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An examination of stripe rust-winter wheat pathosystem in Ontario to improve genetic gain in breeding programs

An examination of stripe rust-winter wheat pathosystem in Ontario to improve genetic gain in breeding programs

Principal Investigator: K Peter Pauls and Ali Navabi

Research Institution: University of Guelph

Timeline: April 2017 – March 2020


  • Monitor the spread of the stripe rust pathogen (Puccinia striiformis) and characterize the races of stripe rust found in Ontario over the course of the project.
  • Study the symptoms of stripe rust in seedling and adult plant stages in a winter wheat breeding population and a winter wheat diversity panel.
  • Conduct a genome-wide search for stripe rust resistance genes in winter wheat.
  • Develop new molecular marker breeding tools as breeder-friendly assays to improve selection for rust resistance genes in breeding and to use these tools in pyramiding resistance to rusts with tolerance against Fusarium head blight (FHB) in wheat.
  • Understand the mechanisms at the molecular level, by which the wheat plant can defeat the attack by the pathogen.


  • The information obtained about the incidence and timing of stripe rust in wheat can be used by growers to choose appropriate disease management solutions. In particular, the finding that most of the commercial wheat cultivars in Ontario are susceptible to stripe rust at the seedling stage could guide producers to apply protective agents to their crops at appropriate stages of development to prevent yield and quality losses from stripe rust outbreaks.
  • The development of new breeding tools, such as molecular markers linked to genes for resistance, may improve the efficiency of selecting lines with resistance to stripe rust and accelerate the development of rust-resistant, high-yielding varieties and may allow breeders to pyramid resistance to multiple diseases such as Fusarium head blight and stripe rust.
  • The introgression of Yr15 seedling resistance into Ontario-adapted winter wheat background, using marker-aided backcrossing, provides interesting germplasm for breeding new rust-resistant wheat lines in the future.
  • The progress in understanding of the molecular mechanism of rust resistance and the genomic locations of resistance genes may ultimately lead to progress in breeding for rust resistance, especially new races.

Scientific Summary:

Stripe rust (caused by Puccinia striiformis) has been spreading to new areas in North America; perhaps because new races of stripe rust in North America are more aggressive and can tolerate higher spring temperatures. This research was designed to address the growing threat from stripe rust by developing a better understanding of the host-pathogen interaction, including: characterization of P. striiformis isolates in Ontario, identification of new sources of resistance to the disease in wheat, and development of molecular markers linked to disease resistance genes to enable breeders to select resistant varieties, even in the absence of disease.

To monitor the spread and virulence pattern of P. striiformis in Ontario, stripe rust-infected plant tissue samples were collected or received from 15 locations in Ontario from mid-May till mid-August. Stripe rust urediniospores from 11 isolates were harvested, purified, multiplied, and tested on a set of wheat stripe rust differential lines at 1-2 leaf stage to identify stripe rust races. The results indicate that the stripe rust races in ON are similar to central and eastern regions of the United States and that the resistance genes Yr1, 5, 10, 15, (24), 26, 28, and (Sp) are still effective in southwest Ontario.

To characterize the phenotypic and genotypic variation in stripe rust resistance in Canadian winter wheat, a Canadian Winter Wheat Diversity Panel (CWWDP; n= 430), which represents the diversity of winter wheat genotypes developed in various regions and different times in Canada, was evaluated for response to a typical Ontario stripe rust isolate in seedling and adult plant stages. The results indicate that, except for the variety Priesley, all Ontario commercial winter wheat varieties are susceptible at the seedling stage, but ~50% of the commercial varieties carry an acceptable level of adult plant resistance. Using SNP markers and a genome-wide association study (GWAS), one adult plant resistant locus on chromosome 3B was identified. The associated locus (at SNP marker RAC875_c3956_659) decreased stripe rust severity by 30% in the field. Further analysis of the chromosomal region linked to this marker identified 44 genes. The closest gene to the marker is (TraesCS3B01G063100), which encodes a protease inhibitor/seed storage/ lipid transfer protein (LTP), which is a member of the pathogenesis-related proteins (PRPs) family and represents an interesting candidate gene for adult plant stripe rust resistance in winter wheat.

To gain an understanding of the genetics of resistance to stripe rust in Ontario winter wheat, a bi-parental population (242 lines) from a cross between resistant and susceptible wheat lines (Priesley x Venture) was screened indoors after vernalization as seedlings and mature plants using the UGWYR16001 isolate. The results showed that 42% of the lines didn’t show any symptoms and 58% showed susceptibility (score of 5-7) as seedlings and at the adult stage  52% of the lines didn’t show any symptoms, 7% were resistant, 9% moderately resistant, 23% moderately susceptible and 7% susceptible. These results indicate that Priesley is a valuable source of resistance for seedling and adult resistance to stripe rust.

