Sugarcane mosaic complex in India: Cause of different viruses/strains.

Abstract

Sugarcane mosaic is one of the most important, more than a century old viral diseases, widely distributed in the world and its economic significance varies between countries. Recently, the association of Sugarcane streak mosaic virus (SCSMV), an unclassified Potyviridae member with sugarcane mosaic was established from the major sugarcane growing Asian countries including India. Often the mosaic symptoms in sugarcane were associated with co-existence of more than one strains of SCMV or SrMV or SCSMV or the strains of the two or three viruses in combinations. Detailed studies were conducted to assess the infection of SCMV and SCSMV in 58 selected varieties exhibiting varying symptoms of mosaic. RNA were extracted from the leaf samples of 58 varieties and an aphid colony (Melanaphis sacchari) infested on sugarcane variety showing mosaic and streak mosaic and RT-PCR was performed for both the viruses using specific primers. Of the 58 samples, a majority of 65.08% were infected with SCSMV alone and only 3.17% infected with SCMV. However, ~27% of the samples were infected with both the viruses. The study clearly revealed that majority of the sugarcane varieties found to have SCSMV infection in the country. Later, the amplified coat protein (CP) amplicon of 51 SCSMV and 26 SCMV were sequenced and characterized to identify the variation in the virus(es). Both these two viruses were also detected and characterized from M. sacchari. The 52 SCSMV-CP gene sequences (SCSMV-CB) were compared with each other as well as GenBank database sequences of Potyviridae members viz., Rymovirus, Potyvirus, Ipomovirus, Tritimovirus and eight sequences of SCSMV. Among the SCSMV-CB isolates sequenced in the study, 85.7-100 and 89.9-100 % sequence identity was observed at nucleotide and amino acid sequence level, respectively and with database sequences of SCSMV, the respective identities were 82.2-97.5 and 89.7-98.6%. Grouping of the isolates by the maximum likelihood with molecular clock model, distributed 60 SCSMV sequences including the eight database sequences in 16 phylogenetic groups sandwiched between Rymovirus and Ipomovirus in a separate cluster. The sequence comparison and phylogenetic studies revealed that the relatedness of SCSMV with the Potyviridae related genera was comparatively low to consider it as a member of earlier described genera of Potyviridae, hence the genus “Susmovirus” (sugarcane streak mosaic virus) has been proposed, with SCMV as the sole species to be included at present. Further, the phylogenetic studies with the 60 SCSMV isolates including the database sequences alone were distributed them in 16 phylogenetic groups under three clusters. In SCMV-CP gene sequence comparison, 90.4-100 and 85.3-100% sequence identities were observed among the SCMV-CB isolates, respectively at nucleotide and amino acid sequence level and in phylogenetic tree constructed with amino acid sequence, they were distributed under three clusters. The recognized strains of SCMV viz., SCMV-A, B, D, E, BRIS, BUND and Isis are in a subcluster and the SCMV-CB isolates of the present study were distributed in three clusters. The present study evidenced that sugarcane mosaic in India is caused by either the strains of SCSMV or SCMV alone or in their combinations.