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National Wheat Improvement Program Cluster, Activity 32, Identification of expression QTLs (eQTLs) for Fusarium Head Blight resistance and susceptibility in wheat

Principal Investigator

Thérèse Ouellet

Research Institution

Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC)

External Funding Partners

This project is part of the $25.2 million National Wheat Improvement Program funded by the Western Grains Research Foundation (WGRF), the Canadian Field Crop Research Alliance (CFCRA), the Alberta Wheat Commission (AWC), and Agriculture and Agri-Food Canada (AAFC) through the Industry-Led Research and Development Stream of the Growing Forward 2 AgriInnovation Program. Grain Farmers of Ontario is a founding member of the CFCRA.

Project Start

April 2013

Project End

March 2018


  • Identify genetic markers associated with gene expression patterns that correlate with resistance or susceptibility to Fusarium Head Blight (FHB) in spring wheat.
  • Identify additional wheat breeding material carrying the expressed quantitative traits (eQTLs) discovered in project by testing spring wheat lines from 6 Canadian breeding programs; this will include a comparative field evaluation for FHB disease resistance over three field seasons at one site.
  • Validate the association between the genetic markers and the expressed genes identifying the eQTLs by testing gene expression in subsets of lines that are contrasting for the presence of the eQTLs.


  • The improvement of FHB resistance in Canadian wheat breeding programs through identification of wheat genes or expressed quantitative traits (eQTLs) associated with increased susceptibility to FHB and with resistance to FHB.
  • The improvement of food security by reducing the incidence of deoxynivalenol (DON) accumulation through the efforts of wheat breeding.

Scientific Summary

Even though a majority of wheat breeding programs in Canada have deployed significant efforts towards improving resistance for Fusarium Head Blight (FHB) during the last 20 years, progress has been slow and FHB still remains a priority problem for the industry. The identification of genetic markers associated with resistance to FHB has accelerated the improvement of resistance to FHB by allowing breeding programs for spring and winter wheat to track genetic loci for quantitative traits (QTLs) contributing to that resistance. QTLs for resistance to FHB have been identified so far from field disease rating and deoxynivalenol (DON) accumulation data. However, the known QTLs for resistance to FHB in wheat capture only part of the resistance observed in the field.

This project uses a different approach, called differential gene expression, to identify genetic markers associated with expression QTLs (eQTLs) that cannot be detected by conventional marker discovery work using field data. Our group at AAFC-ORDC, Ottawa, has developed a database of global gene expression profiles from FHB-susceptible and -resistant wheat varieties/breeding lines when infected by Fusarium graminearum. Comparative analysis of those expression profiles followed by experimental validation has led to the identification of genes contributing to either susceptibility or resistance to FHB. We propose to complement this work by using a high throughput sequencing technology (RNASeq) for comparative expression profiling on a double haploid population segregating for FHB resistance that is being mapped with the 90K wheat SNP chip in a separate project. This will allow us to validate the correlation to resistance or susceptibility for additional candidate genes and identify if they are associated with new or known QTL or new eQTLs identified from this and the mapping work. Genetic markers associated with QTLs/eQTLs for susceptibility or resistance to FHB will be tested on a panel of 120 spring wheat breeding lines and varieties from 6 Canadian spring wheat breeding programs, to identify material that carry the novel QTLs/eQTLs and provide breeders with additional options in their strategies to improve resistance to FHB.