noxB-based marker for Alternaria spp.: a new diagnostic marker for specific and early detection in crop plants.

Alternaria species are a major plant pathogen and their precise detection and identification is crucial for effective management. In the present study, a polymerase chain reaction (PCR)-based diagnostic technique has been developed for detection of Alternaria species. Four primers were designed for four genes viz. noxB, AMK1, AKT3 and NIK1. In gradient PCR, only the primer sets for noxB gene showed specific amplicon of ~ 200 bp in all the isolates of Alternaria, while no amplification was observed in related fungal species such as Ulocladium botrytis, Ulocladium consortiale, Stemphylium vesicarium, Cochliobolus tuberculatus, Curvularia prasadii, and Bipolaris sorokiniana. The noxB primer set was used as diagnostic marker to discriminate and diagnose Alternaria species in nine different crop plants. Real-time assay revealed that the primer set was able to detect Alternaria noxB genes in leaves with no characteristic visible symptoms. Through real-time PCR, the noxB gene of Alternaria could be detected even in 0.5 ng of host DNA. This is the first report of noxB gene for molecular detection of Alternaria spp.