Molecular characterization and genetic variability of Chilli Veinal Mottle Virus and its reaction on chilli pepper genotypes

Chilli pepper (Capsicum annum L) is being grown in diverse climatic conditions throughout India. Nonpersistent aphid transmitted viruses have been implicated as the major factor contributing to low yields of chilli pepper in India. A virus causing symptoms of mosaic mottling, vein banding, and leaf distortion of chilli was isolated from chilli growing areas of Karnataka and Tamil Nadu states of India. Of the six isolates collected all of them were identified as Chilli Veinal Mottle Virus (CVMV) based on host range, serological relationship, electron microscopy and phylogenetic analysis of coat protein sequences. The biological differences among the six isolates were noticed in infecting test hosts Datura metel, Nicotiana glutinosa, N .tabacum, and Capsicum annum. In order to gain an understanding of the molecular variability present among the six isolates of CVMV, RT-PCR coupled with sequence analysis of coat protein region and 3’ non-coding region (NCR) was done. Using primers specific to CP and 3’ NTR of CVMV, resulted in a PCR fragments of 0.8 to 1.2 kb depending on primer combinations from all six isolates. Comparison of nucleotide sequences of six isolates with already reported sequences of CVMV, showed 91-93% nucleotide identity. After mechanical inoculation of CVMV isolates on to 25 genotypes of chilli pepper, three genotypes were found immune, 10 genotypes highly resistant, two genotypes resistant and ten genotypes as susceptible as confirmed by symptoms and ELISA testing. The symptom variation and severity varied among six isolates of CVMV.