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 sugarcane production. We have established a collection of seven prominent sugarcane mosaic potyvirus (SCMV) strains currently causing disease in sugarcane 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 viruses 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 located in the NIb gene, have been sequenced for each of these strains. A comparative analysis of the deduced amino acid sequences in the NIb and coat protein genes and of the nucleotide sequences in the 3'-untranslated region, among these seven viruses and among six other members of the SCMV subgroup, confirms that there are at least four, but suggests that there are five, distinct viruses in the SCMV complex. Based on these seven new sequences and on the available sequence data for six other members of the SCMV subgroup, we have developed group-specific primers for use in RT-PCR-based restriction fragment length polymorphism analysis for rapid discrimination between strains of SCMV and SrMV. This is the first assay for differentiating strains of SCMV and SrMV that does not require interpretation of symptoms on differential hosts