Arable Crop Disease Alert System

Abstract

This multi-disciplinary project aimed to produce an automated air sampling device, able to use a DNA-based method to detect airborne spores of key pathogens and text results for display on a website so that growers can react to smart spray applications. The system was designed for multiple devices to operate as a network to enhance information quality.

The high-volume devices, developed by the Burkard Manufacturing Co. Ltd, (Rickmansworth), sample 300 L/minute of air, and were found to detect spores affecting broad-acre crops in the proximity of a farm-yard, allowing the device to be mains-powered and located in a secure position. The device has excellent collection efficiency for spores as small as 4 µm (aerodynamic diameter) and is programmed by the user to sample for a set period each day.  The collected sample is processed in liquid to burst all spore types to release DNA, a sub-sample is then transferred to a reaction tube where an isothermal DNA-based assay takes place. Two types of DNA-based assay can be used, LAMP or RPA assays, which differ in their reagents and the temperature of the reaction (65-72 or 37-40 ֯C, respectively).  The assay is measured by fluorescence and results are sent wirelessly by an internal 4G router to a server.  Up to three different target pathogens can be tested from the same sample each day.  Weather data, collected by an on-board met station, are also sent by text every 10 minutes.  The data are automatically processed, collated and displayed on a web-portal.  Simple rules applied to the data allow an automated calculation of the spore detection assay, indicating zero, low or high numbers of spores present and an estimation of occurrence of infection conditions can currently be made for yellow rust and Sclerotinia.  Each device requires weekly attendance to replenish reagents and tubes and to perform simple maintenance. 

The project has also developed new LAMP assays for the following pathogens: Pyrenopeziza brassicae Sclerotinia sclerotiorum, Zymoseptoria tritici, Rhynchosporium sp, Oculimacula yallundae & O. acuformis (joint assay), Alternaria solani, and for fungicide insensitivity in Zymoseptoria tritici (assays for reduced DMI sensitivity and separately an assay for multidrug resistance including reduced DMI and SDHI sensitivity).  Other published assays were assessed for sensitivity and specificity to UK pathogens (Phytophthora infestans, Puccinia striiformis and Fusarium graminearum). 

This novel device will lead to a new approach in precision agriculture by providing information in near real-time, on the presence of airborne spores and the weather conditions necessary for infection. The technology will in time, with use of appropriate reagents (DNA primers), be translated to improve disease control in other AHDB sectors and could be available for fungicide resistance monitoring in addition to disease forecasting.