Welcome to The VEGI Informatics Portal

Bridging comparative, population and functional genomics to identify and experimentally validate novel
regulatory regions and genes for crop improvement

Relatively little is known about functionally important non-coding DNA in plants, and even less about their significance to Canadian crops. Genomic methods, pioneered in studies of simple, single-celled organisms, are being applied with great success to important crop plants.

A newly funded collaborative study (The VEGI project) between McGill University and the University of Toronto, under the direction of Dr. Thomas Bureau, aims to study the functionality of normal variation in non-coding DNA regions in several species of the Brassicaceae family.  
 
The VEGI project centers around the vast resources of the model plant Arabidopsis thaliana (mouse-ear cress), a close relative to several crops important to the Canadian economy (e.g., canola), and therefore comparative and population genomics in Arabidopsis species will identify functionally important non-coding DNA regions.  

The functional non-coding DNA sequences will be characterized by a combination of comparative, population and functional genomics approaches by high-throughput sequencing, microarray gene expression analysis, gene disruption via insertion mutagenesis and RNA interference, and detailed phenotype characterization, a major part of our strategy. An agricultural economist (Dr. Anwar Naseem) will be part of the team to evaluate and rank potential traits to be selected.

Several close relatives of Arabidopsis and Canola, such as Sisymbrium, Leavenworthia and Aethionema will be sequenced by Dr. Ken Dewar. After annotation of the newly sequenced genomes (Dr. Paul Harrison), comparative- (Dr. Mathieu Blanchette and Dr. Alan Moses) and population genomics (Dr. Stephen Wright and Dr. Daniel Schoen) will be used to identify regions involved in gene transcription.

Furthermore, high-throughput sequencing of plants in one population will be used to identify single-nucleotide polymorphisms (SNPs) that can be used for gene expression association studies (Dr. Stephen Wright).

We will validate the function of non-coding DNA regions by evaluating the effects of mutations in these regions on the growth characteristics of the affected plants (functional genomics) (Dr. Thomas Bureau, Dr. John Stinchcombe, Dr. Stephen Wright).

We anticipate that our project will identify non-coding DNA regions that will have proven potential for crop improvement. We will also generate valuable data, expertise and trained personnel that will provide the basis for future crop-improvement applications.