Researchers at the Centre for Crop and Disease Management (CCDM) have developed a new system that combines spore trapping with advanced DNA sequencing to confirm fungicide resistance from air samples containing airborne spores.
The integrated approach offers the grains industry a powerful new tool to track resistance and better understand how crop diseases and their resistance to fungicides are evolving across Australian paddocks — a major challenge for growers across the country.
At the centre of the system is a device the size of chocolate bar – a portable DNA sequencer, known as the MinION, which can analyse pathogen genetics in real time.
Researcher Dr Katherine Zulak said the technology allowed scientists to go beyond simply confirming resistance, enabling them to examine entire genes and detect complex mutation patterns.
“With the new sequencing technology, we can read the entire fungicide target gene, which means we can detect new or multiple mutations and get a much clearer understanding of their potential impact in the paddock and how resistance is evolving,” Dr Zulak said.
“Resistance monitoring has traditionally relied on collecting infected plant samples and analysing them in labs, which is effective but time-consuming and is limited by when and where samples are collected.
“If we can monitor which mutations are present in air samples containing spores, we can better understand where resistance is occurring across the landscape and also better characterise these specific sites and their infection sources.”
CCDM fungicide resistance expert Associate Professor Fran Lopez-Ruiz said the breakthrough emerged by combining established sampling tools with advanced molecular diagnostics into a single system.
“Spore traps have been used for years to monitor pathogen spread, but what is new is how we analyse those samples,” Associate Professor Lopez-Ruiz said.
“By bringing together two proven technologies, we’ve created a smarter monitoring system that can complement existing resistance surveillance efforts.
“It’s about giving the grains industry accurate, up-to-date information on which to base decisions about fungicide use and broader disease management strategies.”
The system has already demonstrated its capability by detecting complex resistance mutations from samples of airborne spores, including cases where pathogens carry multiple mutations linked to resistance and reduced fungicide sensitivity.
Field trials are now underway in Western Australia, Victoria and South Australia, where researchers are collecting air samples throughout the growing season using different types of spore traps.
Combined with traditional sampling methods, the data will allow researchers to map where resistance is emerging and track how it spreads across regions.
Monitoring results will be shared with industry through CCDM’s Pesticide Resistance Integrated Mapping tool, providing growers and agronomists with timely updates and guidance.
CCDM Director Professor Mark Gibberd said the research highlighted how integrating new technologies was transforming crop protection.
“By combining continuous environmental sampling with high-resolution sequencing, we’re developing smarter systems to monitor resistance more effectively,” Professor Gibberd said.
“This approach provides a more complete picture of what’s happening in Australian paddocks and supports efforts to protect crop productivity while ensuring the long-term sustainability of fungicides.”
CCDM is a national research centre co-supported by Curtin and the Grains Research and Development Corporation, with the work delivered in collaboration with research partners NIAB (UK), TEAGASC (Ireland), INRAE (France), Wageningen University & Research (Netherlands) and the University of Warmia and Mazury (Poland).