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Agriculture and agribusiness honours projects

Refer to the below for a full list of the Agriculture and Agribusiness honours projects.

When you find a project that interests you, click on the supervisors name which will automatically generate an email message.

Study of fungicide sensitivity shifts in historic and current collections of Botrytis cinerea isolates collected from Western Australian vineyards

Supervisor: Dr Fran Lopez

The aim of this study is to determine if there have been changes in the sensitivity of Botrytis cinerea to major fungicides due to the continuous exposure of the pathogen to key antifungals used by the viticultural industry. We have demonstrated that resistance to certain fungicides is well established in other pathogens such as Blumeria gramisnis f.sp hordei and Ascochytas spp. Australia, but it remains unclear if the resistance developed just recently as a consequence of the increase in production and fungicide consumption, or if it has been present in fungal populations for a longer time. Another question that remains unresolved is if resistance is a phenomenon that originates once and then expands in the population or if it has multiple origins. Sensitivity to key antifungals will be tested by plate reader analysis in different B. cinerea isolate collections existing in our laboratory and in isolates collected from the field by the student. Historical isolates collected 10 to 20 years ago from chemically managed vineyards will be compared to isolates from the 2012/2013 season obtained from organic and chemically managed vineyards. Sensitivity baselines will be established for the different groups of isolates and fungicides to determine if shifts in fungicide sensitivity have occurred. The fungicide target genes of isolates showing fungicide resistance will be screened for mutations and a correlation between the resistance levels and the mutations found will be established.

Adoption of new pasture species across the wheatbelt – Farmer survey update

Supervisors: Dr Sarita Bennett, Dr Phil Nichols (DAFWA, South Perth)

In 2005 a survey was undertaken across the wheatbelt of WA to determine the uptake of the new pasture legume varieties released in the previous 10 years, compared to the traditional subterranean clover (Trifolium subterraneum) and burr medic (Medicago polymorpha). 127 farmers responded across the 300 to 600 mm rainfall zone. It was found that on average 460,000 ha or 6.6% of the total farm area was sown to the new pasture legume species. It is now 7 years since that survey was conducted and there have been another suite of new species released in the last 10 years and so it is important that the survey is repeated to see if uptake of new pasture species is still increasing.

Develop a survey that can be sent and given to farmers across the wheatbelt of WA that assesses their use of pastures, and which species they are using and why. The survey will be sent to farmers, but will also be handed out at field days early in the season. Results will be compared to the results obtained in 2005 and will be an important method of assessing and promoting adoption of new pasture species.

Decay curves for pre-emergent herbicides under dry seeding conditions

Supervisors: Sarita Bennett and Mike Ashworth (Curtin University), and David Minkey (WANTFA)

Pre-emergent herbicides are used increasingly across the wheatbelt of WA to kill weed seeds before the emergence of a cereal crop. However, the true to time to decay of these herbicides in different soil types, and the true impact of them on the germination of the subsequent crop is unclear. This project will involve applying pre-emergent herbicides to different soil types and monitoring their effectiveness on weeds over the season to determine the true decay of the herbicide.

Comparative genomics of fungal mitochondria

Supervisor: Dr James Hane

The mitochondria are the energy production factories of eukaryotic cells. In fungi the mitochondrial are especially significant as they are also one of the main targets of fungicides, the primary means of field-based control of fungal diseases in both agriculture and medicine. In this project you will compare multiple mitochondrial genomes and characterise their gene contents, mutations and other relevant properties. This will result in a comprehensive understanding of fungal mitochondrial genomes, and the distribution of specific mutations that confer higher or lower fungicide resistance across both species and isolates.

