Abstract: Twenty-six fragments of near-full-length coat protein (CP) gene of Sugarcane mosaic virus (SCMV), the main causal agent of sugarcane and maize mosaic diseases in China, were obtained by reverse-transcription polymerase chain reaction (RT-PCR) with templates of total RNA extracted from diseased sugarcane and maize leaves collected from south China. Their nucleotide sequences were determined directly by Sanger’s method and were used for diversity analysis of SCMV-CP gene, with the reported sequences(from GenBank) of representative strains and isolates of SCMV(mainly from China) also included. Study on CP gene nucleotide (nt) identity showed that SCMV isolates in China could be divided into three molecular groups that coincidently correlated to their respective original hosts, namely hybrid sugarcane, maize and noble sugarcane. There were 78%-84% nt identities between two different group and >91% within each one group. The division was supported by the phylogenetic tree based on the CP gene nt data and forming three independent clusters: the first and second cluster respectively belongs to the sugarcane group (SCE group) and maize group (MZ group) founded by Alegria (2003), while the third named noble sugarcane group (NSCE group) was firstly founded in this study. No significant geographical divergence was found among SCMV isolates from Chinese hybrid sugarcane, whereas the MZ group and NSCE group in China could be further divided into some minor groups correlated with geographical origin. The minor groups within MZ group were respectively from East and Middle China, Northwest and Southwest China and South China, while within NSCE group respectively from Zhejiang and South China. Field investigation in mixed growing areas of maize and sugarcane indicated that the cross-infection of SCMV among different original hosts might occasionally occur via aphid-transmission, but on some a certain host there existed relative separation of virus population, suggesting that the selecting pressure from hosts on the evolution of SCMV was on population level, therefore the population perspectives should be kept when studying on those pathogens with rich diversity, such as SCMV. In addition, we have found that two kinds of weeds from south China, Narenga sp. and Miscanthus sp. relationally closed to sugarcane, were infected with SCMV.

Key words: Sugarcane mosaic virus, coat protein gene, sequence analysis, genetic diversity