Diseases of cotton are of a significant constraint to cotton production and have been identified as key areas for investment by the cotton industry. Sustainability of the Australian cotton industry remains dependent on the continued development and adoption of cultivars that are highly resistant against major soilborne pathogens such as Thielaviopsis basicola, Fusarium oxysporum f. sp. vasinfestum and Verticillium dahliae, and a re-emerging Alternaria leaf spot (ALS) pathogen, Alternaria alternata. Incorporating high yielding traits with disease resistance is a difficult long-term process; and with limited resources, it is not always possible to develop a complete resistant cultivar to all diseases. Therefore, effective management of cotton diseases relies on an integrated approach. a key focus of this project was to identify non-cotton fungicides, novel chemistries and biocontrol agents, which can be integrated into management strategies of major diseases in cotton production systems.

This project has identified a number potential candidates/approaches. Several pathological research gaps that could be further investigated for their efficacy and insights into pathogen biology. These are as follows:

• Non-cotton fungicides A-16148-F and Fungicide 2, and a novel plant extract PlantY provided a potential black root rot (BRR) control, but there was a lack of control consistency and required further assessments;

• In response to the leaf spot outbreak on seedlings in 2017/18 season in southern NSW, Alternaria alternata was a predominant pathogen responsible for the outbreak;

• Mancozeb and Tebuconazole have been granted an emergency application permit on both seedling and mature cotton in the event of a future outbreak;

• Incorporation of a brassica crop could provide a potential alternative practice to suppress the V. dahliae population, but this requires a long-term field assessment for inclusive recommendations;

• BRR and Verticillium wilt pathogens are now widely distributed in NSW, but insights of their biology and diversity are largely unknown. Such knowledge is essential for developing an accurate and rapid detection approach, as well as management strategies;

• Assessing for disinfestation efficacy against BRR and Verticillium wilt pathogens of Farmcleanse-alternative products will be vital for farm hygiene practices;

• Studies focused etiology and epidemiology of a sporadic but important boll rot disease should also be a priority.

State-based agencies such as NSW DPI have historically played an important role in providing responses to industry needs and delivering leadership in cotton pathology. This project built and enhanced research capacity by the appointment of an additional cotton pathologist based at NSW DPI Narrabri. The aim was to retain grower confidence in the cotton industry to provide support and leadership of cotton pathology issues. The appointed team including Dr Duy Le and Aphrika Gregson has collaborated with Queensland cotton pathology team, southern NSW Cotton Crop Protection specialist based at Yanco Agricultural Institute and CottonInfo team. Such collaboration allowed us to investigate into a broad array of plant pathology research activities such as disease surveillance, management and diagnostics.