Genome characterization and host range studies of Cucumber mosaic virus belonging to the Subgroup IB infecting chilli in India and screening of chilli genotypes for identification of resistance

Chilli pepper is an important vegetable and spice crop grown worldwide. Chilli is susceptible to various pathogens, among them mosaic disease caused by Cucumber mosaic virus (CMV) is a major constraint for its production. Roving survey was carried out for mosaic disease assessment in chilli at 35 locations comprising five districts of south eastern Karnataka, which was later confirmed for the presence of different viruses in random samples by DAC-ELISA. Results revealed the prevalence of the disease caused by CMV up to 43.00% based on visual assessment. However, only in 64 samples out of 140 infected chilli samples showed CMV infection in DAC-ELISA and revealed the mixed infection of viruses. Mechanical sap inoculation of CMV-Ko isolate induced symptoms on chilli plants, which were similar to the symptoms observed in field. Complete genome sequence of CMV-Ko (RNA1, RNA2 and RNA3) isolate was amplified, cloned and sequenced. Sequence analysis revealed that it shared 83.7–99.1% nucleotide (nt) identity with CMV subgroup IB isolates infecting different crops in India. Recombination analysis of CMV-Ko genome showed that, RNA1 and RNA2 had recombinant origin and not RNA3. Host range studies for CMV-Ko isolate showed its potential of infecting nine host plants out of 21 used for transmission. Fifty advanced chilli lines were screened against CMV-Ko isolate and 27 immune lines to CMV were identified, which can be utilized for management of disease caused by CMV in chilli.