Plant Rust Images: an open photo gallery of rusts from South Africa
This repository is a selection of images of rust diseases assembled by plant pathologists from the University of the Free State, Bloemfontein, South Africa. It is not intended to be a complete checklist of rust fungi in South Africa, but rather pictures of signs and symptoms of rusts studied or collected over several years.
Using Reproducible Research to Revisit Published Results
In which the author revisits a previously published analysis and finds ways to improve it while using reproducible research to illustrate refitting a GAM using random effects to better fit the model to the data.
Dieback-free gravel for road construction
Phytophthora cinnamomi (the dieback ‘fungus’) is an introduced soilborne pathogen associated with the death of native plants. It is spread in infested soil, including gravel. Main Roads WA (MRWA) only uses dieback free gravel for road construction and repair; this is in short supply. One option is to treat gravel to kill Phytophthora.
TraineR2: an evolution of TraineR that uses actual photos
TraineR2 is another Shiny app developed to train users in assessing disease severity, expressed as the percentage of the organ (leaf or fruit) affected by lesions. However, this app distinguishes itself by basing its assessments on actual photographs of disease symptoms.
TraineR: a new app for improving accuracy of severity estimates
TraineR is a Shiny app designed to train users in the assessment of disease severity expressed as the percent area of the organ (leaf or fruit) affected by lesions.
How Much Do We (Plant Pathologists) Value Openness and Transparency?
Our most recent paper examines code and data sharing practices in plant pathology and shares some ideas for what we can do to improve.
Fitting temperature- and moisture-based models to infection data using R
In many processes of the disease cycle, such as infection - one of the most critical components for disease forecasting - the interaction between temperature and the duration of moisture determine the amount of succesful infection sites and resulting disease severity. This post shows how to fit, in R language, a form of the Analytis Beta model to infection data as a function of temperature and an asymptotic regression model to infection as a function of moisture duration.
Polyphagous shot-hole borer in Western Australia – emergency response at the urban interface
Polyphagous shot-hole borer (PSHB; Euwallacea fornicatus) was detected in August 2021 by the Department of Primary Industries and Regional Development (DPIRD) in the Perth metropolitan area of Western Australia (WA). PSHB is an agricultural and environmental pest, with a wide host range (>400 amenity, fruit and nut tree species). This presentation will summarise PSHB biology and DPIRD response activities and explore some of the challenges and opportunities present at the urban forest- residential interface. Kylie will also speak to what it is like to work as a subject matter expert during a plant pest incursion.
Tracking changes from Rmd/Qmd Rendered Files Across Word Document Versions
Writing your manuscripts in RMarkdown or Quarto and rendering to Word for review? Do you need to be able to track your changes in Word in your response to reviews but don't know how to? Read on for how you can still use Rmd/Qmd and satisfy the requirements for tracked changes in your responses when resubmiting to journals for review.
Understanding plant-microbe- soil interactions to improve plant conservation and restoration outcomes
Although soil microbial communities, e.g., fungi and bacteria, are still largely considered a “black box”, their central role in ecosystem processes and function is indisputable. Despite the important role they play in carbon and nitrogen cycling, decomposition, and plant health there have been few attempts to incorporate soil microbial communities into conservation and restoration practice. In this talk, I will give an overview of my research pertaining plant- microbe interactions and how it has the potential to improve our understanding of plant-microbial dynamics in diverse ecosystems. Better understanding plant-microbial dynamics will also inform about the ecosystem-level processes and ecosystem health, e.g., decomposition rate, nutrient cycling, and plant nutrient acquisition. Finally, I will bring examples of our work that has practical applications for improving plant conservation and restoration outcomes.
Advances in understanding the host-mediated defence mechanism in wheat against rust infections
Sambasivam (Sam) Periyannan is a Scientist at the Agriculture and Food division of CSIRO and an Adjunct Associate Professor at the University of Queensland, Australia. After completing his PhD (Agriculture) at the University of Sydney in 2011, Sam started his scientific career as a postdoctoral fellow (2011-2016) at CSIRO, where he eventually became an independent scientist in 2016. Between 2017-2019, Sam took a secondment position at the Australian National University (ANU) to complete his ARC DECRA project. He also served as the “Crop Resistance Genes” team leader at CSIRO from 2019 to 2021. Sam’s research interest is centred on molecular genetics and pathology, focusing on cereal crops and rust pathogens. Apart from publications in top journals such as Science and Nature Biotechnology, Sam is the recipient of prestigious awards such as the Goldacre award from the Australian Society of Plant Scientists and Chairman’s Medal from CSIRO. Currently he is a Senior Editor for Plant Disease and Associate Editor for BMC Biology and Frontiers in Plant Science.
Estimating leaf temperatures for spatial epidemiology
How to obtain leaf temperature estimates world-wide using the R packages, tealeaves and nasapower.
Calculating AUDPS using Julia
Calculating AUDPS in R and Julia.
Introducing Julia to Plant Pathologists
Do you feel the need for speed?
Adaptation of a clonal pathogen - The story of Ascochyta rabiei in Australia
Ascochyta rabiei, a pathogenic fungus and the causing agent of Ascochyta blight of chickpea, is represented by a highly clonal population in Australia, due to the presence of only a single mating type. This presentation will summarise the current knowledge of the patterns and trends found in this unique population structure, as discovered by genetic analysis of isolates collected between 2013-2020 as part of ongoing monitoring studies led by Prof. Rebecca Ford at Griffith University.
