Boosting diagnostics for plant production industries

1. Fusarium oxysporum is an important pathogen, rapid and accurate differentiation between the various formae speciales and between the pathogenic and non-virulent strains will assist disease management in the field, diagnostics and biosecurity. The research aims to identify the various fungal effector molecules associated with fungal virulence that are present in the Australian F. oxysporum species complex and to identify those potential effectors that can be used to differentiate certain strains. This research will provide alternative formae speciales specific molecular detection methods which would be rapid, accurate and could replace labour- and time-intensive disease assays.

2. Building capability in cyst nematode identification The project will be a PhD study. The aims are three-fold:

1. to build capability in cyst nematode taxonomy,
2. to utilise suitable genomics approaches to identify suitable molecular markers for species identification and possibly biotype identification, and
3. to develop diagnostic tests that can be used to detect key cyst nematodes in soil and in planta for diagnostics and molecular epidemiology.

3. Surge capacity for high priority plant pathogenic bacteria and viruses HTP and in-field diagnostic assays (e.g. LAMP) will be developed for a range of high priority bacteria and viruses that threaten horticulture crops. These assays will be validated as part of an industry driven "blitz" activity where field samples are collected and submitted for testing.

Currently Grapevine red blotch virus poses a threat to Australian viticulture and there is no diagnostic capability to detect this pathogen. Existing molecular assays developed off-shore will be validated and adopted for use in Australian diagnostic laboratories together with the development of an in-field diagnostic assay, such as LAMP, recombinase polymerase amplification (RPA) or PCR, to support in-field triage activities.

As part of a national plant bacteriology project focussing on the Xanthomonas genus, AVR staff will develop high throughput diagnostic protocols for X. fragariae, a high priority pest that threatens the Australian strawberry industry. This assay, together with a LAMP assay will be incorporated into the NDP for X. fragariae

This activity will build capacity amongst Australian diagnostic laboratories to cope with sample surge during an incursion through provision of NDPs. A workshop will be held to train a range of stakeholders including diagnosticians, biosecurity officers and industry to build national capability and capacity for in-field diagnostic testing to detect GRBV and X. fragariae

5. Spotted winged Drosophila (Drosophila suzukii)

The proposed work will develop and evaluate metabarcoding for spotted wing drosophila (SWD) diagnostics.

Molecular markers for SWD have already been developed, and in this research project we will:

1. develop laboratory protocols to enable diagnostic molecular marker/s to be used for simultaneous identification of multiple Drosophila species (i.e. identification of SWD, and other drosophilid pest and non-pest species),
2. validate these protocols on known bulk samples to examine limits of detection and sensitivity,
3. apply these methods to real trap catches, including preserved traps samples obtained from overseas, as well as spiking Australian traps with dead SWD
4. optimise in-field rapid diagnostics technology (LAMP) for the identification of SWD larvae, and
5. incorporate SWD LAMP surveillance protocols into the current SWD NDP.