Indian Journal of Virology

Sugarcane mosaic is the most widely prevalent disease in all the sugarcane growing regions of India and has the potential to cause severe losses, adversely affecting the economy of the sugar industry. An extensive survey of sugarcane mosaic disease was conducted during 2003–2004 to 2006–2007 in Tamil Nadu, Maharashtra, Haryana, Andhra Pradesh, Punjab, Uttar Pradesh and Kerala states of India. The varieties viz., Co740, CoM 9006 and Co 62399 showed maximum incidence of the mosaic disease were taken for comparative coat protein nucleotide sequence analysis. The RNA of mosaic isolates was extracted from crude extract of mosaic-infected leaves of sugarcane. The isolated RNA of Isolate-I (Co 740), Isolate-II (CoM 9006) and Isolate-III (Co 62399) appeared near about 9.8+0.1 kbp on 1% agarose gel. For further study, specific coat protein region of three virus isolates were amplified from cDNA by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) with SCMV-F3 (5’-TTT YCA CCA AGC TGG AA-3’) and SCMV-R3 (5’-AGC TGT GTG TCT GTC TGT ATT CT-3’) primer pairs as upstream and downstream primers. Amplication of Isolate-1, Isolate-2 and Isolate-3 resulted in the production of amplicon size about 0.9 kbp.

The coat protein nucleotide sequences of the three isolates had single ORF of 899 bp. A region of 0 to 800 bp (amplicon without primer sequences) from the coat protein encoding region was used for phylogenetic analysis with additional sequences for the same region that were obtained for other SCMV isolates from different countries, viz., Egypt, Cameroon, Pakistan, China, India, Brazil, Australia, USA, Thailand, South Africa and Germany. The clustal algorithm of MegAlign from the DNASTAR package (version 3.1, USA) was used to align complete sequences. Phylogenetic relationships of our three SCMV isolates with other 11 SCMV strains/isolates from sugarcane were examined. The Indian isolates SCMV isolates were closely related with each other showing 80–96% homology with each other and forming a distinct group.

The isolates (I, II & III) used in the present study had made one cluster along with Thailand (AY 630923). While, sequences from China (DQ 227694) and USA ((AJ 491966) have made another cluster. The SCMV isolates from Brazil (AY 819716) and South Africa (AJ 491973) clustered into another group. The isolates from India (AY 241923) and Australia (D 00948) clustered together Isolates from Germany (AJ 006199) remained alone and did not cluster with any of the SCMV isolates from other part of the world. The phylogenetic relationship of the virus in the study with other characterized Sugarcane mosaic virus isolates indicated that the SCMV isolates in the present study definitely belongs to SCMV subgroup of Potyvirus.