Living with the cereal killers of New South Wales: a four-year journey with NSW-DPI Wagga Wagga

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

Diagnosing plant diseases: what do we ask and why do we ask for it? [Online community]

Diagnosing a plant disease or other injury is like going to a medical doctor who must ask several questions before making an accurate diagnosis and recommending a treatment. If you withhold information, it can lead to a misdiagnosis. The same goes for crop diseases. Plant pathologists, specifically diagnosticians, are often asked “What is wrong with my plant; followed by, what can I do to manage the problem?” In most cases it may be too late to save the specific plant, but a correct diagnosis is important to prescribe methods that prevent the problem on other plants or in the future. So how do we go about diagnosing plant diseases? Proper identification of diseases and of the causal agents is vital in prescribing a sound disease management strategy, avoiding further losses and preventing the waste of time and money. Often, we rely on symptoms for the identification of a disease. As similar symptoms can be produced by different causal agents, the use of symptoms alone in most cases is an inadequate method for disease identification. While other methods for identification are available, it may also take a week or more to accurately identify the disease-causing agent. So, what can diagnosticians do? Asking many questions related to the plants’ environmental and cultural factors to help eliminate or identify possible causes of the problem. To help gather this information we provide disease diagnosis request forms for you to fill out when requesting our free diagnostic services. It is important that you use the form relevant to the laboratory you are submitting a sample to. QDAF Plant Disease Enquiry Form USQ Centre for Crop Health Plant Disease Diagnosis Submission Form Disease testing services around Australia Information gathered from these forms is crucial in helping narrow the problem down to a few suspects, which will require further study in the laboratory before making a final diagnosis. Regardless of the outcome, a recommendation will be given as to what should be done with the problem

Whole genome data from Curtobacterium flaccumfaciens pv. flaccumfaciens strains associated with tan spot of mungbean and soybean reveal diverse plasmid profiles

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

Characterizing the Saltol quantitative trait locus for salinity tolerance in rice

This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na +/K + homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for markerassisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress

Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery of Salmonomyces as a New Lineage of the Erysiphales

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

Final Report: Soilborne Pathogens of Sesame

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 shown several soilborne fungal and bacterial species present in representative paddocks across southeast Queensland. Distribution and identities of these microorganisms were determined to identify which ones could potentially affect sesame production

Botryosphaeriaceae in Australian cereal grains: An overview

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

Integrated disease management tools to manage summer crop diseases in the northern region

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 categories based on PREDICTA®B test results and its associated yield loss. Several indigenous Trichoderma strains have displayed the ability to inhibit mycelial growth of M. phaseolina in vitro. However, in vivo, only one Trichoderma strain showed potential to minimise charcoal rot development as seed treatment. The commercially available Trichoderma-based products evaluated as seed treatment were not able to minimise the sorghum charcoal rot disease. The in vitro bioassay demonstrated the mycelial growth inhibiting ability of different fungicides at varying rates. However, when applied as seed treatment, the fungicides were not able to minimise the charcoal rot infection in sorghum, which can be attributed to the short post-infection activity of the systemic fungicides evaluated. Most Trichoderma strains evaluated for biocontrol mechanisms displayed the antibiosis ability by lytic enzymes, but not as host resistance inducer. Further studies are needed to include other biocontrol mechanisms tests to identify the Trichoderma strains that can potentially be used for biocontrol. No significant difference among the different M. phaseolina inoculum densities in their ability to cause charcoal rot disease was observed in the 'sick soil method' of inoculation. The 'toothpick method' of inoculation guarantees consistent infection and more disease, while the 'sick soil method' is comparable to natural infections taking place under natural outdoor conditions. However, the inconsistency of the 'sick soil method' in causing infection needs to be addressed. The existence of interactions among the host, pathogen and environmental conditions highlights the need for additional studies to improve the reproducibility of these methods. In vitro, 30°C is the optimum temperature for growth of most northern region M. phaseolina strains, with some growing well at 40°C and at 15°C mycelial growth is significantly affected. The use of species-specific primers to identify M. phaseolina have shown that they can be used for the selective and specific identification that is rapid, easy, accurate and cost-effective. The project’s research allowed for a wide range of effective tools and recommendations to be developed. The tools were not just for growers and agronomists, but also for breeding programs, which will benefit growers and other researchers in the future. This provides both immediate and long-term benefits that will provide lasting impact

Extent, distribution and cause of peanut kernel shrivel (PKS) syndrome in the Bundaberg and Northern Queensland regions

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