In 2024, CRDC launched the Australian Cotton Disease Collaboration (ACDC), a groundbreaking $13 million research, development and extension (RD&E) program.
This ambitious initiative has brought many aspects of disease research under one major project to provide a comprehensive RD&E effort, previously not seen in the industry.
ACDC's primary goal is to reduce the economic impact of current and emerging diseases to less than five per cent of the cost of production. Projects are now underway across four key research areas - systems-based disease control packages, understanding pathogen behaviour, spatial data analytics and advanced modelling, and improving understanding of fungicides and mediators of plant defence. These four areas involve a varied team of specialist researchers.
Managing disease effectively means growers understand the impact of their farming system on disease development and severity and have access to rapid and accurate diagnostics, and that researchers have improved knowledge of pathogen behaviour and diversity and can create more efficient means of detecting diseases in in the field.
With the formation of the ACDC, CRDC has established long-term strategic partnerships with the University of Southern Queensland (UniSQ), led by ACDC Director, Associate Professor Sam Periyannan, and Qld DPI, led by senior cotton industry pathologist and ACDC Deputy Director, Associate Professor Linda Smith.
Diseases are ranked into two tiers. Tier 1 diseases include Fusarium wilt, Verticillium wilt, black root rot and Alternaria leaf spot. Tier 2 diseases are any other emerging or existing diseases, such as reoccurring wilt.
"Diseases such as Verticillium, black root rot and Fusarium are having a huge impact on our industry," CRDC Senior Innovation Broker Susan Maas said.
"It is really exciting to see the first projects starting - translating the strategic vision of ACDC into on ground research.
"We are also building collaborations with CottonInfo and other research providers and will look to host a disease symposium later this year to support industry coordination and collaboration on this critical issue."
Systems approach
The ACDC will have a number of field studies this season to better understand disease in the farming system context.
Qld DPI senior plant pathologist Linda Scheikowski is investigating the impact of irrigation and nutrition management on cotton wilt disease incidence. While irrigation and nutrition management is known to have a large impact on wilt diseases, the evidence for this is anecdotal in Australia. Linda is working with UniSQ's irrigation and water management researcher Associate Professor Joseph Foley.
"We want to quantify the impacts of Verticillium and Fusarium wilts and incorporate this knowledge into grower management recommendations for irrigation and nutrition," Linda said.
"This will contribute to reduced yield loss through understanding improved wilt management options, increased water use efficiency when irrigating with a higher soil water deficit, and increased profit through reduced fertiliser application and reduced disease incidence."
Linda is also investigating how post-harvest cotton residue/trash impacts inoculum carryover, as the pathogens that cause Verticillium, Fusarium, and Eutypella wilts can survive in cotton residues. Post-harvest management is therefore crucial to disease management.
"Currently, there is no clear understanding of the contribution these crop residues have on inoculum build-up and disease," Linda says.
"To understand the persistence of pathogens on cotton trash after various levels of decomposition, molecular methods to quantify the pathogens are required.
"We are currently reviewing past research to identify suitable methodologies to quantify pathogens in cotton residues and scoping potential project partners with specialist skills to quantify levels of pathogen inoculum."
AI for wilt identification
In this project machine vision systems will be developed to detect and differentiate Verticillium and Fusarium wilts. Identifying wilt pathogens is of increasing importance as more fields are being found to have both pathogens present, yet diagnosing them in a field is still manual, time consuming and requires sound identification skills. Furthermore, the disease is not detected until symptoms are clearly visible and management options, particularly post-harvest are quite different.
Researchers have therefore looked to machine vision sensing to differentiate wilts and predict severity before visual symptoms show. The project is being undertaken with Associate Professor Alison McCarthy from UniSQ's Centre for Agricultural Engineering, who is undertaking a separate project with support from CRDC into sensing, machine learning and artificial intelligence.
This will enable field mapping to identify predicted high disease areas, assisting growers to make decisions around farming practices, such as nutrition and irrigation management to manage these diseases.
Diagnostics under the microscope
Rapid and accurate diagnostic capability is a key aspect of disease control.
"This goes hand in hand with support for growers and their consultants," Qld DPI plant pathologist Dr Dinesh Kafle said.
"Modern, rapid molecular diagnostics are being developed and validated for all major soil-borne and leafspot pathogens affecting Australian cotton production (including the new production regions in northern Australia) to reduce the time for accurate disease diagnostics and increase the effectiveness of disease management strategies."
Isolates of various pathogens will be stored and pathogenicity assays will be conducted to confirm new and emerging pathogens. The isolates will be available for future genetic diversity studies, pathogenicity tests and population genetics studies.
