Nature Communications<\/a>, provide the clearest genetic explanation yet for how major stem rust outbreaks emerge.<\/p>\n
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\n ![\"A](\"https:\/\/www.newsbeep.com\/au\/wp-content\/uploads\/2026\/02\/1771836314_372_Stem_rust_close_up.jpg\")
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\n Stem rust, also known as cereal rust, black rust, red rust or red dust, is caused by the fungus Puccinia graminis.
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Using advances in long-read DNA sequencing and chromosome-level genome assembly, the research team reconstructed complete, phased genomes for the two stem rust strains behind these outbreaks. What they found was striking. Neither strain was, in fact, a descendant of Ug99. Nor were they closely related to each other. Instead, each had emerged independently, shaped by its own evolutionary path.<\/p>\n
\u201cWe elucidated the origin of Ug99 back in 2019,\u201d said Dr Melania Figueroa, Principal Research Scientist at CSIRO.<\/p>\n
\u201cThe origin of these new strains is driven by different genetic changes in the pathogen.\u201d<\/p>\n
Understanding where these outbreaks came from \u2013 and why resistance broke down \u2013 has been one of the biggest unanswered questions in crop disease research.<\/p>\n
Now, CSIRO researchers together with international collaborators have uncovered a crucial part of the answer by reading the pathogen\u2019s genome in unprecedented detail.<\/p>\n
\u201cThis disease can decimate wheat fields,\u201d Dr Figueroa said. \u201cWhen outbreaks occur, it\u2019s not enough to know that resistance has failed \u2013 we need to understand how and why it happened, at the molecular level.\u201d<\/p>\n
A molecular alarm system<\/p>\n
Wheat stem rust is caused by a fungus that infects plants by secreting proteins during infection. Dr Peter Dodds, Chief Research Scientist at CSIRO and co-lead of the project, explained that in resistant wheat varieties, specific resistance genes act as molecular sentinels, detecting those proteins and triggering a defence response before the disease can take hold, saving the plant.<\/p>\n
\u201cPlants don\u2019t have immune systems like humans, but the principle is very similar,\u201d Dr Dodds said. \u201cJust as vaccines help our bodies recognise disease, resistance genes allow plants to recognise a pathogen early and respond.\u201d<\/p>\n
The challenge is that pathogens evolve. Small genetic changes can alter the fungal proteins enough to escape recognition. When that happens, resistance that once worked in farmers\u2019 fields can suddenly fail.<\/p>\n
\u201cThat\u2019s when you see outbreaks or epidemics,\u201d he said. \u201cThe pathogen has effectively learned how to slip past the plant\u2019s defences.\u201d<\/p>\n
Cracking a complex genome<\/p>\n
Tracing those changes has long been difficult. The wheat stem rust fungus carries two separate genomes within each cell, making it challenging to link genetic variation to real-world disease outcomes.<\/p>\n
Recent advances in genomics have changed that. By resolving and assembling each genome separately \u2013 down to individual chromosomes \u2013 the researchers were able to pinpoint variation in a small but critical set of avirulence genes. These genes determine whether a wheat plant recognises the pathogen and triggers a defence response, or remains vulnerable to infection.<\/p>\n
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\n ![\"A](\"https:\/\/www.newsbeep.com\/au\/wp-content\/uploads\/2026\/02\/1771836315_542_CERC-Postdoctoral-Fellow-Dr-Camilla-Langlands-Perry.jpg\")
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\n CERC Postdoctoral Fellow Dr Camilla Langlands-Perry, one of the first authors of the publication, holds a petri dish while cloning an avirulence gene from stem rust at the CSIRO Black Mountain
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\nMelania Figueroa
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The team then tested how dozens of avirulence gene variants behaved in the lab, creating what is now the most comprehensive atlas of these genes for any rust species.<\/p>\n
\u201cFor the first time, we have a clear set of genes to watch if we want to understand how stem rust causes epidemics,\u201d Dr Dodds said. \u201cThat gives us a powerful new way to connect genetics to what\u2019s happening in the field.\u201d<\/p>\n
