Detection of three major RNA viruses infecting sugarcane by multiplex reverse transcription-polymerase chain reaction (multiplex-RT-PCR)

A multiplex reverse transcription-polymerase chain reaction (multiplex-RT-PCR) was developed for the detection of Sugarcane mosaic virus (SCMV), Sugarcane streak mosaic virus (SCSMV) and Sugarcane yellow leaf virus (SCYLV), three of the major RNA viruses widely prevailing in the sugarcane-growing regions around the world. Primers designed from the coat protein genes of the respective viruses amplified fragments of similar to 860 bp (SCMV), similar to 690 bp (SCSMV) and similar to 615 bp (SCYLV) in multiplex-RT-PCR. In this study, we could specifically detect the target viruses in disease-suspected sugarcane cultivars. Of nine samples tested, four were found infected with all three targeted viruses, two had infections of SCMV and SCSMV and the remaining three samples had the viruses found separately. Furthermore, multiplex-RT-PCR was found to be equally efficient to uniplex-RT-PCR to amplify the target viruses from sugarcane. This is the first report on detecting three viruses together in a single PCR reaction in sugarcane and this will have immense application in sugarcane quarantine programs.