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Pathogenicity testing of the soilborne fungi, Corynespora cassiicola and Macrophomina spp. were conducted to determine their ability to cause diseases on two sesame cultivars, using different methods of inoculation. At the same time, glasshouse experiments were conducted to test the resistance responses of sesame cultivars to the root-lesion nematodes, Pratylenchus thornei or P. neglectus, as well as an experiment to test the growth response of sesame to arbuscular mycorrhizal fungi (AMF). The C. cassiicola isolate used was found to be pathogenic to the two sesame varieties, white cv. '6855' and black cv. 'Black Savannah', both as a root rot and target spot causing fungus using different methods of inoculation. The root dipping inoculation with C. cassiicola for root rot disease displayed inconsistencies due to the harmful effect of root wounding which could be misconstrued as effect of the fungal inoculum. Macrophomina phaseolina and M. tecta were found pathogenic, causing charcoal rot in sesame. Moreover, the results of inoculation methods evaluation in this study provided a basis for selecting methods for use in sesame pathology research. Sesame cvs black and white were rated as provisionally resistant to P. neglectus. Insufficient numbers of plants grew to maturity in the P. thornei experiment to assess resistance/ susceptibility. Modifications have since been developed to improve plant germination and establishment for future glasshouse experiments. White sesame cv. '6855' was highly dependent on AMF for plant biomass and height and black sesame cv. “Black Savanah” was moderately dependent. Future experiments with root-lesion nematodes should also investigate the effect of the addition of AMF to the soil to improve plant growth and for effects on nematode reproduction. In addition, on a separate USQ on-going disease scoping sesame trap crop trials with the Broadacre Cropping Initiative project, under the Queensland Department of Agriculture and Fisheries, have

Currently, 100 percent of sesame seed and sesame oil of Australia is being imported, which had a combined value in excess of $26.5 million in 2016 and demand has only been increasing. Sesame production is an emerging industry for Australia, with about two million tonnes traded globally each year, it is well positioned to take advantage of adopting commercial sesame production, as it has the potential to be a high-value summer cropping alternative for grain growers. Add to that the big global market for sesame with the top importers being China, Japan and South Korea, markets that are looking for high-quality whole seed and oil. The northern regions of Australia, northern NSW and southern and central Queensland, are prime candidates for production as sesame is a heat and drought tolerant crop that could be grown as a summer crop and tap into existing farming systems and infrastructure. As an emerging industry in Queensland, evaluation of new sesame genetics and development of management practices for these new varieties was initiated in 2016. Sesame agronomy trials and herbicide screening trials for weed control options have started and is expected to continue over three years. However, there has been no attempt yet in scoping potential diseases that could pose problem for sesame in the identified candidate areas for production. Foliar diseases such as bacterial blight, Cercospora leaf spot, Alternaria blight, powdery mildew and phyllody; and root diseases such as damping off and root rots are reported in sesame growing countries. These diseases are also common in most summer broadacre crops in Australia, and it is imperative to identify which among these diseases will have the potential to have great impact in Australia’s sesame production.

Despite the substantial economic impact of Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) on legume productions worldwide, the genetic basis of its pathogenicity and potential host association is poorly understood. The production of high-quality reference genome assemblies of Cff strains associated with different hosts sheds light on the genetic basis of its pathogenic variability and host association. Moreover, the study of recent outbreaks of bacterial wilt and microevolution of the pathogen in Australia requires access to high-quality, reference genomes that are sufficiently closely related to the population being studied within Australia. We provide the first genome assemblies of Cff strains associated with mungbean and soybean, which revealed high variability in their plasmid composition. The analysis of Cff genomes revealed an extensive suite of carbohydrate-active enzymes potentially associated with pathogenicity, including four carbohydrate esterases, 50 glycoside hydrolases, 23 glycosyl transferases, and a polysaccharide lyase. We also identified 11 serine peptidases, three of which were located within a linear plasmid, pCff119. These high-quality assemblies and annotations will provide a foundation for population genomics studies of Cff in Australia and for answering fundamental questions regarding pathogenicity factors and adaptation of Cff to various hosts worldwide, and, at a broader scale, contribute to unravelling genomic features of Gram-positive, xylem-inhabiting bacterial pathogens.

