Plant Pathogen Detection
DNA Auto Spore Sampler
The DNA auto spore sampler is the world's first automated field analyser specifically designed for early warning system for the detection of crop disease pathogens within crop growing environments. One analyser can monitor a wide geographic area of around 100 Ha (dependant on local environmental conditions) and can be configured to detect multiple crop disease pathogens. Each in-field analyser transmits 4G mobile data for analysis in the cloud. This technology was developed as a result of Innovate UK funding in partnership with Agri Samplers Ltd. Polygenyn Ltd and Rothamsted Research.
The DNA auto spore sampler combines innovative technologies from Agri Samplers Ltd and Polygenyn Ltd. The spore sampler can capture, sample and analyse airborne pathogens within the machine in real-time without the need for human intervention for up to 8 days.
The auto spore trap samples 300 litres of air per minute, collecting airborne particles, such as fungal spores and bacteria into a sampling tube. The spore trap can be flexibly configured by the user to sample for defined period within a 24-hour period into each pot (usually 6am to 6pm which mirrors the spore release times),
Once the sample has been collected, the instrument starts the analysis cycle automatically. It doses a predetermined volume of lysis buffer into the sample chamber. It then physically breaks open the spores releasing the spore DNA for analysis.
The instrument then collects a known volume of sample for further processing. The resulting purified DNA is pipetted into a reaction tube which contains all the constituents needed to carry out a pathogen DNA test in freeze dried form. This tube is heated to 65oC, and the fluorescence of the sample measured over a 60-minute period. The resulting amplified DNA is quantified by the measurement of a fluorescent signal that correlates to the amount of DNA bound to a fluorescent dye in the reaction tube.
If airborne pathogens are detected which reach a level that creates a risk to crops an SMS alert is sent to the grower. An alert is also sent to the on SpraySaver.co.uk web site portal so that preventative action can be taken. Currently the instrument is capable of detecting up to 4 pathogens from a single spore sample simultaneously. The instrument is effective within a 5-mile radius of the sampling site, helping to monitor and protect multiple crops on a farm throughout key times of the year.
Crops Currently Covered
The following DNA assays have currently been developed for use with the DNA Auto Spore Sampler:
- Potato late blight (Phytophthora infestans).
- Sclerotinia spores, which affect oilseed rape (canola), sunflowers and a range of vegetables, carrots. lettuce, beans, celery, chicory, cucumbers, tomatoes and peas.
- Yellow Rust (Puccinia striiformis) wheat and barley.
- Brown Rust (Puccinia triticina) wheat.
- Septoria tritici, wheat, rye, cucumbers, melons and tomatoes.
- Botrytis cinerea, grapes and soft fruits, strawberries, raspberries, blueberries.
- Grape powdery mildew, vineyards.
We are currently developing and testing a range of other different DNA assays covering more plant pathogens such as onion downy mildew and cercospora beticola in sugar beet.
Pathogen Early Warning System
Installing the DNA Auto Spore Sampler on a building or raised platform provides an effective early warning system and allows growers to react swiftly to impending crop infections by spraying only when required. The ability to load the machine with more than one type of DNA test marker means that multiple crops can be protected using one device.
Rather than spraying regularly on a preventative basis regardless of infection risk, the early warning reactive approach means less chemicals are required resulting in considerable cost savings and fewer harmful chemicals being used unnecessarily, where it may affect other beneficial species.
Benefits for Growers
With the DNA Auto Spore Trap, growers receive an early warning of rising pathogen risks. This, combined with weather data, can help determine whether to spray the crop, delay spraying or even not spray at all.
The benefit of this system means significantly less chemicals are used in the protection of crops. The grower can move from a costly regular prophylactic prevention-based spraying to a more cost-effective responsive reaction-based approach.
The system can cost-effectively improve disease surveillance and forecasting to allow fungicide applications before a significant level of crop infection occurs. Accurately targeting fungicide use only, when necessary, saves significant costs per hectare on fungicides and reduces unnecessary crop spraying, while improving crop yields. It can also remove the use of fungicides in unnecessary applications, thereby protecting biodiversity and the environment for future generations.
Benefits for Researchers
The DNA Auto Spore Sampler is an extremely useful tool, able to monitor far more crops than previous non-autonomous systems. These savings include time in the field as well as the speed and efficiency of collating and analysing the data. With this new machine, data can be collected almost on a real-time basis adding an extra significant dimension to the data set and potential modelling of the pathogen.
Benefits for Chemical Industry
Modelling the efficacy of current pesticides in the field in real situations and weather events in near real-time can significantly enhance the development of new chemical-based crop protection. The new DNA Auto Spore Trap is the tool that enables far more detailed monitoring on an automated basis, reducing costs and improving data modelling.
Stabilisation of LAMP Assay Reagents
Polygenyn has successfully stabilised and freeze dried the complex reagent mix for the LAMP assays required for the detection of potato blight, sclerotinia, yellow rust, brown rust, septoria, botrytis and grape powdery mildew . These tests have now been produced for field trials in 2024 and new field trials are planned for 2025.
12 months stability of the potato blight LAMP assay at room temperature. The results show the LAMP assay specificity and sensitivity remains unchanged compared with the freshly manufactured reagents. The LAMP assay reagents have also been tested at elevated temperatures. We have stability data that shows no change in LAMP assay sensitivity when stored at 40oC for 2 months. These products have been successfully deployed in field trials and have shown to remain active over a growing season of 4 months.
Contact us for supply of stabilised Lamp Reagents. guido@polygenyn.co.uk
PathoScout
Pathoscout is our Portable Pathogen analyser, the next generation testing platform based on the DNA auto sampler. This instrument is under development as part of a 2 year Innovate UK development programme. This system incorporates all the sample preparation steps and analysis into a microfluidic chip which is measured using the Pathoscout portable instrument.
This instrument enables the grower or agronomist to walk the fields or polytunnels with the instrument which can carry out air analysis or leaf analysis on site. Results are obtainable within 60 minutes. This technology is in direct competition with laboratory tests for these pathogens which typically take up to 5 days. The results from the portable instrument are saved to the instruments internal memory and sent to the user by SMS warning of early disease outbreak. This early warning system enables pathogen detection before visible signs of disease are detectable on the crops.
Following the successful development of the DNA auto spore sampler, we were inspired to make a simpler portable filed testing instrument combining the air sampling expertise of Agri Samplers Ltd. the diagnostic assay development and stabilisation technology of Polygenyn Ltd. The academic expertise in LAMP assay development and aerobiology of Rothamsted Research under the guidance of Professor Jon West and the microfluidics expertise of MicroBritt Ltd.
It became obvious that the only institutes that could analyse the captured spores were academic institutions. Rothamsted Research had already developed a number of LAMP DNA assays in order to detect plant disease pathogens. Following discussions with a number of growers, Rothamsted Research and Polygenyn Ltd. a consortium was put together to apply for Innovate funding to address the lack of a field based automated spore pathogen analysis system. As a result, the DNA autospore trap and the Pathoscout instruments were created that could automate field-based DNA LAMP assays for a number of specific plant pathogens.
The microfluidic chips will incorporate field stable LAMP assays for the detection of plant pathogens such as: Potato blight, sclerotinia, yellow rust, brown rust, septoria, botrytis and grape powdery mildew.
The institutions involved in the creation of the DNA autospore sampler and the PathoScout portable analyser include Agri Samplers ltd. Polygenyn Ltd. Rothamsted Research and Microbritt Ltd. The Spraysaver and PathoScout and projects were funded by Innovate UK.