Detection and Quantification of Bremia lactucae by Spore Trapping and Quantitative PCR

• DOI: 10.1094/phyto-03-16-0143-r
• Publication Date: 2016-07-08T13:20:41Z
• Authors: Sridhara G. Kunjeti; Amy Anchieta; Frank N. Martin; Young-Joon Choi; Marco Thines; Richard W. Michel...; Steven T. Koike; Cayla Tsuchida; Walt Mahaffee; Krishna V. Subbarao; Steven J. Klosterman
• Keywords: Spores; 2. Zero hunger; 0303 health sciences; Geography; Air Microbiology; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Fungicides, Industrial; Plant Leaves; 03 medical and health sciences; Oomycetes; DNA Primers; Lactuca; Plant Diseases

Bremia lactucae is an obligate, oomycete pathogen of lettuce that causes leaf chlorosis and necrosis and adversely affects marketability. The disease has been managed with a combination of host resistance and fungicide applications with success over the years. Fungicide applications are routinely made under the assumption that inoculum is always present during favorable environmental conditions. This approach often leads to fungicide resistance in B. lactucae populations. Detection and quantification of airborne B. lactucae near lettuce crops provides an estimation of the inoculum load, enabling more judicious timing of fungicide applications. We developed a quantitative polymerase chain reaction (qPCR)-based assay using a target sequence in mitochondrial DNA for specific detection of B. lactucae. Validation using amplicon sequencing of DNA from 83 geographically diverse isolates, representing 14 Bremia spp., confirmed that the primers developed for the TaqMan assays are species specific and only amplify templates from B. lactucae. DNA from a single sporangium could be detected at a quantification cycle (Cq) value of 32, and Cq values >35 were considered to be nonspecific. The coefficient of determination (R2) for regression between sporangial density derived from flow cytometry and Cq values derived from the qPCR was 0.86. The assay was deployed using spore traps in the Salinas Valley, where nearly half of U.S. lettuce is produced. The deployment of this sensitive B. lactucae-specific assay resulted in the detection of the pathogen during the 2-week lettuce-free period as well as during the cropping season. These results demonstrate that this assay will be useful for quantifying inoculum load in and around the lettuce fields for the purpose of timing fungicide applications based on inoculum load.