This project developed capabilities to improve traceability of diagnostic samples and support rapid detection of significant crop diseases.
A prototype fit-for-purpose phone App was developed to increase ease, efficiency, traceability, and reliability of managing diagnostic samples. The App was designed to enable collection of sample specific metadata and full traceability from the field to the laboratory via a QR code system. Testing and refinement of the App are underway.
A rapid near field testing capability to support crop management decisions was developed by transferring SARDI existing high throughput technology and quantitative PCR (qPCR) tests to a portable platform. The new capability was first evaluated and optimised in laboratory settings using wheat foliar diseases yellow leaf spot, Septoria tritici and Stagonospora nodorum as a proof of concept. The technology was successfully used to diagnose other diseases, including scald (Rhynchosporium commune) and Black leg (Leptosphaeria maculans). SARDI partnered with Elders to demonstrate the technology; staff were trained to deliver the technology in a near-field setting and demonstrated the capability on several occasions to other agronomists and growers. The range of diseases and crops can be expanded in the future, to include leaf diseases of other cereals, pulses, vegetables, and pesticide resistance.
Project description:
This project developed capabilities to improve traceability of diagnostic samples and support rapid detection of significant crop diseases.
Diagnostic sample traceability and integrity are integral to the diagnostic process. However, the metadata associated with the samples is generally manually collected; it can be illegible and is vulnerable to transcription errors when entered in the laboratory information management system. Samples can be badly handled, affecting the reliability of the diagnostics. The project developed a phone App to enable accurate collection of sample metadata and support the diagnostic laboratory to better manage sample flow. Dedicated sample kits each including a bag and unique QR code were designed.
The App and associated recommendations allow the end user to collect appropriate sample metadata by scanning the bag QR code and inputting sample specific details, while recording GPS coordinates in the background. The App also timestamps crucial timepoints such as sample collection and submission. A prototype App has been developed and demonstrated to several key pathology and Elders SA staff. SARDI is eager to pursue the completion and delivery of the App as funding allows and this will be offered to those that complete the PREDICTA® B training, as well as other grower and agronomist contacts throughout SA. Additionally, this will be used by researchers as a valuable tracking tool for their samples. Sample kits will be made available to end users once the App is accessible online.
Enabling accurate disease diagnostic outside the laboratory is generating significant interest from the industry. Near or in-field rapid diagnostics can facilitate agronomists and growers inspecting crops and support decision making. Such capability is particularly suited to leaf disease diagnostics where timely detection underpins effective and efficient management decisions to minimise losses. Testing samples in or near field allows for faster turnaround time by simply eliminating the transport time to the central laboratory.
With more than 150 quantitative PCR (qPCR) tests for a broad range of plant pests, diseases, and beneficial organisms available, the SARDI molecular diagnostic centre (MDC) has been delivering high throughput molecular diagnostic to the industry for many years. Using the results of the high throughput platform as a benchmark, the project successfully transferred a few selected tests to the Biomeme portable qPCR platform. The proof of concept first evaluated and optimised the Biomeme platform in laboratory settings using wheat foliar diseases yellow leaf spot, Septoria tritici and Stagonospora nodorum as a proof of concept. When using the same PCR conditions as in the high throughput lab (with minor volume modifications), all assays performed well on the Biomeme, as measured by comparing positive controls across platforms. Optimisation focused on simplifying the protocol to facilitate use in a near field setting. In particular, the preparation of stabilised qPCR reaction tubes precoated with key reagents drastically streamlined the workflow, further reducing the risk of cross contamination and pipetting errors. The technology was further used to diagnose other diseases, including scald (Rhynchosporium commune) and Black leg (Leptosphaeria maculans).
To deliver this capability in the regions, the MDC partnered with Elders and trained select members of their staff to carry out the tests. Elders staff members were able to demonstrate their capability on several occasions, delivering tech-demos to other agronomists and growers.
For Septoria tritici, a correlation between percentage infected leaf area and our test results was established, demonstrating the potential of the technique to quantify infection in the field with further work on sampling strategy. To determine the applicability of testing leaf samples from the field over the course of a season, nine Elders staff collected one hundred 20-leaf samples for testing using established tests for Yellow leaf spot and Septoria tritici. Over the season, a trend of increasing pathogen levels on the leaves became evident in some areas. However, it was also noteworthy that leaves were also testing positive in paddocks prior to symptoms emerging later in the season. This indicates that the process could be useful as an early detection tool during the pathogens latent phase in the plant. The range of diseases and crops can be expanded in the future, to include leaf diseases of other cereals, pulses, vegetables, and pesticide resistance. Elders SA and SARDI are continuing to investigate applications of the portable qPCR technology, specifically looking into known resistance genes of fungal pathogens.
Key achievements and results:
The Biomeme portable qPCR machine can be used to run small numbers of samples using established foliar disease tests developed by the SARDI-MDC. The project over-delivered in this area, validating six tests on the Biomeme system. The extraction protocol for a 20-leaf sample is effective and consistent (when comparing between laboratory staff), with the potential to monitor for errors using an internal control test specific to the host plant. Zymoseptoria tritici can be detected in non-symptomatic leaf material, providing the opportunity for early detection.
Two Elders team members have been trained in independently carrying out the tests, which has demonstrated further work is required in: contamination control; homogenisation techniques; sample/test identification and tracking; internal controls (for hosts other than wheat), and subsequent result interpretation that will be required with this. There has also been further interest regional testing capabilities for monitoring wheat powdery mildew, rust and blackleg of canola. In particular, interest around monitoring known resistance in plant pathogens (e.g. fungicide resistance) is an area of future opportunities.
Although the app is not yet able to be distributed, the prototype running outside of the myPIRSA system and app stores is functional. SARDI are committed to finalise the app in collaboration with DataEffects and PIRSA.
Further information: