Differentiation of cucumber mosaic virus subgroups by RT-PCR RFLP

A new cucumber mosaic virus (CMV) subgroup based on recent sequence data has been proposed by Palukaitis and Zaitlin (1997) to distinguish between some strains in the former subgroup I. The three subgroups are tentatively named IA, IB and II. Here we describe a simple and rapid procedure based on the reverse transcriptase-polymerase chain reaction (RTPCR) followed by enzymatic digestion (RFLP) to identify and classify CMV isolates accurately into the three subgroups. Two specific primers that target CMV RNA-2, amplify a DNA fragment of approximately 650 bp which yields three different restriction patterns after digestion with MluI. Each pattern proved specific for CMV strains of each subgroup. This method proved innovative in differentiating CMV strains in subgroups IA, IB and II rather than only in subgroups I and II and may provide a simple way to investigate the dynamics of CMV populations in nature.