Transient expression by agroinfiltration in faba bean, Vicia faba, and characterisation of a putative Ascochyta fabae effector protein

Supervisors: Dr Robert Lee, Dr Bernadette Henares and Dr Robert Syme

Ascochyta fabae causes ascochyta blight in faba bean. Effector proteins and necrosis-inducing proteins of necrotrophic fungal pathogens mediate disease in plants by initiating a hypersensitive response that can be detected as necrosis or cell death in plant tissues. We have developed a system for expressing fungal proteins in plant leaf tissues and we have demonstrated necrosis in faba bean leaves using proteins characterised as necrosis-inducing proteins in dicot plants. In this project you will characterise necrosis-inducing protein(s) from A. fabae using the agroinfiltration method and correlate the plant response to effector proteins with susceptibility to A. fabae. Techniques in molecular biology, plant pathology and biology, microscopy and bioinformatics will be employed in this project.

The effect of glyphosate on the viability and carpogenic germination of the fungal plant pathogen Sclerotinia sclerotiorum

Supervisors: Dr Matt Denton-Giles and Dr Mark Derbyshire

Greater than 20% of canola grown in Western Australia (WA) has a genetic modification that allows it to persist in the presence of the herbicide glyphosate. This technology is becoming ever more popular in WA as it allows for better weed control in broad acre agriculture. We are interested in investigating the interaction between glyphosate and the soil-borne plant pathogen Sclerotinia sclerotiorum.
The specific aims of this project are:

  1. To determine the environmental variables that promote/inhibit carpogenic germination of Western Australian S. sclerotiorum isolates.
  2. To test the effect of glyphosate in the germination of Western Australian S. sclerotiorum isolates.
  3. To use genomic and metagenomic data to investigate the interaction between glyphosate and S. sclerotiorum.

Geographic monitoring for agricultural crop disease

Supervisor: Dr James Hane

Spatial and temporal information relating to pathogen distribution and risk of outbreak will enhance farm management and increase profitability. Using cutting edge computational biology techniques to identify unique DNA sequences specific to individual microbial species and/or subspecies, you will apply this unique data resource to novel DNA detection technologies and explore development of on-farm sensor prototypes for field-based pathogen detection. Integrating species presence data within a national GIS framework, you will also identify trends in pathogen distribution, spread, evolution, etc. This will fortify national and international efforts to safeguard our future food security from the emergence of new and fungicide resistant pathogen species.

Pathogenicity effector discovery via large-scale protein sequence and structure similarity searches

Supervisor: Dr James Hane

Proteins that interact with a plant host and cause disease are called “effectors” and although a handful are known, their prediction remains one of the major goals of plant pathology. One of the most successful methods of widely assigning or predicting the function of related proteins has been sequence similarity (similar sequence = similar biological function). However many proteins have similar functions and yet have different sequences. But in some cases these are still similar in their 3D structure (similar shape = similar biological function). This project uses highly sensitive HMM-based search algorithms capable of detecting both sequence and structural homology. Through use of supercomputing resources you will apply this method to discover distantly related protein families of relevance to agriculture and protection of valuable crops from microbial diseases.

Comparing two establishment methods, seedlings and direct seeding of six native grass species and monitoring their palatability and recovery after grazing

Supervisors: Dr Sarita Bennett, Dr Susan Low, Jo Wheeler, David Collins

Many perennial grass species that are native to Western Australia and have declined in prevalence due to land clearing for annual cropping and grazing. Many of these species have the potential to compliment other native shrub and ground cover species identified as having value as a source of fodder especially during the autumn feed gap (CSIRO ENRICH project). With improvements in direct seeding machinery the option to establish native grass by seed could become a viable establishment method. Preliminary trial work conducted by Greening Australia to date has shown that these species will establish as tubestock seedlings and will recruit naturally once reintroduced to a favourable site. Little or no work has been conducted in these species to determine the palatability/attractivness of these grass species when other fodder shrubs are available and their recovery after grazing. This information would be invaluable in determining the most opportune time to graze.