RNAi vaccines for sustainable plant protection
RNA interference (RNAi) vaccines are an emerging environmentally-friendly crop protection platform that are effective against agricultural pests and pathogens. The approach involves applying pathogen-specific double-stranded RNA (dsRNA) to the host plant to trigger RNAi and silence targeted pathogen genes, inactivating the pathogen and protecting the plant. When applied as BioClay(TM), in combination with clay particles that bind dsRNA, RNAi vaccines can provide plants with protection for more than 20 days, making a single spray a commercially feasible and lasting approach to protect crops.
Sources and quantification of flower blight pathogens in macadamia
Raceme blights also known as flower blights are used to describe diseases and disorders of macadamia inflorescence worldwide. Flower blights reduce fruit set and control measures are limited. Knowledge of the disease cycle and epidemiological parameters is required.
The interesting things we find during cotton disease surveillance in Queensland
Cotton is susceptible to many yield-limiting diseases. To understand the importance and impact of diseases present, disease surveys are conducted early and late season across all cotton growing regions to monitor the distribution and incidence of diseases. The surveys also maintain the surveillance for exotic pathogens. Surveys have been conducted in Queensland for 20 consecutive years. Data provided by annual surveys have shown the relative importance of each of the diseases in a region and that specific diseases continue to be a challenge to manage, resulting in significant yield losses.
The power of electrochemical biosensors in Botrytis Grey Mould pathogen diagnostics
Plant pathogens cause enormous economic loss and potential unintended environmental impacts through excessive or off-target chemical management practices. Thus, early diagnosis and quantitation of the causal pathogen species for accurate and timely disease control is crucial. Botrytis Grey Mould (BGM), caused by Botrytis cinerea and B. fabae, can seriously impact production of temperate grain legumes separately or within a complex. Accordingly, several immunogenic and molecular probe-type protocols have been developed for their diagnosis, but these have varying levels of species-specificity, sensitivity, and consequent usefulness within the paddock. To substantially improve speed, accuracy and sensitivity, advanced nanoparticle-based biosensor approaches have been employed and through translation of human biomedical diagnostics tools. These new tools provide accurate and quantitative diagnosis in the field and long before visual symptoms appear. This presentation will outline progress towards the development and validation of BGM species-specific molecular-electrochemical coupled diagnostics, and next steps towards their incorporation in IDM strategy.
Linear modelling of soil temperature effects on root lesion nematode population densities in R
Pratylenchus thornei, the root-lesion nematode, is widely distributed in wheat (Triticum aestivum) growing areas of many countries and is of particular concern in sub-tropical environments. These nematodes penetrate roots to feed and reproduce in the root cortex leading to loss of root function, which affects nutrient and water uptake of nutrients and water causing nutrient deficiency and water stress. In the original paper the population response of P. thornei in Queensland, Australia wheat to temperature is modelled using a linear and quadratic equations by Thompson (2015). The study aimed to investigate the effects of soil profile temperatures after different sowing dates on reproduction of the nematodes in susceptible and moderately resistant wheat cultivars in the subtropical grain region of eastern Australia. This document recreates the models for population densities of P. thornei as described in the original paper.
Characterization of Pyrenophora teres isolates and mapping of virulence genes
Characterization of _Pyrenophora teres_ isolates and mapping of virulence genes _Pyrenophora teres_ is the causative agent of net blotch of barley and one of the most economically important fungal pathogens affecting the Australian barley industry. Buddhika discusses her PhD researsch on genetic characterisation and identification of virulence genes of a barley fungal pathogen, _Pyrenophora teres_. Presented for the Queensland Chapter of the Australasian Plant Pathology Society (APPS).
Diagnosis of African Citrus Greening
African citrus greening (or also known as African greening) is a serious, debilitating, insect-transmissible citrus disease associated with the heat sensitive, phloem-limited, non-cultured bacterial species _Candidatus_ Liberibacter africanus (CLaf). To fill the Australian capability and capacity gaps for diagnostics of African greening, I undertook a two-week diagnostic training at Citrus Research International (CRI), Nelspruit, South Africa in June 2019. This presentation will show what I had gained from the training. Presented for the Queensland Chapter of the Australasian Plant Pathology Society (APPS).
Mycorrhizal fungi improve yield, biomass and nitrogen fixation by rhizobia but increase population densities of the root-lesion nematode Pratylenchus thornei in mung bean
Mung bean is a short-season, high-value legume crop in eastern Australia that is susceptible to the plant-parasitic root-lesion nematode _Pratylenchus thornei_. It also forms associations with the beneficial soil-borne arbuscular mycorrhizal fungi (AMF) which increases plant uptake of phosphorus (P) and zinc (Zn) in exchange for photosynthates. Interactions with AMF and biotic stressors in previous studies suggested that AMF may induce a biocontrol effect to reduce symptom severity and Pratylenchus population density in crops. Presented for the Queensland Chapter of the Australasian Plant Pathology Society (APPS).
{hagis}, an R package for analysis of pathogen gene-for-gene virulence data
{hagis} is a new R package, designed for analysis of pathogen gene-for-gene virulence data that is collected from pathogen surveys or experiments. This package provides users with tools to explore their virulence data and identify the distribution of susceptible reactions, pathotype complexity, pathotype frequency as well as alpha and beta-diversity measurements in an easy-to-use format. Austin shares how this package came into being and how it's being used in this guest post.
