A prompt-moving wheat stem rust outbreak in Sicily in 2016 and a severe epidemic in Ethiopia between November 2013 and January 2014, initially appeared to be linked to the highly virulent Ug99 strain that has threatened global food security since the late 1990s. However, new genomic research reveals these outbreaks stemmed from independently evolved strains, challenging existing disease tracking methods and highlighting the pathogen’s rapid adaptive capacity.
The findings, published in Nature Communications, detail the complete reconstruction of the genomes of the stem rust strains responsible for the outbreaks in Ethiopia and Italy. Researchers at CSIRO, in collaboration with international partners, discovered neither strain was a descendant of Ug99, nor closely related to each other. This indicates the emergence of new threats through distinct evolutionary pathways.
“We elucidated the origin of Ug99 back in 2019,” said Dr. Melania Figueroa, Principal Research Scientist at CSIRO. “The origin of these new strains is driven by different genetic changes in the pathogen.”
Wheat stem rust, caused by the fungus Puccinia graminis, can cause near-total crop loss, as seen in Ethiopia in 2013-2014 where the widely grown wheat cultivar ‘Digalu’ experienced yield losses approaching 100%, according to a 2015 study published in PubMed.
The research team’s breakthrough involved resolving and assembling the complex wheat stem rust genome – which carries two separate genomes within each cell – down to the individual chromosome level. This allowed them to pinpoint variations in a critical set of avirulence genes. These genes determine whether a wheat plant recognizes the pathogen and mounts a defense, or remains vulnerable.
Dr. Peter Dodds, Chief Research Scientist at CSIRO and co-lead of the project, explained that resistant wheat varieties rely on these resistance genes to act as “molecular sentinels,” detecting proteins secreted by the fungus during infection. “Plants don’t have immune systems like humans, but the principle is very similar,” he said. “Just as vaccines help our bodies recognise disease, resistance genes allow plants to recognise a pathogen early and respond.”
The team created a comprehensive atlas of avirulence genes for the rust species, testing how dozens of variants behaved in the lab. This atlas revealed that a complete deletion of a single avirulence gene in the Italian outbreak strain allowed it to infect durum wheat varieties that previously relied on a specific resistance gene. “That one genetic change effectively switched off the plant’s alarm system,” Dr. Figueroa said. “Once you see it in the genome, the outbreak suddenly makes sense.”
The research also identified resistance genes that may offer more durable protection. One target was recognized by every strain analyzed, suggesting the pathogen would require two independent genetic changes to overcome it – a significantly higher evolutionary hurdle. “That kind of information helps us make smarter choices about which resistance genes to deploy,” Dr. Figueroa added. “It’s about staying ahead of the pathogen, not constantly catching up.”
Beyond breeding, the genomic approach has implications for disease surveillance. Traditional monitoring relies on observing fungal samples on a limited set of wheat lines, potentially missing subtle genetic changes. Sequence-based surveillance, by focusing on key genes, offers a more proactive approach. “If we know which genes matter most, we can monitor how they’re changing over time,” Dr. Dodds said. “That allows us to anticipate risk, rather than responding only once an epidemic is underway.”
In Australia, genetic resistance to cereal rusts is estimated to save the national economy approximately $1.09 billion annually, underscoring the potential economic impact of new, virulent strains. The research, supported by the Grains Research and Development Corporation (GRDC) and international funding, involved collaboration between CSIRO scientists and researchers in the United States and the United Kingdom.
The Stakman-Borlaug Center (SBC) for Sustainable Plant Improvement at the University of Minnesota has been involved in collaborative research and education to combat wheat stem rust in Ethiopia since 2014, following the 2013 and 2014 epidemics. The center aims to provide Ethiopian scientists and farmers with the tools and knowledge needed to combat the disease.
Dr. Figueroa emphasized the significance of the breakthrough, stating, “Solving rust genomes has been a long journey… Now we can, and we’re finally seeing the benefits of all the effort.” The team is now applying these advances to other crop pathogens, aiming to strengthen Australia’s preparedness for future disease threats.
