# Allelic variation of Avr genes in highly virulent strains explains severe wheat stem rust epidemics

## TL;DR

Researchers identified genetic changes in wheat stem rust fungi that explain recent severe outbreaks and provide tools for tracking the disease.

## Contribution

The study provides a detailed Avr gene atlas for Pgt strains ETH2013-1 and ITA2018-1, revealing allelic variations linked to virulence and epidemic outbreaks.

## Key findings

- ETH2013-1 and ITA2018-1 have unique nuclear haplotypes unrelated to Ug99 and Pgt21.
- Variation in Avr genes and AvrSr33 explains virulence phenotypes and outbreaks of TTRTF.
- ITA2018-1 lacks AvrSr13, enabling virulence on durum wheat cultivars with Sr13b.

## 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.

Here the authors present a compendium of avirulence genotypes for epidemiologically significant strains of wheat stem rust based on nuclear phased genome assemblies and functional assays to inform resistance gene deployment and pathogen surveillance.