A survey of South African sugarcane mosaic virus (SCMV) strains based on coat protein gene sequence analysis

Sugarcane mosaic potyvirus (SCMV) infection can severely reduce sucrose yie ld in susceptible sugarcane varieties in South Africa. Knowledge of prevale nt South African strains of SCMV is poor but strategically important for th e development of better diagnostic procedures and transgene induced resista nce. Since most strain variation resides in the capsid structure, molecular analysis of relative homology in nucleotide and inferred amino acid sequen ces in the most variable (N-terminal) coat protein region is the method of choice for distinguishing strains. Total RNA was extracted from symptomatic leaves collected from various regions. Viral RNA was reverse transcribed a nd a large fragment at the 3' end of the SCMV genome amplified by PCR using previously designed primers. Fragments, both cloned and uncloned, were cyc le sequenced using dye terminator chemistry. Analysis of the sequences was performed using an ABI Prism 310 Genetic Analyser and related computer soft ware. Consensus sequences of the first 240-360 bases of the coat protein ge ne were obtained and compared against international databases. The results indicate that SCMV strains in South Africa belong to the SC, E and A cluste r.