Detection and partial molecular characterization of sugarcane mosaic virus infecting sugarcane genotypes

• Published in: Journal of environmental biology 2017-05, Vol.38 (3), p.409-417
• Main Authors: Holkar, S.K., Kumar, A., Meena, M.R., Lal, R.J.
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; Amino acid sequence; Amino acids; Cloning; Clustering; Coat protein; Corn; Crop diseases; Digestion; Electron microscopy; Environmental science; Fragments; Genes; Genomes; Genotypes; Infections; Mosaic disease; Nucleotide sequence; Particle physics; Polymerase chain reaction; Primers; Proteins; Sorghum; Sugarcane; Virions; Viruses
• ISSN: 0254-8704; 2394-0379
• DOI: 10.22438/jeb/38/3/MS-219

Sugarcane mosaic virus (SCMV) is one of the causal agents of mosaic disease ofsugarcane in India. Present investigation was carried out to detect association of specific virus with SMD and its molecular characterization. Thirty eight sugarcane genotypes showing mild, severe and necrotic mosaic symptoms were confirmed with the association of flexuous filamentous virion particles by electron microscopy. Of 38 symptomatic sugarcane samples only four samples were subjected to RT-PCR using Potyvirus universal primers which covers amplification of genomic regions viz., partial Nib, full CP and 3'UTR of approximately 1800 bp products. PCR amplicons were cloned in pGEMT Easy vector system. Seven recombinant clones were confirmed by colony PCR, restriction digestion with EcoRI and sequencing. Of these seven recombinant clones, restricted with EcoRI restriction enzyme, in two clones two fragments of approximately 1600 and 200 bp sizes were obtained, whereas rest of the five recombinant clones showed three restricted fragments of approximately 950, 550 and 300 bp which confirmed the variability in the genome of SCMV isolates infecting sugarcane genotypes. The sequence analysis of partial Nib, full CP and full 3'UTR region of the Karnal, Haryana isolate (KF531632) revealed that, 93-96% sequence identity was found at nucleotide level and 97-98 % identity at amino acid level with the corresponding regions of other SCMV isolates in GenBank. The phylogenic analyses of coat protein (CP) gene showed the clustering of present SCMV_Kar isolate with other SCMV isolates originating from different locations. The present study confirms the association of SCMV with mosaic disease and partial characterization of SCMV Karnal isolate in India.