Comparison of real-time PCR detection systems using naturally infected Botrytis cinerea berry samples

Plant disease surveillance systems with proper diagnostic tools can lead to a better understanding of the dynamics of disease development on crop hosts and also help in applying effective management practices to control crop diseases. Advances in the use of molecular quantification techniques have allowed for the rapid detection of pathogens in planta and monitoring airborne plant pathogens. Real time quantitative PCR (qPCR) is commonly used to quantify the amount of pathogen DNA in infected plant samples and quantify the pathogenic conidia in air samples. However, this technique requires expensive equipment and reagents. Miniaturization of the equipment and the use of smaller reagent volumes has helped to decrease the cost associated with using qPCR-based detection. The aim of this study was to compare the use of the Bio-Rad qPCR system with the microchip-based AriaDNA system. The AriaDNA system uses disposable microchips containing lyophilized reagents and small (са. 2 µL) volumes of DNA. Both systems were compared to detect Botrytis cinerea (Pers.) in naturally infected berry fruits of strawberries, raspberries, and blueberries as well as detection of the air-borne conidia from air samplers placed in berry fields. Similar results were obtained from the AriaDNA and the Bio-Rad CFX Connect qPCR systems to detect B. cinerea from host tissues and air samplers. The AriaDNA microchip was easier to prepare, required miniature volumes of DNA and reagents, and results were obtained quicker than with the Bio-Rad system.