Reverse transcription loop-mediated isothermal amplification based rapid detection of Sugarcane mosaic virus and Sugarcane streak mosaic virus associated with mosaic disease of sugarcane

Sugarcane mosaic virus (SCMV) and Sugarcane streak mosaic virus (SCSMV) belonging to the family Potyviridae are the causal agents of mosaic disease complex of sugarcane reported from different Asian countries which causes significant economic losses to sugarcane production. In the present study, a sensitive RT-LAMP based assay was developed for rapid diagnosis of SCMV and SCSMV causing mosaic disease of sugarcane. Primers were designed to amplify the six different regions of the coat protein genes of SCMV and SCSMV and both the viruses were successfully detected by this technique. Comparative analysis of RT-LAMP with the conventional reverse transcription polymerase chain reaction (RT-PCR) and quantitative real time PCR (RT-qPCR) showed that RT-LAMP was more sensitive than the other methods due to its rapid visual detection of the viruses. The sensitivity of RT-LAMP assay developed in the present study was tenfold more than that of conventional RT-PCR and RT-qPCR techniques. This is the first report of RT-LAMP based diagnosis of SCMV and SCSMV from India. © 2020, Indian Phytopathological Society.