Journal of Environmental Biology

Detection and partial molecular characterization of

sugarcane mosaic virus infecting sugarcane genotypes

S. K. Holkar¹*, A. Kumar¹, M. R. Meena² and R. J. Lal¹

¹Division of Crop Protection, ICAR-Indian Institute of Sugarcane Research, Lucknow?226 002, India

²Division of Plant Breeding, ICAR-Sugarcane Breeding Institute, Regional Station, Karnal, Haryana-132 001, India

*Corresponding Author E-mail: somnathbhu@gmail.com

? 

Key words

Genome characterization,

Phytogenic analyses,

Potyvirus,

Saccharum spp.,

Sugarcane mosaic virus

Publication Data

Paper received : 03.12.2015

Revised received : 12.04.2016

Re-revised received : 04.10.2016

Accepted : 05.11.2016

Abstract

Aim: Sugarcane mosaic virus (SCMV) is one of the causal agents of mosaic disease of sugarcane in India. Present investigation was carried out to detect association of specific virus with SMD and its molecular characterization.

Methodology: 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.

Results: 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.   

Interpretation: 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. 

Copyright ? 2017 Triveni Enterprises. All rights reserved. No part of the Journal can be reproduced in any form without prior permission. Responsibility regarding the authenticity of the data, and the acceptability of the conclusions enforced or derived, rest completely with the author(s).