simultaneously interfere with the expression of single or multiple genes via a Dicer mechanism targeting common transcript sequences. We are also in the process of developing novel approaches to assess and characterize the regulatory pathways that are subject to hierarchical control via the 26S ubiquitinylation-mediated activity of select ASK genes.
Read More