The past and future of stem rust epidemics<\/p>\n
One of the clearest insights explains the 2016 outbreak in Italy. The strain responsible carried a complete deletion of a single avirulence gene, allowing it to infect durum wheat varieties that relied on a specific resistance gene.<\/p>\n
\u201cThat one genetic change effectively switched off the plant\u2019s alarm system,\u201d Dr Figueroa said. \u201cOnce you see it in the genome, the outbreak suddenly makes sense.\u201d<\/p>\n
Just as importantly, the atlas highlights resistance genes that may prove more durable. One resistance target was recognised by every strain analysed, meaning the pathogen would need two independent genetic changes to overcome it \u2013 a much higher evolutionary hurdle.<\/p>\n
\u201cThat kind of information helps us make smarter choices about which resistance genes to deploy,\u201d she said. \u201cIt\u2019s about staying ahead of the pathogen, not constantly catching up.\u201d<\/p>\n
How genomics can make wheat defences last<\/p>\n
Beyond breeding, the work has major implications for disease surveillance. Traditional monitoring relies on observing how fungal samples behave on a limited set of wheat lines. While effective, that approach can miss deeper genetic changes, particularly when different genomes combine within a single strain.<\/p>\n
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\n Image of protoplast cells isolated from wheat to test recognition of avirulence proteins secreted by stem rust.
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Sequence-based surveillance offers a way forward.<\/p>\n
\u201cIf we know which genes matter most, we can monitor how they\u2019re changing over time,\u201d Dr Dodds said. \u201cThat allows us to anticipate risk, rather than responding only once an epidemic is underway.\u201d<\/p>\n
In Australia, genetic resistance to cereal rusts \u2013 including stem rust \u2013 is estimated to save the national economy about $1.09 billion a year, highlighting the scale of potential losses should new, more virulent strains take hold. Because recent epidemic-forming strains are not descendants of Ug99 and have emerged independently, their impact could be greater or faster than expected for Ug99 \u2013 a strain Australia has prepared against for years.<\/p>\n
Because the stem rust strains studied are not present in Australia, the work relied on long-standing international partnerships and specialised biosecurity facilities overseas.<\/p>\n
The research brought together CSIRO scientists with collaborators in the United States and the United Kingdom, supported by a mix of public and philanthropic funding from Australia, the US and the UK, including Australia\u2019s Grains Research and Development Corporation (GRDC). This collaborative approach also supported the training of early-career researchers in Australia, USA and UK.<\/p>\n
Solving one of crop science\u2019s hardest puzzles<\/p>\n
For Dr Figueroa, the study represents the culmination of years of work to decode some of the most complex genomes in plant pathology.<\/p>\n
\u201cSolving rust genomes has been a long journey,\u201d she said. \u201cIt was like unlocking a book where the answers and secrets were written \u2013 but we couldn\u2019t read the language.\u201d<\/p>\n
\u201cNow we can,\u201d she said. \u201cAnd we\u2019re finally seeing the benefits of all the effort, from the people who built the tools to the teams who contributed along the way.\u201d<\/p>\n
Extending genomic surveillance beyond wheat rust<\/p>\n
The approach demonstrated in this research can now be applied to other high-risk crop pathogens. Dr Figueroa and her team are working to leverage these advances to strengthen Australia\u2019s preparedness for future disease threats.<\/p>\n
\u201cThis work shows we\u2019re ready,\u201d Dr Figueroa said. \u201cWe can deploy this technology, make informed decisions, and help protect agriculture.\u201d<\/p>\n
In an era of increasing disease pressure and global movement, that readiness may be just as important as resistance itself.<\/p>\n
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<\/p>\n","protected":false},"excerpt":{"rendered":"
By\u00a0
Smriti Daniel
23 February 2026
6 min read
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