Crop diseases in the GRDC Northern Region cost growers at least $400 million p.a. As growers rely on tighter margins more than ever, effective disease management is a must. With current global and climate change, pathogens affecting crops are changing requiring new management methods to be developed and made available. The project’s research was conducted in several levels, from basic pathogen identification, host range and host-pathogen interaction, novel methods of disease management, to insect-vector investigation and yield loss caused by disease. The project found that the Fusarium species associated with Fusarium wilt in mungbean are capable of surviving in the asymptomatic roots of other crops, including barley, chickpea, cotton, soybean, and to a lesser extent sorghum. It was also demonstrated that plant growth and pod production was reduced when the Fusarium wilt pathogens infected mungbean when the root lesion nematode, Pratylenchus thornei was also present. Evidence was provided to show that phytoplasma infection in peanut is a causal agent for symptoms typical of peanut kernel shrivel (PKS), and demonstrated that the leafhopper Orosius orientalis is a vector of the most commonly found phytoplasma species in grain legumes, Ca. P. aurantifolia. A strong relationship existed between the incidence of charcoal rot and percent lodging, supporting the notion that charcoal rot is one of the causative agent in lodging of sorghum. Low levels of Macrophomina load results to low level of charcoal rot and consequently low level of damage. Variation in the pathogen densities between pre-sowing and pre-harvest soil samples is influenced by location and environmental factors. Rainfall and location were shown to influence lodging rate, and some varieties of sorghum may be less susceptible to charcoal rot than others. While this study has provided useful information, it has highlighted the need for further data collection to be able to develop a reliable disease risk categ

In contrast to Eurasia and North America, powdery mildews (Ascomycota, Erysiphales) are understudied in Australia. There are over 900 species known globally, with fewer than currently 60 recorded from Australia. Some of the Australian records are doubtful as the identifications were presumptive, being based on host plant-pathogen lists from overseas. The goal of this study was to provide the first comprehensive catalog of all powdery mildew species present in Australia. The project resulted in (i) an up-to-date list of all the taxa that have been identified in Australia based on published DNA barcode sequences prior to this study; (ii) the precise identification of 117 specimens freshly collected from across the country; and (iii) the precise identification of 30 herbarium specimens collected between 1975 and 2013. This study confirmed 42 species representing 10 genera, including two genera and 13 species recorded for the first time in Australia. In Eurasia and North America, the number of powdery mildew species is much higher. Phylogenetic analyses of powdery mildews collected from Acalypha spp. resulted in the transfer of Erysiphe acalyphae to Salmonomyces, a resurrected genus. Salmonomyces acalyphae comb. nov. represents a newly discovered lineage of the Erysiphales. Another taxonomic change is the transfer of Oidium ixodiae to Golovinomyces. Powdery mildew infections have been confirmed on 13 native Australian plant species in the genera Acacia, Acalypha, Cephalotus, Convolvulus, Eucalyptus, Hardenbergia, Ixodia, Jagera, Senecio, and Trema. Most of the causal agents were polyphagous species that infect many other host plants both overseas and in Australia. All powdery mildews infecting native plants in Australia were phylogenetically closely related to species known overseas. The data indicate that Australia is a continent without native powdery mildews, and most, if not all, species have been introduced since the European colonization of the continent.

The bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is the cause of tan spot (in some regions known as ‘wilt’) on mungbean (Vigna radiata) and other legumes worldwide. The pathogen was first reported in mungbean paddocks in Queensland in 1984, and subsequently in New South Wales in 1986, causing yield losses of up to 25% in hot and dry seasons. No chemical control is available, and disease management relies on pathogen exclusion, through the use of clean seed, and deployment of moderately susceptible varieties. Breeding programs are currently working to incorporate better resistance into new mungbean varieties. The success of breeding programs depends on a thorough understanding of the genetic diversity and evolution of the pathogen population(s). This project was designed to elucidate the genotypic diversity of Cff population(s) and investigate sources of inoculum that contribute to tan spot epidemics in the northern grains region (Queensland and northern New South Wales). Whole genome re-sequencing of 100 Cff isolates detected moderate genotypic diversity, with a narrower genetic background compared to the global Cff population. One highly adapted clonal lineage was found to dominate the population with a frequency of 45%. This study showcases how population genomics studies can be used to test hypotheses relating to disease epidemiology and provide useful information for resistance breeding programs. The results provide insights on Cff population structure and epidemiology, and have direct application for breeding programs by providing a set of Cff isolates that represent the genetic diversity of the pathogen population(s) in the northern grains region.

