Detection and diagnosis of tomato leaf curl virus infecting tomato in Northern Karnataka

Abstract

Tomato (Lycopersicon esculentum Mill.) is an important and most widely grown vegetable crop in India. The begomo viruses’ affecting tomato in India is the most devastating and is a major limiting factor in the tomato production. The tomato leaf curl virus (ToLCV) was present in almost all fields of Belgaum, Dharwad and Haveri districts surveyed with the disease incidence ranged from 4-100% in rabi and was in severe form ranging from 60-100% during summer. All the five representative symptomatic samples collected from the different regions of North-Karnataka were found positive for polymerase chain reaction (PCR) amplification with specific primers for deoxyribonucleic acid (DNA); a component of tomato leaf curl Bangalore virus (ToLCBV). To examine the diversity of the sequences, phylogenetic trees were generated for the four CP sequences together with representative sequences available in gene Bank. The isolates under study clustered into two groups. The Dharwad isolate and Belgaum- 2 isolate were closely related (99.4% nucleotide similarity) and formed in to one cluster in which Haveri and Belgaum-1 isolates had comparatively less homology (97.30% nucleotide homology) between themselves and clustered into another sub group. The isolates under study had lowest nucleotide sequence homology of 53.50 to 53.90% with ToLCV 19.Patna (AJ 810358) followed by ToLCV 18.Malvastrum.Pa (AJ 810357) (53.50-54.00%), ToLCV 17. Nasik (AJ 810356) (53.90-54.30%), while they had highest homology of 92.40-96.00% with ToLCBV-AVT 1 (AY 428770). The results revealed that these isolates are entirely different from North Indian isolates and there is some variability within the isolates collected from a geographical location, indicating that there will be continuous variability in gemini viruses.