Dinesh will also look into novel methods of disease detection. Spore trapping in collaboration with the South Australian Research and Development Institute (SARDI) is being investigated as a tool for detecting leaf spot pathogens of cotton and the novel Eutypella species which cause reoccurring wilt.
"Spore trapping is used to capture airborne spores, primarily for monitoring and detecting fungal diseases in crops, allowing for early intervention and preventative measures," Dinesh said.
Through the ACDC, a national collection of all pathogens of cotton in Australia is being established. This collection is crucial for understanding the evolution and spread of existing and new pathogenic strains and for screening cotton germplasm for broad-spectrum disease resistance.
Led by UniSQ's Dr Cassy Percy, the collection will provide valuable resources for creating reference genomes to identify strain-specific diagnostic markers for rapid disease surveillance, understanding pathogen population dynamics and the evolution of new strains.
Cassy is also overseeing the collection of plant varieties or other host organisms with known resistance or susceptibility profiles to different strains or races of a specific pathogen. This information is not currently available for all key pathogens, and information on the host range of cotton pathogens is incomplete.
"This information is crucial for identifying and characterising unknown pathogen strains, understanding their virulence patterns and developing effective disease management strategies," Cassy said.
"It will improve the capacity to develop resistant cultivars and phenotype key pathogens and Australian cotton growers will benefit from tactical disease management strategies developed in this project."
CottonInfo links R&D to growers and consultants
CottonInfo are supporting and working closely with the ACDC to ensure that the science being conducted by researchers is effectively extended to growers. To help achieve this, they are providing a regional perspective of disease issues, facilitating the collection of samples to support research into changes in pathogenicity, and continuing on-farm trials to investigate potential management practices that may reduce disease incidence and severity.
"Disease is one of our highest priorities this season, with activity delivered by CottonInfo Biosecurity and Disease Technical Lead Sharna Holman and our Regional Extension Officers (REOs)," says CottonInfo Program Manager Janelle Montgomery.
"Our REOs are undertaking different on-farm trials, with some already underway.
"In the Namoi, REOs Bob Ford and Blake Palmer have developed on-farm farming systems trials in collaboration with local growers to assess the effect of different practices and rotations on Verticillium wilt, while in the Gwydir, REO Greg Bramley will have a trial to better understand how different soil ameliorants and the biological product Sero-X impact this disease."
The CottonInfo team will work with crop managers to ensure high-quality disease samples are submitted for diagnostics. The benefits are two-fold as correct identification supports a grower's decision-making and appropriate management, and the samples contribute to the ACDC-curated reference collection and support the detection of shifts in pathogenicity over the long-term.
"Taking high-quality samples for diagnostics is essential because it enables researchers to accurately isolate the pathogen of concern," Sharna said.
"This information, which is provided back to growers and consultants, enables them to make informed management decisions which can vary depending on the disease, particularly for post-harvest management and non-host rotation crops.
"The CottonInfo team will use a mix of approaches to help ensure disease research information gets out to growers and the industry, including the updating of CottonInfo's online resources, regionally-focused newsletters and local face-to-face meetings.
"We also recognise there are lots of disease research activities underway such as the Cotton Seed Distributors' (CSD) Richard Williams Commercial Research Initiative which is working with Crown Analytical Services. As well as collaborating on regional extension, CottonInfo will bring organisations together in October to further this collaboration and coordination."
Addressing issues as they arise is also a core remit for the ACDC and CottonInfo, according to CRDC Senior Innovation Broker Susan Maas.
"CottonInfo really boosts the capacity of the ACDC to stay connected to regional disease issues and considerations and in getting timely advice out," she said.
"For example, in early September, based on enquiries about boll rot, Central Qld REO Tami Buranda organised a visit from Qld DPI scientists to meet with growers and consultants.
"The REOs are also running trials with growers, which means they get to see the results first-hand in relation to problems the growers themselves have highlighted - results they can then share with other growers in their valleys.
"We are also going to build on past and ongoing research to get to the heart of long-standing issues such as black root rot for southern growers.
"This will involve working with Southern Valleys REO Kieran O'Keeffe, Macquarie REO Rochelle Field and local agronomists so we can combine practical, current, on-the-ground knowledge with academic pathology.
"We know it is important to have capacity in the south to manage black root rot and the ACDC is in process of contracting a southern focused disease project."
CottonInfo is developing a suite of practical, ready-to-use resources focused on the industry's key diseases of concern to highlight where research is currently underway in different ACDC projects. They are also sharing current best management practices to reduce the incidence and severity of cotton diseases. Most recently, CottonInfo hosted a disease webinar to update growers and consultants on the projects and research trials planned for this season. Growers and consultants that missed the webinar can catch up online.
This article first appeared in the Spring 2025 edition of CRDC's Spotlight magazine.