The trial site has been selected at the property of Dean Butler situated between Koorda and Cadoux west of the Cowcowing Lakes. The property owner will undertake site preparation works such as weed and insect control. Greening Australia will assist/collect seed of 6 native grass species in Wongan Hills and Northam locations recording GPS and soil type information. Once the seed samples have been dried and cleaned representative sub samples will be x rayed at Kings Park to determine the estimated percentage of viable seeds, this will be confirmed by germinating these samples in a petri dish experiment (T. Bennett 2013). The remainder of the seed will be stored in a controlled temperature and humidity environment until needed for planting in trays for seedlings (November 2014) or direct seeded at the trial site (May/ June 2015). After seeding in May/ June 2015 exclusion area sub plots will be established to prevent any grazing from stock or wildlife. The site will be managed to control weeds, insects and grazing until November 2015 when stock will be introduced for a week/weeks then removed. Observations/measurements will then be made on grazing that occurred and compared to the grazing protected areas.

High-throughput gene orthology calculation and phenotype-based data mining

Supervisor: Dr James Hane

Orthologs are genes from two diverged species, which originated from the same gene in their last common ancestor species. Our research relies on application of this technique to up to 1000s of species, requiring supercomputing scale resources. In the study of fungal pathogens of crops, orthology analysis can be applied to discovering genes common to sub-groups of species (e.g. pathogens of wheat, but not pathogens of other crops) and from this we may broadly infer their biological role. This method also efficiently identifies laterally-transferred genes, which may be involved in crop disease.

Hunting for viral sequences and viral remnants in fungal genomes and RNA-seq next-generation sequencing data

Supervisor: Dr James Hane

Viruses of fungi, or mycoviruses, are capable of either reducing or increasing the virulence of fungal pathogens that cause crop disease, but are still relatively poorly studied. They integrate into host genomes, and may be detected through sensitive homology searches, or may also be detected within fungal RNA degradomes. Using enhanced sequence similarity search algorithms, you will search across multiple genome and RNA datasets to enable discovery of novel mycoviruses. Mycoviruses are believed to be common to fungal habitats, and may be responsible for otherwise unexplained variability between both crop-growing regions and experimental replicates.

Characterisation of Ascochyta lentis necrosis-inducing proteins in lentil, Lens culinaris, and related plant species

Supervisors: Dr Robert Lee, Dr Bernadette Henares and Dr Robert Syme

Ascochyta blight is a major disease of lentil, and is caused by Ascochyta lentis. Agroinfiltration is a method by which single fungal proteins can be expressed in host-plant leaves and detection of necrosis or cell death indicates a role for the candidate protein in causing plant disease. Using this system, you will characterise a necrosis-inducing protein from A. lentis. You will develop constructs for transient gene expression in lentil, characterise the necrosis reaction in susceptible host plants using plant-based assays, and light and fluorescence microscopy. You will employ bioinformatics analyses to look for similar proteins across the ascochyta species and fungal plant pathogens more broadly. Homologous genes in closely related species will be tested in both lentil and in their natural host plant species.

Establishing bioinformatic database resources for pathogenicity effectors that will help improve crop resistance to fungal and bacterial pathogens

Supervisor: Dr James Hane

Bioinformatic databases are fundamental to advancing modern biology, the best known example being GenBank – the database of almost all known DNA/RNA/protein sequences which underlies the extremely popular sequence similarity search tool BLAST. Scientific knowledge advances quickly and periodically new knowledge from independently published research needs to be aggregated into data repositories so that it can be considered as a whole and inform future research. Effectors are extremely important proteins in agriculture which cause disease in a host, independently of the pathogen that produced it. Effector sequences are extremely different from each other, therefore they are still not well understood or easily predicted computationally. In this project, you will compile a list of plant “cell-killing” protein toxins, and use the newly aggregated dataset to discover novel patterns and signatures common to effector proteins.

