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Bridging Comparative, Population and Functional Genomics to Identify and Experimentally Validate Novel Regulatory Regions and Genes for Crop Improvement


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Competition in Applied Genomics Research in Bioproducts or Crops (ABC)

Genome Centre(s)



Project Leader(s)

Fiscal Year Project Launched


Project Description

Genomic methods, pioneered in studies of simple, single­celled organisms, are being applied with great success to important crop plants. Genomics provides a way to examine and analyze all of the genes (i.e., the genome) that define the crop with a view to enhance yield and productivity, while reducing production costs. In recent years it has become clear that the genome is more than the sum of genes that code for cellular proteins. Indeed, the regions (“non­coding DNA”) between the protein coding genes are important for regulating their activity.

Studies in plants, humans and other animals now suggest that many of these noncoding DNA regions may have profound significance, harbouring the very elements that regulate genes or provide novel functionality.

Our goal is to use genomics as a means to identify, characterize and validate noncoding DNA regions that have a direct role in determining characteristics that are important for Canadian crops. We have chosen to concentrate on a plant called Arabidopsis for two reasons. First, more is known about the genetics and genomics of this plant than any other in the world. Second, Arabidopsis is a close relative of several crops important to the Canadian economy (e.g., canola). Thus, through the comparison of Arabidopsis with other plants, we can identify important non­coding DNA regions, including those relevant for Canadian crops. We will approach this by determining the whole­genome sequence of several close relatives of Arabidopsis and canola, using this information for within species and between species comparative studies. Non­coding DNA regions will be identified by computer­based predictions and will be validated by experiments that use population genetics and genomic methods. Important findings will be protected for further exploitation.

We anticipate that our project will identify non­coding 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 crop­improvement applications.

Integrated GE3LS Research Component:  The Integration of Genomics with Plant Breeding
GE3LS Project Leader:  Anwar Naseem, McGill University

The use of genomic methods to improve crops has implications for Canadian society. As the demand for food rises, crops with traits that allow them to thrive in marginal conditions, such as cold tolerance, drought tolerance and low-nitrogen will become increasingly important. In order for scientific knowledge to be brought safely and effectively to practical application, the GE3LS component of the project will pursue several research themes to address economic, policy and legal questions related to agricultural genomics.

First, to inform and guide the scientific aspects of the overall project, a socio-economic impact analysis of the traits that are coded by the target genes will be conducted, so that the genes that hold the greatest societal benefit are selected. Second, we will develop methods of estimating the value of genomics patents to the agricultural industry. We will carry out case studies of five selected patents that are likely to come from the genomic research component of this project. We will consider several indicators, such as economic value, impact on knowledge creation and expert analysis of specific patents.

Finally, we will explore how advances in genomics have affected the productivity of the plant breeding process by comparing the economic returns to marker assisted breeding with conventional breeding methods. The outcomes of this phase of the research will be widely applicable to crop-improvement generally and in providing guidance on ways to improve the breeding efficiency. Our research will have important policy implications for the future of agricultural genomics in Canada, and how the integration of genomics with plant breeding can best be realized.