Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics
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.
Authors
- Jibril Lubega
- Taj Arndell (ORCID: https://orcid.org/0000-0002-6540-2006)
- Eric S. Nazareno (ORCID: https://orcid.org/0000-0001-5192-2644)
- Rebecca Spanner (ORCID: https://orcid.org/0000-0002-4735-9649)
- Zhouyang Su (ORCID: https://orcid.org/0000-0003-1270-0429)
- Kanyuka Kostya
- Eva C. Henningsen (ORCID: https://orcid.org/0000-0001-9619-3705)
- Li Chen Cheah (ORCID: https://orcid.org/0000-0002-0072-2885)
- Camilla Langlands-Perry (ORCID: https://orcid.org/0000-0003-2635-6905)
- Megan A. Outram (ORCID: https://orcid.org/0000-0003-4510-3575)
- Nino Virzì (ORCID: https://orcid.org/0000-0003-2502-9259)
- Thomas Vanhercke (ORCID: https://orcid.org/0000-0003-1397-7622)
- Peter N. Dodds (ORCID: https://orcid.org/0000-0003-0620-5923)
- Brian J. Steffenson (ORCID: https://orcid.org/0000-0001-7961-5363)
- Alexis Feist
- Jana Sperschneider
- Oadi Matny
- Jian Chen
- Eric Stone
- David D. Lewis
- Ming Luo
- Michael Ayliffe
- Melania Figueroa
- Feng Li
Institutions
- Australian National University (AU)
- Commonwealth Scientific and Industrial Research Organisation (AU)
- University of Minnesota (US)
- National Institute of Agricultural Botany (GB)
- University of Minnesota, Waseca (US)
- Cereal Research Centre (IT)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-02-13
- DOI
- https://doi.org/10.1038/s41467-026-69508-8
- Primary Topic
- Wheat and Barley Genetics and Pathology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- U.S. Department of Agriculture
- University of Minnesota
- Commonwealth Scientific and Industrial Research Organisation
- Grains Research and Development Corporation
- National Institute of Food and Agriculture
- Biotechnology and Biological Sciences Research Council