Dissecting the mechanism of fungal pathogenicity

Supervisors: Dr. Kar-Chun Tan and Prof. Richard Oliver

Parastagonospora nodorum is a serious necrotrophic fungal pathogen of wheat. In Australia, the pathogen is responsible for $108 million in yield loss of wheat per annum. In a recent study, the CCDM have identified a group of genes that are strongly expressed during infection. These genes are implicated in plant cell wall degradation, nutrient assimilation, effector function and signal transduction. The aim of the Honours project is to deduce the role of these genes in fungal pathogenicity using a molecular approach to generate gene knockout mutants.

Mutants will be assessed for pathogenicity and developmental defects using a wide range of molecular techniques. The project will provide the candidate with excellent training in molecular biology, bioinformatics, biochemistry, proteomics, metabolomics, microbiology, histology and plant pathology. These skills are sought after by many lifescience laboratories and pharmaceutical companies in Australia.

Modelling and Decision Support Systems for assessment of fungal diseases in climate change scenarios

Supervisors: Dr Fran Lopez Ruiz, Dr Miriam Munoz-Rojas

In a scenario of changing climate conditions, it is anticipated that cereals pathogen distribution will adapt to the new environment and that new virulence will emerge. As a result, control strategies will need to be improved in order to respond to the new hazard. Fungal diseases remain a major threat to cereal crop production in Australia being controlled at present by a combination of host genetic control, cultural methods and pesticide applications. The use of integrated pest management strategies significantly reduce the number of fungicide treatments and thus resources spent on crop disease control (Pautasso et al., 2012). However, the recent spread of fungicide resistance to major chemical groups in grain fungal pathogens in Australia threatens current control strategies (Tucker et al., 2013; Lopez-Ruiz et al., 2013).

Further research on climate change and assessment of plant diseases needs to be undertaken, developing new tools and involving multiple factors to provide effective measures for land management. A system able to fill the gap between environmental factors such as climate, soil or land use and management and crop protection strategies is, arguably, one of the major requirements that the Australian cereal industry needs to overcome the risk of competitiveness loss as a consequence of increased crop disease.
In this context, predictive models can be extremely useful for the estimation of crop-diseases interactions and to explore different scenarios under a variety of climate and management conditions (Stokes and Howden, 2008; Muñoz-Rojas et al., 2013). Models predicting the incidence of the disease at key stages of the crop cycle allow farmers and advisors to optimize crop-protection strategies, such as fungicide application (Cohen et al., 2012).

The objective of the project is to improve the management of crop diseases caused by fungal pathogens in Australia through the development of new tools for prediction and assessment of the fungal infection, severity and distribution, under different scenarios of climate and land management. This research will focus on cereals, in particular wheat and barley, due to their economic importance to the Australian farming system, and major cereal fungal diseases will be assessed.

Using fodder shrubs to rehabilitate degraded farmland

Supervisors: Dr Sarita Bennett and Dr Sue Low (Curtin University), David Collins (Greening Australia, Jo Wheeler (Wheatbelt NRM)

Various projects with a focus on:

  • Plant growth, nutrition and feed availability
  • Sheep pregnancy rates, lambing rates and lamb survival
  • Improving plant biodiversity
  • Improving soil health
  • Micro-climate advantages for soil health and animal welfare

Please note: These projects may involve some field work. The student is required to have a current driver’s license and contribute their own transport to the project, as well as being willing to undertake fieldwork in potentially remote locations.

Regulation of postharvest life and quality of stone fruits using ethylene antagonists

Supervisors: Prof Zora Singh and Dr Alan Payne

More than 30% of horticultural produce is lost before it reaches to consumers. Postharvest losses are estimated to be 2.4 billion $ to Australian Horticulture industry. Ethylene management plays an important role in extending storage life, maintaining quality and reducing postharvest losses in horticultural produce. Previously, we have identified some potential ethylene antagonists and their role in mitigating the adverse effects of ethylene in pome fruits has been investigated. There is prospective opportunity for honours student to investigate the role of new robust ethylene antagonists on ethylene production, respiration rate, storage life and quality of stone fruits (peach, nectarine or plum).

