In 2013, farmers in the Ethiopian highlands began to notice something disturbing. Well-known varieties of wheat are failing in an unfamiliar way.

Stems weaken, plants fall, and fields that once held up well to disease suddenly become vulnerable. Three years later, the same fears surfaced thousands of miles away, when Sicily’s wheat crops (including a prized durum variety made for pasta) were succumbed to an outbreak of a rapidly aggressive stem rust that baffled local farmers.

At first glance, these outbreaks seemed like echoes of known threats. Since the late 1990s, a highly virulent wheat stem rust strain known as Ug99 has threatened global food security, and its spread has been closely tracked by scientists and surveillance networks. But when researchers looked more closely at what happened in Ethiopia and Italy, things started to change.

The results of the survey were recently published nature communications provides the clearest genetic explanation to date of how large-scale stem rust outbreaks occur.

The research team used advances in long-read DNA sequencing and chromosome-level genome assembly to reconstruct the complete step-by-step genomes of the two stem rust strains behind these outbreaks. What they discovered was surprising. In fact, neither strain was a descendant of Ug99. Nor were they closely related to each other. Instead, each emerged independently, shaped by its own evolutionary path.

“We uncovered the origin of Ug99 in 2019,” said CSIRO Principal Scientist Dr Melania Figueroa.

“The origin of these new strains is caused by different genetic changes in the pathogen.”

Understanding where these outbreaks come from and why resistance breaks down is one of the biggest unanswered questions in crop disease research.

Now, CSIRO researchers, working with international collaborators, have uncovered a key part of the answer by reading the pathogen’s genome in unprecedented detail.

“This disease can devastate wheat fields,” Dr. Figueroa said. “When an outbreak occurs, it’s not enough to know that resistance has failed; we need to understand at the molecular level how and why it happened.”

molecular alarm system

Wheat rust is caused by a fungus that infects plants by secreting proteins during infection. Dr Peter Dodds, CSIRO’s principal investigator and project co-lead, explained that in resistant wheat varieties, specific resistance genes act as molecular sentinels, detecting these proteins before the disease spreads and triggering a defense response to save the plant.

“Plants don’t have immune systems like humans, but the principles are very similar,” Dodds says. “Just as vaccines help our bodies recognize diseases, resistance genes allow plants to recognize and respond to pathogens early.”

The challenge is that pathogens evolve. Small genetic changes can alter fungal proteins enough to escape recognition. If this happens, the resistance that has been working in farmers’ fields may suddenly stop working.

“That’s when you see outbreaks and epidemics,” he says. “The pathogen has effectively learned how to bypass the plant’s defenses.”

Deciphering complex genomes

Tracking these changes has long been difficult. The wheat stalk rust fungus maintains two separate genomes within each cell, making it difficult to link genetic variation to real-world disease outcomes.

Recent advances in genomics have changed the situation. By analyzing and assembling each genome individually down to its individual chromosomes, the researchers were able to pinpoint mutations in a small but important set of nontoxic genes. These genes determine whether the wheat plant recognizes the pathogen and mounts a defense response, or remains vulnerable to infection.

The team then tested how dozens of avirulent gene variants behaved in the lab, creating what is now the most comprehensive atlas of these genes for any rust species.

“For the first time, we have a clear set of genes to look at if we want to understand how stem rust causes epidemics,” Dr. Dodds said. “This gives us a powerful new way to connect genetics to what’s happening in the field.”

Past and future of stem rust epidemics

One of the clearest insights describes the 2016 outbreak in Italy. The causative strain completely lacked a single avirulence gene, allowing it to infect durum wheat varieties that depended on specific resistance genes.

“That one genetic change effectively turned off the plant’s alarm system,” Dr. Figueroa said. “Once you see that in the genome, this epidemic suddenly makes sense.”

Equally important, the atlas highlights resistance genes that may prove more durable. One resistance target was recognized in all analyzed strains. This means that two independent genetic changes are required for the pathogen to overcome it. This poses a much higher evolutionary hurdle.

“Such information can help us make smarter choices about which resistance genes to introduce,” she said. “It’s about staying ahead of the pathogen, not always trying to catch up.”

How genomics can sustain wheat defenses

This research has great implications beyond breeding and disease monitoring. Traditional monitoring relies on observing how fungal samples behave on a limited number of wheat accessions. Although effective, this approach can miss deeper genetic changes, especially when different genomes are combined within a single strain.

Sequence-based monitoring offers a way forward.

“Once we know which genes are most important, we can monitor how they change over time,” Dr. Dodds said. “This allows us to anticipate risks rather than only reacting after an outbreak begins.”

In Australia, genetic resistance to cereal rust (including stem rust) is estimated to save the national economy around $1.09 billion a year, highlighting the potential scale of losses if new, more virulent strains become established. Because the strain forming the recent outbreak is not a descendant of Ug99 and emerged independently, its impact may be greater or faster than expected for Ug99, which Australia has been preparing for this strain for many years.

The stem rust strains studied do not exist in Australia, so the research relied on long-standing international partnerships and specialist biosecurity facilities overseas.

The research brought together CSIRO scientists and US and UK collaborators, with support from a combination of public and philanthropic funding from Australia, the US and the UK, including the Australian Grain Research and Development Corporation (GRDC). This collaborative approach has also supported the training of junior researchers in Australia, the US and the UK.

Solving one of crop science’s most difficult puzzles

For Dr. Figueroa, this study marks the culmination of years of work to decipher some of the most complex genomes in plant pathology.

“Unraveling the rust genome has been a long journey,” she says. “It was like unlocking a book with answers and secrets. But we couldn’t read the language.”

“You can do it now,” she said. “And we’re finally seeing the fruits of all that hard work, from the people who built the tools to the teams who contributed along the way.”

Expanding genomic surveillance beyond wheat rust

The approach demonstrated in this study can now be applied to other high-risk crop pathogens. Dr Figueroa and her team are working to leverage these advances to strengthen Australia’s preparedness for future disease threats.

“This study shows we are ready,” Dr. Figueroa said. “We can deploy this technology to make informed decisions and protect agriculture.”

In an era of increasing disease pressure and global movement, preparedness may be as important as resistance itself.