Progress in sugarcane virus research in India vis-à-vis developments in molecular diagnostic tools

Abstract

During 1990s suspected occurrence of Sugarcane bacilliform virus (SCBV) reported in Saccharum officinarum and other Saccharum spp clones through ISEM studies. These studies gave authentic confirmation on SCBV infection in sugarcane from India. Recently, molecular studies conducted at SBI clearly demarcated five different SCBV species, at least three new species, SCBBbV, SCBBoV and SCBBruV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam infecting sugarcane and the virus genome ranged from 7553 to 7884 nucleotides in size. Earlier based on serology and differential host studies presence strains of several Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SCMV) were reported. Detailed molecular studies conducted at SBI established that sugarcane mosaic in India is caused by SCMV and Sugarcane streak mosaic virus (SCSMV) in combination or separately. Molecular characterization of several SCMV and SCSMV isolates established variation in coat protein genome of the respective viruses for the first time in India. SCSMV was characterized as a new genus “Susmovirus” in the family Potyviridae based on its distinct coat protein genome. Recently ICTV, has renamed the genus as Poacevirus based on host range of the species in the genus. Recently complete nucleotide sequence of an SCSMV isolate from India, SCSMV-IND was determined. It is a linear single stranded positive sense RNA genome of 9786 nucleotides in length (excluding the Poly A tail). Among the viral diseases, yellow leaf disease (YLD) caused by Sugarcane yellow leaf virus (SCYLV) is the recently identified disease and it has caused more damage than any other viruses in India. Recently complete genomes of four isolates of SCYLV (5875 nt) were sequenced and phylogenetic analyses established that all the isolates belong to the genotype SCYLV-IND. Overall, with the adoption of molecular biological tools, virus etiology with the diseases and genomic variation in the viruses was established beyond doubt. Also knowledge on virus genome helped us in developing precise diagnostic tools to index different viruses in sugarcane. Meristem tip culture along with RT-PCR is recommended to eliminate SCYLV from sugarcane while developing YLD-free nurseries. This practice has helped many sugar industries to revive severely degenerated varieties and SBI plays a pivotal role in indexing for sugarcane viruses in the country. Additionally, to simplify virus diagnostics, recombinant antisera were raised against SCSMV-coat protein and DAC-ELISA and immuno capture RT-PCR were developed for the diagnosis of the virus.