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DNA testing innovation to reveal new insights

The South Australian Research and Development Institute’s Alan McKay with a DNA-testing PCR instrument that will enable better surveillance of disease pathogens.
Photo: Brad Collis

Key points

  • New DNA tests are being developed to better identify pathogens collected during surveillance activities
  • These insights are already shedding new light on pathogen behaviour and distribution

Work has begun on developing a new, comprehensive pathogen surveillance system to identify organisms behind visual disease symptoms and allow growers and advisers to make far more accurate diagnoses than what is currently possible with visual identification.

The planned surveillance system will be an extension of the revolutionary PREDICTA® B test for soil and stubble-borne pathogens. PREDICTA® B was developed by the South Australian Research and Development Institute’s (SARDI) Molecular Diagnostics Centre (MDC).

The centre, which is a GRDC and SARDI investment, is now adapting this technology further to detect foliar pathogens in plant samples or spores collected from the air in spore traps. It has the potential to enable a comprehensive pathogen surveillance system to identify the organisms behind visual disease assessments and to clarify mixed infections.

The MDC is developing this plant health surveillance approach in collaboration with the NSW Department of Primary Industries (DPI) and in a national Rural R&D for Profit project, iMapPESTS.

The new DNA tests detected pathogens in mixed infections and in senescing crops that were not easily distinguished by visual assessments.

The objective is to overcome the misdiagnosis and missed diagnosis that can happen with visual inspections or when symptoms are mild or masked by other plant diseases and stresses.

A system that can detect the presence of a wide range of multiple plant pathogens would provide an early warning system for the risk of disease incidence by location and time.

It would also enable rapid mapping of new pathogen incursions and support disease-free status claims to enable market access.

The new testing protocols use qPCR – or quantitative Polymerase Chain Reaction – to detect and quantify the nucleic acids specific to a pathogen’s DNA. This technology is able to quantify how much of the pathogen is present in a sample and may, in future, help inform the development of economic thresholds.

Improving surveillance

The MDC has developed qPCR tests for the leaf and stem pathogens that cause Fusarium head blight, Septoria tritici blotch and Septoria nodorum blotch of wheat, scald and Ramularia leaf spot of barley and a general rust test to support NSW DPI’s cereal surveillance program.

Collected tillers were visually assessed for disease symptoms and supplied to the MDC for further DNA analysis. The tests confirmed the visual assessments and also detected pathogens in mixed infections and in senescing crops that were not easily distinguished by visual assessments.

For example, the DNA tests highlighted that co-infection by Fusarium crown rot and common root rot appeared to mask underlying lower levels of take-all infection in 93 per cent of wheat crops surveyed in NSW in 2019.

There was good correlation between the levels of pathogen DNA detected by the qPCR tests and the visual assessments of disease. For instance, crops with higher incidence of basal browning associated with Fusarium crown rot had elevated Fusarium DNA levels in the qPCR tests.

New tests were also developed for spore trap samples for iMapPESTS, a proof-of-concept project to demonstrate how national cross-industry surveillance data can alert growers when crops are exposed to potential infection by specific airborne pathogens and pests. Tests developed include Ascochyta in lentils, Botrytis grey mould, chocolate spot, Sclerotinia and Septoria tritici blotch.

Early results demonstrate the benefits of data-rich surveillance activities to inform growers and underpin further research.

More information: Dr Alan McKay, 08 8429 2216,; iMapPESTS

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