Genome Prairie

Functional Genomics of Abiotic Stress

The FGAS project undertook research activities to identify genes that provide improved resistance to cold and drought in cereal and canola crops.

The Functional Genomics of Abiotic Stress (FGAS) project used a range of genomics and proteomics technologies to study how plants respond to various abiotic (environmental) stresses at the gene level - particularly cold - but also heat, drought and nutrient stress. Two crops of importance to Canada, Wheat and Canola along with the model plant Arabidopsis thaliana, are being used as experimental systems.
The FGAS project goals included the implementation of an array of tools including field genetic resources, protein analytical technologies, DNA sequence databases and microarrays that will empower the elucidation of biological mechanisms governing stress adaptation in crops. The project team sequenced over 100,000 Expressed Sequence Tags (ESTs) in support of the wheat cold-acclimation research and are in the process of mining this data set for lead-candidate genes of possible importance to the regulation of cold tolerance in temperate cereals. Proteomics analyses are being used for identification of lead-candidate gene products whose expression correlates with cold acclimation in both Brassica and wheat plant systems. FGAS has also implemented an effective informatics infrastructure that permits the secure organization, analysis and exchange of data within and between the 2 project themes (wheat and Brassica).

Through a genomic approach, many of the genes that respond to the various stresses and increase the ability of these plants to withstand these environmental stresses were identified. Through a proteomic approach, the proteins that appear in various tissues in response to stress were isolated and analyzed. An integral component of the project was also the implementation of a bioinformatics platform used to analyze and interpret the data collected. The team was also interested in finding out whether these two very different plants utilise similar strategies and also whether there is any commonality in the strategies used for different stresses.

Environmental stress is the primary factor that limits both the range of crop plants that can be grown and the yield and quality of those crops. The knowledge gained is helping researchers apply genomics to plant improvement, through both conventional and genetic engineering approaches. This knowledge can also be applied to other crops, not just wheat and canola, and lead to a more sustainable agricultural system. In addition, the genes and proteins identified by the project may have application in areas as diverse as frozen foods and cryopreservation.

Research ResultsResearch Results

With regards to the wheat research on Low Temperature (LT) tolerance, 82,000 (ESTs) from specialized libraries have been sequenced and deposited in the public domain as a strategic contribution to the international wheat genomic effort. This data set has been used in the design of a 17,300-feature LT enriched oligonucleotide array in collaboration with 3 international partners. Protocols for high throughput identification of promoters and transcription factors have been developed and protein interaction maps have been constructed. A 1.27 million clone Bacterial Artificid Chromosome (BAC) library has also been produced and provides 5.5X coverage of the hardy wheat cultivar 'Norstar' genome and three 500-loci mapping populations are in place that have been specifically designed to assist in the discovery of key LT tolerance genes.

With regards to the Canola research, five custom Arabidopsis Serial Analysis of Gene Expression (SAGE) libraries have been completed and 500,000 tags have been identified. Furthermore, a 25,000-feature Arabidopsis Oligo microarray has been developed. Molecular genetic analyses have revealed over 400 genes differentially expressed upon short-term cold stress. Functional characterization is underway for several candidate genes.

An investigation of the genetic mechanisms of how plants protect themselves against abiotic stresses—cold, heat, and drought - led to several developments that mitigate against crop losses. A key receptor involved in a wide range of abiotic stresses was discovered. This critical discovery eluded researchers for over 50 years, and will undoubtedly be the basis for further developments of hardier crops. Scientists produced plant lines that protect themselves against flooding and crop lines that demonstrated increased yields.


Notable OutcomesNotable Outcomes

  • The FGAS team has submitted two patents for approval: Plant Proteins having an abscisic acid binding site and Methods of Hormone Profiling.
  • This project contributed to the creation of the Proteomics Core Facility at the University of British Columbia as well as developed a partnership between the University of Saskatchewan and the University of British Columbia.
  • Over 160 proteins identified associated with low temperature or osmotic stress
  • 180,000 tags extracted from 3 SAGE libraries

Quick Facts

Project Leaders:

William Crosby, University of Windsor

Project Manager:

Elizabeth Nanak, University of Saskatchewan
Amit Shukla, University of Saskatchewan

Project Value:

$15.45 Million

Genome Canada Contribution:

$9.7 Million

Provincial Funding (SK):

$600,000

Provincial Funding (MB):

$190,000

Other Funding Partners:

$5 Million

Project Status:

Status (Dates)

Competition:

Genome Canada 2001-2002 Competition I