Development of a Diagnostic Assay for Differentiation Between Genetic Groups in Clades I, II, III, and IV of Puccinia graminis f. sp. tritici

Les J Szabo, Pablo D. Olivera, Ruth Wanyera, Botma Visser, Yue Jin

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Wheat stem rust has reemerged as a serious disease caused by new variants of Puccinia graminis f. sp. tritici. Variants with significant virulence and broad geographic distribution (Africa, Central Asia, and Europe) include the Ug99 race group, race TTRTF, and TKTTF race group. Genetic analysis has placed isolates representing these critical new virulent races into 12 genetic groups that make up clades I to IV. Development of molecular diagnostic assays for these 12 genetic groups will be an important component of global surveillance efforts. A single-nucleotide polymorphism database was mined for candidate markers that would differentiate between these 12 genetic groups. Thirty-five candidate markers were screened, and a core set of 17 markers was tested against a set of 94 isolates representing a broad range of genotypes and race phenotypes. These core markers were 100% accurate in identifying the 12 genetic groups for 52 isolates in clades I to IV, and no false positives were observed with nontarget isolates. The assay has built-in redundancy so that minor genetic changes or errors in genotyping calling will not affect the accuracy of the results. This assay is also effective in identifying the genetic groups in clade V from Germany and Georgia, the three main subgroups in North American clade VI, and clade VII consisting of race TTTTF found in North and South America. This assay provides a rapid diagnostic tool for both living and nonliving samples to detect these critical new races or race groups of P. graminis f. sp. tritici.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Original languageEnglish (US)
Pages (from-to)2211-2220
Number of pages10
JournalPlant disease
Issue number8
StatePublished - Aug 2022

Bibliographical note

Funding Information:
Funding: This study was financially supported by the U.S. Department of Agriculture Agricultural Research Service, Durable Rust Resistance in Wheat and Delivering Genetic Gain in Wheat projects (grant nos. DRRW-OPPGD1389 and DGGW-OPP1133199), and the Bill and Melinda Gates Foundation and the United Kingdom Foreign, Commonwealth & Development Office.

Publisher Copyright:
© 2022 The Author(s).


  • genotyping
  • surveillance
  • wheat stem rust
  • Basidiomycota/genetics
  • Puccinia
  • Disease Resistance/genetics
  • Plant Diseases/genetics

PubMed: MeSH publication types

  • Journal Article


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