Presentation on the activities by the GRDC-funded project on Integrated Disease Management Tools to manage summer crop diseases in the Northern Region.

A report on the fungicide resistance research in Queenland and what needs to be done.

A report on the INTEGRATED DISEASE MANAGEMENT TOOLS TO MANAGE SUMMER CROP DISEASES IN THE NORTHERN REGION, (USQ-1907-001RTX)

The bacterium Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) is the cause of tan spot (in some regions known as ‘wilt’) on mungbean (Vigna radiata) and other legumes worldwide. The pathogen was first reported in mungbean paddocks in Queensland in 1984, and subsequently in New South Wales in 1986, causing yield losses of up to 25% in hot and dry seasons. No chemical control is available, and disease management relies on pathogen exclusion, through the use of clean seed, and deployment of moderately susceptible varieties. Breeding programs are currently working to incorporate better resistance into new mungbean varieties. The success of breeding programs depends on a thorough understanding of the genetic diversity and evolution of the pathogen population(s). This project was designed to elucidate the genotypic diversity of Cff population(s) and investigate sources of inoculum that contribute to tan spot epidemics in the northern grains region (Queensland and northern New South Wales). Whole genome re-sequencing of 100 Cff isolates detected moderate genotypic diversity, with a narrower genetic background compared to the global Cff population. One highly adapted clonal lineage was found to dominate the population with a frequency of 45%. This study showcases how population genomics studies can be used to test hypotheses relating to disease epidemiology and provide useful information for resistance breeding programs. The results provide insights on Cff population structure and epidemiology, and have direct application for breeding programs by providing a set of Cff isolates that represent the genetic diversity of the pathogen population(s) in the northern grains region.

Peanut Kernel Shrivel (PKS) is a currently undiagnosed condition affecting peanut crops in the Bundaberg and North Queensland growing regions. PKS is currently costing the peanut industry more than $4M+ p.a. and is a potential threat to Australian peanut industry. Previous investigations into the cause of PKS have ruled out nearly all abiotic factors and most biotic factors. The GRDC/USQ/PCA collaborative research project was aimed at investigating the extent, distribution and cause of peanut kernel shrivel (PKS) syndrome. The survey by PCA showed peanut crops to have the PKS symptoms in all regions surveyed. USQ’s investigation, based on culturable microorganisms, showed that there appears to be no clear cut involvement of plant pathogenic bacteria and fungi in the PKS syndrome, but revealed Fusarium spp. as the more prevalent fungal genera in PKS affected plants. Furthermore, the soil metagenomics study aimed at determining the relationship between soil microbial profile and PKS syndrome revealed that Fusarium spp. was the most abundant fungal communities, where Fusarium oxysporum species complex was the most common fungal species and considered as possible suspect in the PKS syndrome. However, this still needs to be validated via pathogenicity testing (Koch’s postulates). Results of this test will assist in developing PKS management strategies.

White grain disease is an economically important disease of wheat, infecting wheat head and grains. WGD are known to be associated with a complex of closely related fungi (Eutiarosporella spp.).Losses is estimated to be $100M. Stubble management and crop rotation could provide useful levels of control. The disease has been in existence for almost 20 years and yet we know very little about the: host range, infection process, exact conditions that lead to disease, distribution of the disease in the region, resistance status of cultivars' cultural control methods effectiveness of fungicides.

A presentation on what my role and activities are when I was professional officer at NSW DPI Wagga wagga working on winter cereals pathology.