New study reveals how wheat stem rust overcomes genetic resistance

Wheat stem rust

Niab is part of an international research team, led by Prof Melania Figueroa of the Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia, that has created a detailed map of avirulence (Avr) genes in wheat stem rust – the fungal disease responsible for some of the most damaging wheat epidemics worldwide. The study shows how changes in these pathogen genes can allow new strains to infect wheat varieties that were previously protected by resistance genes.

Wheat stem rust is caused by the fungus Puccinia graminis f. sp. tritici (Pgt). It remains a major threat to global wheat production because new races can appear suddenly and bypass resistance genes (Sr genes) that breeders have deployed in wheat. Understanding exactly how this resistance breakdown happens is essential for faster surveillance and for breeding wheat with longer-lasting protection.

In a paper published in Nature Communications, the researchers generated high-quality, chromosome-scale genome references for two Pgt isolates linked to recent epidemics: ETH2013-1 (race TKTTF, associated with the 2013 Ethiopia outbreak) and ITA2018-1 (race TTRTF, associated with outbreaks in Europe, including Sicily). By resolving the genomes in fine detail, the team was able to identify genetic differences in several known Avr genes and link those differences to whether the pathogen could infect wheat lines carrying the corresponding Sr resistance genes.

A key outcome of the work is an “Avr gene atlas”: a catalogue of Avr gene variants in the pathogen and the specific wheat Sr genes that recognise them. The study also reports a newly identified avirulence gene, AvrSr33, discovered through a high-throughput screen of pathogen effector proteins and then confirmed using multiple experimental approaches.

Niab’s contribution (Drs Jibril Lubega and Kostya Kanyuka) focused on rapid functional validation directly in wheat. Using a virus-based delivery method, the team expressed candidate Avr effector proteins in whole wheat plants using a barley stripe mosaic virus (BSMV) overexpression system (VOX). This helped confirm that AvrSr33 is recognised in wheat and supported validation of additional Pgt Avr effectors against their corresponding wheat Sr genes. Such functional testing is a critical step in turning genome data into practical tools for monitoring pathogen populations and supporting resistance breeding.

“Being able to test effector recognition directly in wheat is crucial for translating genome discoveries into practical disease resistance strategies,” said Dr Kostya Kanyuka (Niab). “Our BSMV VOX assays helped validate AvrSr33 in the host plant and confirm recognition patterns for multiple effectors, supporting efforts to stay ahead of emerging stem rust races.”

Overall, the findings help explain real-world epidemic outbreak patterns, for example, how the loss or alteration of a particular Avr gene can enable a new rust race to infect wheat varieties that carry previously effective resistance. The Avr gene atlas also lays groundwork for sequence-based diagnostics, which could strengthen and speed up pathogen surveillance and guide the deployment of more durable resistance in wheat breeding programmes.

Read the paper