The seedling resistance gene Yr15, which is originally derived from emmer wheat, has remained effective all across the world. We initiated a crossing block to introgress Yr15 into Ontario-adapted winter wheat background, using marker-aided backcrossing. Avocet+Yr15 was crossed with OAC-SRW-03, OAC Constellation (OAC-SRW-04), Princeton, and Gallus. F1 plants were backcrossed to the elite parents. The second round of backcrossing was performed, and seeds were harvested and have been placed in the cold storage for further development of elite wheat lines with resistance to rust at the seedling level.

This project also provided an opportunity to access additional funding through SOSCIP to conduct research on the molecular aspects of resistance against stripe rust and FHB. For this work, two near-isogenic lines Avocet-S (Susceptible) and Avocet+Yr15 (carrying the Yr15 seedling resistance gene) plants were grown in greenhouse conditions and were inoculated at the seedling stage. Mock and infected leaves were sampled at four-day post-inoculation. High-quality RNA samples were prepared and sent to a sequencing company to obtain RNA-seq data. In addition, several infection trials and accompanying microscopic analyses were conducted, including DAB staining to detect defense-associated hydrogen peroxide molecules, epi-fluorescence microscopy for detecting cell wall fortifications, and bright field microscopy for detecting HR reaction. The results indicate that Avocet+Yr15 plants carry a unique form of resistance, characterized by a non-hypersensitive response to stripe rust isolate UGWYr16001.

The project progressed, as planned, with no major issues. The information obtained about the stripe rust pathosystem, the molecular markers that were developed, as well as the germplasm that was developed will be useful to plant breeding programs selecting elite wheat lines with seedling and mature plant stripe rust resistance for Ontario producers. The finding that most of the commercial wheat cultivars in Ontario are susceptible to stripe rust at the seedling stage could guide producers to apply protective agents to their crops at appropriate stages of development to prevent yield and quality losses from stripe rust outbreaks.

External Funding Partners:


Ontario Ministry of Agriculture, Food and Rural Affairs

Southern Ontario Smart Computing Innovation Platform (SOSCIP)

“Computations were performed on the SOSCIP Consortium’s [Blue Gene/Q, Cloud Data Analytics, Agile and/or Large Memory System] computing platform(s). SOSCIP is funded by the Federal Economic Development Agency of Southern Ontario, the Province of Ontario, IBM Canada Ltd., Ontario Centres of Excellence, Mitacs and Ontario academic member institutions”

Ontario Centre of Innovation (at the time of this work the organization was referred to as: Ontario Centres of Excellence (OCE))

OCE is a member of the Ontario Network of Entrepreneurs (“ONE”)

Project Related Publications:

Peer-reviewed publication

  1. Seifi H, Serajazari M, Kaviani M, Pauls P, Booker H and Navabi A (2021). Immunity to stripe rust in wheat: A case study of a hypersensitive response (HR)-independent resistance to Puccinia striiformis f. sp. tritici in Avocet-Yr15, Canadian Journal of Plant Pathology, DOI: 10.1080/07060661.2021.1907448

Conference abstracts, presentations & posters

  1. Serajazari, M., H. Sidhu, J. Follings, N. Wilker, K.P. Pauls and A. Navabi. (2019). A potential QTL on Chromosome 3BS with major effect on adult plant resistance to stripe rust in a Canadian winter wheat diversity panel. Plant Canada conference, Guelph, Ontario, Canada.
  2. Harlow E., Serajazari M., Kaviani M., Navabi A. (2019). A genetic study of resistance against new races of stripe rust in Eastern Canada. Submitted as a poster presentation for 1st International Wheat Congress. Saskatoon, Canada.
  3. Serajazari M., Hilker B., Sing Sidhu H., Follings J. and Navabi A. (2018) Host-pathogen interaction in the winter wheat-stripe rust pathosystem in Ontario. 4th Canadian Wheat Symposium and 9th Canadian Workshop on FHB. Winnipeg Manitoba, Canada.
  4. Seifi H. S., Serajazari M., Kaviani M. and Navabi A. (2018) Yr15-mediated resistance against stripe rust in wheat: Evidence of An Hr-Independent Mechanism. 4th Canadian Wheat Symposium and 9th Canadian Workshop on FHB. Winnipeg Manitoba, Canada.


  1. Elijah Dalton (2018) Stripe Rust Video, submitted to Canadian Phytopathological Society.  Won 2nd prize.
  2. Carolyn King (2019) Preparing for an Emerging Threat, Top Crop Manager in April 2019. An interview about the stripe rust project.