Identification of new variants of SCMV causing sugarcane mosaic in India and assessing their genetic diversity in relation to SCMV type strains

Abstract

Sugarcane mosaic virus (SCMV) is one of the two causative viruses of mosaic in sugarcane, a sugar crop widely grown under tropical and subtropical conditions worldwide. Although molecular characterization of SCMV strains was reported from many countries, strains occurring in India, a major sugarcane producer have not been reported so far. Twenty-six sugarcane samples represented by seven major sugarcane growing states in India and USA were subjected to reverse-transcription polymerase chain reaction (RT-PCR) using a pair of newly designed coat protein specific primers. Among them 17 were found positive to the SCMV infection. The lengths of the sequences derived in this study using the new set of primers varied between 812 and 866 nt. The amino acid sequence comparison of 30 Indian SCMV isolates showed wide range of sequence similarities in core region (88.80-100%) and hyper variable region (51.3-100%). In the N-terminal region of the five Indian isolates, a deletion of 12 aa residues between aa 11 and 30 was observed, whereas the deletion was between aa 45 and 50 in SCMV-B and -D and between aa 61 and 70 in SCMV-A. The phylogenetic analyses performed with 46 SCMV CP sequences for both hyper variable region and core region separated the isolates mostly according to their geographical origin. The 30 Indian SCMV isolates were included exclusively in four groups besides SCMV-IND, which was grouped with SCMV-SC, a type of strain from Australia. Nearly 97.0% of the Indian isolates have no signs for close relationships with previously characterized SCMV type strains (SCMV-A, -B, -D, -E, and -SC) reported from other countries. Our studies revealed that the sugarcane mosaic in India are caused by at least nine new SCMV variants (IND-CC1, -CC2, -CC3, -CC4, -CO1, -CO2, -CP, -CS, and -J) and a type strain SCMV-SC represented by SCMV-IND. This is the first report on the variability and occurrence of new SCMV population in India.

High sequence conservation among Odotoglossum ringspot virus isolates from orchids

“…This might be in part explained by the fact that the tubers from the same origin are disseminated for multiplication of orchid production, leading to the high degree of observed CP conservation. In contrast to ORSV, some studies showed geographic variation of a few plant viruses, based on the determination of only CP sequences of virus isolates and various analyses of the determined sequences [22][23][24][25][26][27]. These studies support that the validity of our analysis of CP gene sequences is sufficient for investigating geographic variation of ORSV isolates.…”

Molecular Diversity Analysis of Pretty Interesting Potyviridae ORF (PIPO) Coding Region in Indian Isolates of Sugarcane streak mosaic virus

“…To confirm the SCSMV infection and to rule out other prevalent and co-existing diseases (Prabu et al 2008), the collected plant samples were tested for SCSMV, sugarcane mosaic virus (SCMV), and sugarcane grassy shoot phytoplasma (SCGS) infection by RT-PCR and PCR using the reported specific primers (Viswanathan et al 2009;Xu et al 2010). Presence of SCSMV infection in the plant materials used in this study has been confirmed (data not shown).…”

Phosphoproteomic analysis of the resistant and susceptible genotypes of maize infected with sugarcane mosaic virus

“…It appears that virus mixtures are more virulent than single infections (Xu et al 2008). In addition, new strains or genomic variants of SCMV continue to be reported in different countries (Perera et al 2009;Viswanathan et al 2009;Gao et al 2011;Padhi and Ramu 2011). These outbreaks indicate that even though SCMV has been long known, it remains an agricultural threat (Wu et al 2012).…”