Molecular characterization of Cucumber mosaic virus infection in chilli (Capsicum annuum L.) and its phylogenetic analysis

Abstract

Cucumber mosaic virus (CMV) is the most serious viral pathogen affecting chilli (Capsicum annuum L.) worldwide. The proper diagnosis of virus infection using visual observations alone makes the management of CMV very difficult. In order to find the occurrence, field samples exhibiting the symptoms of necrosis, leaf malformation, stunting and reduction in plant size were collected. To study the nature of CMV infection, samples were diagnosed by reverse transcriptase polymerase chain (RT-PCR). Total RNA was isolated from leaves of infected plants and used in RT-PCR reaction with a primer specific to CMV coat protein region. The results revealed that a viral amplicon of expected 800 bp size were obtained from infected plants and phylogenetic relationship determined by the comparison of coat protein gene nucleotide sequences with other CMV isolates reported from India and worldwide. Sequence analysis of the coat protein gene had nucleotide similarity of 96 to 94 per cent with known strains of CMV. The multiple sequence alignment revealed that high homology between the isolates, further confirms the placement of the chilli strain of CMV in a single subgroup with India isolates. The proper diagnosis of CMV infection through molecular approaches could help in timely adoption of management strategy.