Incorporating the perennial Tedera (Bituminaria bituminosa) into wheatbelt farming systems of WA using APSIM

Supervisors: Dr Sarita Bennett, Dr David Ferris and Dr Daniel Real (DAFWA, South Perth), Dr Roger Lawes (CSIRO)

Tedera is a perennial forage legume, originally from the Canary Islands that has been shown to have potential in the wheatbelt of WA, particularly in lower rainfall areas. Trials have been conducted over the last 10 years on variety selections. The work has now progressed to expanding results across the wheatbelt of WA with a cultivar ready for release.
APSIM (Agricultural Production Systems sIMulator (APSIM) is internationally recognised as a highly advanced simulator of agricultural systems. It was developed by CSIRO and has now been used extensively overseas as well as across the agricultural regions of Australia.

Using field trials sown and managed by DAFWA in a number of locations around the wheatbelt, collect required data on plant growth, soil water use and grazing habit, so that Tedera can be built into the APSIM model to model its fit across various mixed farming systems in WA and into a number of different agro-environments.

Effect of cutting and grazing on messina (Melilotus siculus) regrowth and production

Supervisors: Dr Sarita Bennett, Dr Phil Nichols

Messina (Melilotus siculus) is a very promising new annual pasture legume with high tolerance of both salt and waterlogging, which is undergoing varietal selection trials to select a new cultivar for agriculture. There is considerable variation in growth habit between varieties and this is likely to lead to differences in their ability to recover from grazing or cutting. Furthermore, grazing and cutting management strategies need to be devised to give guidance to farmers. This project will be important in helping develop these guidelines and for making a final selection decision on which genotype to release as a new cultivar.
Field trials of a number of accessions from collections in Spain and Israel were sown in the wheatbelt in 2011. These sites will be used for studies looking at the recovery of Messina after grazing or simulated cutting. Samples of the plots will be cut at various times and with a range of recovery times over the winter and early spring period to determine the accessions that are the most persistent and show the best recovery after grazing. There may also be the opportunity to sow plots of Messina with a variation of growth habits at Bentley for more detailed simulated grazing experiments.

Characterisation of Ascochyta rabiei necrosis-inducing proteins in chickpea, Cicer arietinum

Supervisors: Dr Robert Lee, Dr Bernadette Henares and Dr Robert Syme

Ascochyta blight is a major disease of chickpea, and is caused by Ascochyta rabiei. Effector proteins and necrosis-inducing proteins of necrotrophic fungal pathogens mediate disease in plants by initiating a hypersensitive response that can be detected as necrosis or cell death in plant tissues. We have developed a system for expressing fungal proteins in plant leaf tissues and have identified several proteins that may be important for development of disease in ascochyta blight-causing species. In this project you will characterise a necrosis-inducing protein from A. rabiei using techniques in molecular biology, plant-based assays, light and fluorescence microscopy, protein chemistry and genetics. You will employ bioinformatics analyses to look for similar proteins across the ascochyta species and fungal plant pathogens more broadly.

Comparative genomics of fungal pathogens of an emerging crop, narrow-leaf lupin

Supervisor: Dr James Hane

Lupin is an emerging crop of significance in agriculture, livestock and human health. It is used in crop rotations where over a period of years it can improve the profitability of wheat and other crops. Its ability to fix atmospheric nitrogen is also useful for soil improvement and its rotation also provides a ‘disease break’. It is also used as livestock and aquaculture feed and is growing as a human health food. Yet there are a number of limitations that hold back this crop’s potential to be widely adopted, one of which is risk of crop disease. Its two major fungal pathogens, commonly known as anthracnose and phomopsis (Colletotrichum lupini and Diaporthe toxica) cause significant yield and quality losses. They also produce toxins that are harmful to both livestock and human health. In this project, you will help establish new genomic resources for these pathogens and perform comparative genomics versus related species to identify genes relevant to pathogenicity.