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Updated: Feb 15, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics
Rebecca E Spanner1, Eva C Henningsen2, Camilla Langlands-Perry2
1Department of Plant Pathology, University of Minnesota (UMN), St. Paul, MN, USA.
Abstract:
Wheat stem rust is a disease of global importance caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt). Here we generate chromosome-level, nuclear-phased genome references for Pgt isolates ETH2013-1 and ITA2018-1, representing races TKTTF and TTRTF respectively, that have caused major epidemics in Africa and Europe. The nuclear haplotypes of ETH2013-1 and ITA2018-1 are unique and unrelated to those of Ug99 and Pgt21. Pgt nuclear haplotypes show extensive variation in sequence and copy number of six known Avr genes and AvrSr33, which we identify through an effector gene library screen. Recognition properties of 22 novel Avr gene variants explain the race virulence phenotypes and the outbreak of TTRTF on durum cultivars containing Sr13b, since ITA2018-1 carries a homozygous deletion of AvrSr13. This work establishes an Avr gene atlas for Pgt that can inform wheat breeding and enable development of sequence-based virulence diagnostic tools for pathogen surveillance.
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