SEQUENCE AND RELATIONSHIPS OF SUGARCANE MOSAIC AND SORGHUM MOSAIC-VIRUS STRAINS AND DEVELOPMENT OF RT-PCR-BASED RFLPS FOR STRAIN DISCRIMINATION

Sugarcane mosaic is the most widespread virus disease affecting sugarc ane production. We have established a collection of seven prominent su garcane mosaic potyvirus (SCMV) strains currently causing disease in s ugarcane throughout the world and originally found in sugarcane in the United States. This collection includes SCMV strains A, B, D, and E, and the sorghum mosaic virus (SrMV) strains SCH, SCI, and SCM. These v iruses were propagated on Sorghum bicolor cv. Rio and purified. Cloned cDNAs representing 2.0 kb of the 3' termini, obtained after a reverse -transcriptase-polymerase chain reaction (RT-PCR) on purified virions using an oligo(dT) primer and degenerate primers with sequences locate d in the NIb gene, have been sequenced for each of these strains. A co mparative analysis of the deduced amino acid sequences in the NIb and coat protein genes and of the nucleotide sequences in the 3'-untransla ted region, among these seven viruses and among six other members of t he SCMV subgroup, confirms that there are at least four, but suggests that there are five, distinct viruses in the SCMV complex. Based on th ese seven new sequences and on the available sequence data for six oth er members of the SCMV subgroup, we have developed group-specific prim ers for use in RT-PCR-based restriction fragment length polymorphism a nalysis for rapid discrimination between strains of SCMV and SrMV. Thi s is the first assay for differentiating strains of SCMV and SrMV that does not require interpretation of symptoms on differential hosts.