Skip to content

Molecular marker development for Gibberella ear rot resistance and DON accumulation

Principal Investigator: Aida Kebede

Research Institution: Agriculture and Agri-Food Canada (AAFC)

Timeline: April 2022 – July 2023   


  • Identify quantitative trait loci (QTLs) associated with Gibberella ear rot (GER) disease severity and DON accumulation using genome-wide association study.
  • Assess DON-3G:DON ratios in a diverse set of corn genotypes and identify QTLs contributing to high DON-3G:DON ratios.
  • Compare different inoculation methods and inoculum concentrations for effective GER screening.
  • Design KASP assay for use in marker assisted selection in corn breeding programs.


  • The use of molecular markers in the breeding process can reduce the time required for hybrid development and can allow farmers to gain access to newly released GER resistant hybrids quicker.
  • QTLs and resistance genes associated with GER, DON accumulation, and DON-3G:DON ratio will be identified.
  • Breeder-friendly markers will become available using KASP assay for marker assisted selection in the corn inbred breeding program.
  • Molecular markers will be provided to private breeding programs which obtain AAFC germplasm to aid in confirmation of GER/DON resistance trait insertion.
  • Growing GER resistant hybrids secures income for the corn grower by reducing yield loss from mouldy grains that are contaminated with mycotoxins and limiting pesticide application while building resiliency in the Ontario grain marketing sector and exporter confidence.
  • The best Fusarium graminearum inoculation technique and inoculum concentration will be recommended for future resistance screening efforts (e.g., Ontario Corn Committee) resulting in consistent GER/DON hybrid ratings.
  • Improved confidence by farmers when selecting DON hybrids.
  • Reduced reliance on fungicides at R1 timing, allowing for targeted fungicide application for other disease issues such as tar spot without the need for multiple applications thus reducing costs and increasing farmer profits.

Scientific Summary:

The prevalence of corn, wheat and other cereal crops in Ontario has led to frequent epidemics of Gibberella ear rot (GER) and Fusarium head blight caused by the broad host pathogen Fusarium graminearum. Screening corn hybrids for GER resistance is a time consuming and laborious process highly affected by the environment. Molecular markers can improve breeding efficiency by eliminating the environmental effect, increasing the genetic gain, and shortening the time required to release a new corn hybrid. There are close to 550 diverse inbred lines developed by AAFC. These inbred lines represent the global gene pool from which new inbred lines can be developed in a public corn breeding program. A subset of these lines was recently screened to identify resistance to ear, foliar and stalk diseases. The panel of diverse corn inbred lines will be used in a genome-wide association study to identify markers associated with GER disease severity and DON accumulation. QTL mapping of GER resistance/susceptibility using a bi-parental mapping population had been done in our research group. The QTLs identified in the previous study will be validated using the diverse panel of inbred lines and even more QTLs could be identified.

The level of QTL detection accuracy is as good as the phenotypic data used for analysis. Silk channel injection of inoculum with a concentration 2.5 × 105 spores/mL has been routinely used when screening for GER resistance. Some researchers suggest direct silk spray as an alternate method of inoculation because it mimics the natural method of disease infection. Testing the relative efficiency of different inoculation techniques and inoculum concentration on QTL detection can improve the efficiency of resistance screening and optimize selection.

When considering marker assisted selection, the genotyping platform determines the cost effectiveness and feasibility for routine application in a breeding program. KASP (competitive allele specific PCR) assay has been one of the most preferred genotyping methods in cereal breeding. The assay utilizes a novel, homogeneous, fluorescence-based reporting system to detect SNPs and small InDels. KASP can be scaled from 96 to 1536 – well plates and can be applicable in small and large capacity breeding programs.

DON is commonly glycosylated by plant hosts into deoxynivalenol-3-glucoside (DON-3G) as part of a defense mechanism to detoxify and sequester mycotoxins. A recent study by our group surveyed the incidence and ratio of DON-3G to DON in Canadian corn inbreds. The results showed that the level of disease severity was positively correlated with DON accumulation and negatively correlated with DON-3G:DON molar ratio (means ranging from 3.1 to 19.7%). GER resistant genotypes had relatively lower total DON content and higher DON-3G:DON ratios. Genes responsible for DON glycosylation have been identified in barley and wheat, but not in corn. QTL mapping for high DON-3G:DON ratio will identify candidate genes responsible for DON glycosylation. With the current study, the relationship between GER disease severity and DON can be verified and QTLs co-localized for the two traits can be used in marker assisted selection for low GER disease severity and DON content.

External Funding Partners: