Research Projects
The research domains identify focus on industry need to build upon fundamental research historically conducted by the cotton industry and research partners.
Domain A: Systems-based disease control
Domain B: Understanding pathogen behaviour
Domain C: Spatial data analytics and modelling
Domain D: Fungicides and plant defense mediators
The research priortises diseases including:
Tier 1 diseases
Black root rot, Fusarium and Verticillium wilt and Alternaria leaf spot
Tier 2 diseases
Rhizoctonia rot, reoccurring wilt, target spot, grey mould and boll rot
Browse our research projects below and download the ACDC Research Projects Flyer for clear summaries of each project.
Location
Field Sites: North Star (Qld) and Darling Downs (Qld) for field sites
Glasshouse Trials: Toowoomba (Qld)
Researcher locations: Brisbane and Toowoomba
Project Leads
Linda Scheikowski (Qld DPI)
Associate Professor Joseph Foley (UniSQ)
About the project
Impacts of irrigation and nutrition have a huge impact on wilt cotton diseases, but are currently based on anecdotal evidence in Australia. This project aims to quantify the impacts of Verticillium and Fusarium wilt and incorporate this into grower management recommendations.
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.
Location
Brisbane and Toowoomba, Qld
Project Leads
Dr Dinesh Kafle (Qld DPI)
Dr Murray Sharman (Qld DPI)
About the project
In this project, modern rapid molecular diagnostics are being developed and validated for all major soil-borne and leafspot pathogens affecting Australian cotton production (including new production regions in far northern Australia) to reduce the time for accurate disease diagnostics and increase the effectiveness of disease management strategies.
Representative 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.
Location
Brisbane and Toowoomba, Qld
Project Lead
Linda Scheikowski (Qld DPI)
About the project
The pathogens that cause Verticillium, Fusarium, and Eutypella wilts can survive in cotton residues. Currently, there is no clear understanding of the contribution these have on inoculum build-up and disease. To understand the persistence of pathogens on cotton trash after various levels of decomposition, molecular methods to quantify the pathogens are required.
In this project, the literature is being reviewed to identify suitable methodologies to quantify pathogens in cotton residues. Potential project partners with specialist skills to quantify pathogen inoculum in plant residues are also be identified.
Location
Central and northern Queensland for field sites to conduct spore trapping and Brisbane (Qld), Toowoomba (Qld), Urrbrae (SA) for researcher locations
Project lead
Dr Dinesh Kafle(Qld DPI)
About the project
Spore trapping is a method used to capture airborne spores, primarily for monitoring and detecting fungal diseases in crops, allowing for early intervention and preventative measures. Spore trapping is being investigated as a tool for detecting leaf spot pathogens of cotton and the novel Eutypella sp. which cause reoccurring wilt. If spore trapping is validated as an effective tool for monitoring the dispersal and distribution of aerial spores of cotton pathogens, the findings will assist in understanding the etiology of these pathogens and direct research to investigate management options.
Location
NT DAF (Katherine)
WA DPIRD (Kununurra)
Project Leads
Dr Dinesh Kafle (Qld DPI)
Sarah Nolan-Gorman (WA DPIRD)
Dr Edward Mwando (NT DAF)
About the project
This project addresses understanding disease pressure in extending cotton cultivation in Northern Territory and Western Australia. The expected industry outcomes and impact are key and emerging cotton pathogens identified in Northern Australia to assist with the development of effective management strategies. The expected output is cotton pathology capacity built through establishment of diagnostic service, disease surveillance and pathology training.
Location
UniSQ (Toowoomba Campus)
Project Lead
Dr Cassy Percy (UniSQ)
About the project
This project will establish a nationalised collection of all pathogens of cotton in Australia, crucial for understanding the evolution and spread of existing and new pathogenic strains and for screening cotton germplasm for broad-spectrum disease resistance. The collection will provides 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.
Location
Narrabri, NSW
Project Lead
Prof Sambasivam Periyannan (UniSQ)
About the project
There is a lack of pathology support for New South Wales cotton growers. The expected industry outcomes and impact of this project are that NSW cotton growers will have access to disease diagnostics services, and an improved understanding of pathogen spread, evolution and the influence of farming systems on disease outbreaks.
Location
UniSQ (Toowoomba Campus)
Project Lead
Dr Alexandros Georgios Sotiropoulos (UniSQ)
About the project
This project, by monitoring the pathogen genomic diversity, will provide fungal cotton pathogen populations to rapidly monitor and compare changes in pathogen migration patterns and adaptation to alternate hosts, new cotton lines, and the environment, identifying diverse and virulent pathogens. Population genomic resources for cotton fungal pathogens are being created, making it easier to understand virulent fungal populations emerging in a region and creating datasets of pathogen genomes for comparisons in pathogen diagnostics in the future.
Location
UniSQ (Toowoomba Campus)
Project Lead
Dr Alexandros Georgios Sotiropoulos (UniSQ)
About the project
Berkeleyomyces rouxiae is a pathogen that impacts cotton yield. Eutypella spp. and Corynespora spp. are other fungi pathogens causing reoccurring wilt and leaf blight. Generating chromosome-scale assembly and genome annotation provides insight into genome architecture and virulence gene profiles. Australian cotton growers will have an improved understanding of the virulence of these pathogens and will be better equipped to develop diagnostic markers. The new genomic resources will assist in population studies and will be used as references for monitoring the emergence of highly virulent or mutant isolates that could potentially cause more harm (e.g. epidemics).
Location
Charles Sturt University (CSU) (Wagga Wagga) and Cotton Farms (Griffith), NSW
Project Leads
Dr Sadegh Balotf (UniSQ)
Dr Ben Stodart (CSU)
About the project
Black root rot disease emerged as a serious threat to sustain cotton cultivation in NSW, particularly the southern region. Cotton pathology capacity will be built in southern NSW to understand black root rot disease pressure. The etiology of black root rot will be understood to assist with the development of effective management strategies.
Location
UniSQ (Toowoomba Campus)
Project Lead
Dr Cassy Percy (UniSQ)
About the project
Cotton differential sets are not available for all key pathogens, and information on the host range of cotton pathogens is incomplete. cotton growers will benefit from tactical disease management strategies developed in this project using foundational resources. Cotton germplasm resources and a differential set will improve the capacity to develop resistant cultivars and phenotype key pathogens.
Location
UniSQ (Toowoomba Campus)
Lead
Dr Sadegh Balotf (UniSQ)
About the project
Many cotton diseases are caused by multiple pathogens, contributing to complex disease dynamics. Co-infection complicates disease management and often leads to more severe symptoms and higher seedling mortality rates, which directly impacts yield. This project will equip cotton growers with evidence-based, practical insights on how these pathogens interact and contribute to disease severity, enabling more informed decisions to manage complex disease threats, and providing the tools necessary to detect and quantify co-infection.
Location
UniSQ (Toowoomba and Springfield Campus)
Project Lead
Prof Ravinesh Deo (UniSQ)
About the project
Cotton production in Australia faces significant threats from plant diseases, which can impact yield and profitability. Effective disease management requires accurate tools to predict and monitor outbreaks across varying scales. In this project, new spatial data analytic tools with statistical and artificial intelligence (AI)-driven modelling will be developed and integrated to generate key outcomes to support the Australian cotton industry. These tools will advance disease management practices through enhanced capability to predict and visualise the disease incidences at multiple spatial and temporal scales, but also by data-driven findings that guide and lead to specific, meaningful strategic intervention.
Location
UniSQ (Toowoomba Campus)
Project Lead
A/Prof Alison McCarthy (UniSQ)
About the project
Identifying Verticillium and Fusarium wilt pathogens is of increasing importance as more fields are being confirmed to have both pathogens present. Diagnosing wilt pathogens in a field is still manual. This study aims to develop machine vision sensing to differentiate wilts and predict severity before visual symptoms show. Australian cotton growers will have new technology available to identify the wilt diseases in-field before symptoms are visible. This will enable field mapping to identify predicted high disease areas and implementation of farming practices, such as nutrition and irrigation management
Location
UniSQ (Toowoomba Campus)
Project Lead
Prof Levente Kiss (UniSQ)
About the project
This project will provide Australian cotton growers and industry representatives with an improved understanding of the efficacy of the fungicides and plant defence mediators against cotton pathogens. The industry will be provided with a comprehensive and critical analysis of the efficacy of fungicides and plant defence mediators used in cotton production in Australia and overseas.
Location
UniSQ (Toowoomba Campus)
Project Lead
Professor Levente Kiss
About the Project
This project will deliver critically needed (must-have) data on the efficacy of up to 50 fungicides and other plant protection products (PPPs) against up to 14 significant fungal pathogens of cotton in Australia. The industry will be provided with a comprehensive database and critical analysis of the efficacy of a total of up to 50 new and currently registered fungicides and other PPPs against the most important fungal pathogens of the Australian cotton.