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African Journal of Agricultural Marketing ISSN 2375-1061 Vol. 9 (2), pp. 001-007, February, 2021. Available 
online at www.internationalscholarsjournals.org © International Scholars Journals 

 

Author(s) retain the copyright of this article. 
 
 

Full Length Research Paper 

 

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

 
Reddy, A. B.1*, Patti, M. S.1, Reddy, K. M.2 and Venkataravanappa, V.2 

 
1
Department of Plant Pathology, UAS, Dharwad-05, India. 

2
Division of Plant Pathology, IIHR, Hesaraghatta, Bangalore-89, India. 

 
Accepted 02 November, 2020 

 
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. 

 
Key words: ToLCV, detection, diagnosis, cloning, nucleotide sequence. 

 
INTRODUCTION 

 
Tomato (Lycopersicon esculentum Mill.) is an important 
and most widely grown vegetable crop in India. Virus 
diseases are the major production constraints. Among the 
virus diseases, tomato leaf curl disease; tomato leaf curl 
Bangalore virus (ToLCBV), tomato leaf curl New Delhi 
virus (ToLCNDV), tomato leaf curl Karnataka virus  
 
 
 
 
*Corresponding author. E-mail: arb_agri@yahoo.co.in. 

 
Abbreviations: ToLCV, Tomato leaf curl virus; PCR, 
polymerase chain reaction; DNA, deoxyribonucleic acid; 
ToLCBV, tomato leaf curl Bangalore virus; ToLCNDV, tomato 
leaf curl New Delhi virus; ToLCKV, tomato leaf curl Karnataka 
virus; ToLCGV, tomato leaf curl Gujarat virus; TLCB, twolined 
chestnut borer; ORF, open reading frame. 

 
 
 

 
(ToLCKV) and tomato leaf curl Gujarat virus (ToLCGV) 
are the important begomo viruses which limit the tomato 
production.  

The begomo viruses affecting tomato in India are the 
most devastating and the early work on the geographical 
distribution of twolined chestnut borer (TLCB) species 
within India has shown that the begomo viruses affecting 
tomato in northern India are bipartite and those affecting 
tomato in Southern India are monopartite (Muniyappa et 
al., 2000; Kirthi et al., 2002). These two groups of viruses 
are quite distinct in their biological activity and genomic 
organizations.  

The incidence of ToLCV has become a major limiting 
factor and challenge to farmers and scientists. The 
tropical climate in Southern India allows year-round 
tomato cropping, which together with the presence of 
perennial host plants for both TLCBs and B. tabaci 



2 

 

 
 
 

 

(Ramappa et al., 1998; Sastry et al., 1978), enables the 
easy carry-over of ToLCD between growing seasons. 
Until the late 1990s, the main control method employed 
against ToLCD was the intensive use of insecticides 
targeted at viruliferous immigrant adult B. tabaci that 
spread TLCBs into and within tomato crops. The 
existence of variability among the virus isolates is the 
main reason for the break down of resistance in the ruling 
varieties.  

In order to manage the deployment of these resistant 
varieties to improve the efficacy of the ToLCD-resistant 
material, an improved understanding of the diversity and 
distribution of TLCBs present in a region is required. 
Though the disease has been known for quite a long 
period with a good amount of literature on various 
aspects of the disease, the information regarding the 
extent of diversity among the different isolates of the 
ToLCV in the tomato growing areas of North Karnataka 
was lacking. Considering that the present work is initiated 
in identification of ToLCD isolates in North Karnataka and 
development of reliable detection method suitable for 
development of various management strategies. 
 
 
MATERIALS AND METHODS 
 
Survey for disease incidence 
 
A roving survey was conducted during rabi 2005 and summer 2006 
in major tomato growing districts of North Karnataka. In each visited 
field, a plot area of 10 x 10 m area was selected and the total 
number of plants and infected plants showing leaf curl symptoms 
was recorded separately and the percent disease incidence was 
calculated. Three such plot areas were selected randomly in each 
field and mean of three plots was calculated. The overall disease 
incidence and severity was recorded based on visual symptoms. 

 

Collection of ToLCV isolates and DNA extraction 
 
A survey was undertaken to collect the samples of ToLCV and the 
leaves and twigs exhibiting typical symptoms were collected from all 
the fields visited in Belgaum, Dharwad, Gadag and Haveri districts 
of North Karnataka. The samples showing some variations in 
symptoms within a cultivar were chosen for further analysis. The 
total deoxyribonucleic acid (DNA) was extracted from the 
representative field samples, following standard DNA extraction 
protocols of Cetyl trimethyl ammonium bromide method (Srivatasva 
et al., 1993). The extracted DNA was quantified for the 
concentration and was diluted appropriately in sterile distilled 
deionised water before being subjected to polymerase chain 
reaction (PCR) amplification using tomato leaf curl specific primers. 

 

PCR amplification and cloning 
 
The total DNA extracted was used for PCR amplification of ToLCV 
DNA. Further, the PCRs were carried out in 25 µl of reaction 
mixture containing DNA template (50-60 ng) -1.0 µl, deionised 
nuclease free water-16.0 µl, 10X PCR buffer (supplied with 
enzyme)-2.5 µl, 2 mM dNTPs -2.0 µl, 25 mM MgCl2 - 2.0 µl and 
primers- forward primer (20 pmol/µl)- 0.5 µl, reverse primer 20 
pmol/µl) -0.5 µl and Taq DNA polymerase (1.5 U/µl) - 0.5 µl. All the 
reaction components were procured from MBI Fermentas, 

 
 
 
 

 
Germany.  

The PCR amplification was carried out in a thermal cycler 
(Biometra) with initial-denaturation at 94°C for 2 min followed by 35 
cycles each consisting of denaturation at 94°C for 45 s, annealing 
at 55°C for 1 min followed by extension at 72°C for 1.30 min with 
final extension at 72°C for 20 min. Amplified DNA fragments were 
electrophoresised in 0.8% agarose gel according to the procedure 
outlined by Sambrook and Russel (2001). 

 

Sequence of tomato leaf curl specific primers used 
 
Forward primer (ToLCBV33F): 5’ GGT CCC CTC CAC TAA ATCAT 
3’ (20 nt)  
Reverse primer (ToLCBV1070R): 5’CAG TTG GTT ACA GAA TCG 
TAG AAG 3’ (24 nt) 

 

Cloning of PCR product 
 
After gel elution of amplified DNA fragment using gel extraction kit 
(Qiagen, Germany), the PCR amplified DNA fragment was cloned 
into the plasmid vector pTZ57R/T using T/A cloning kit (MBI, 
Fermentas) following the manufacturer's instructions. The vector 
also contains the ampicillin resistant gene for antibiotic selection 
and the lacZ gene that allows blue/white selection of recombinant 
colonies by a α- complementation. Ligation was carried out at 22°C 
for 16 h. The ligation mixture was used for transformation. The 
competent cells of Escherichia coli strain DH5 α were prepared by 
calcium chloride method as described by Sambrook and Russel 
(2001). 

 

Screening of clones 
 
Colony PCR was carried out by using the specific primers to 
confirm the clones carrying the insert. The confirmed colonies were 
then grown in 3-5 ml LB containing ampicillin (100 mg/ml) at 37°C 
overnight in a rotary shaker at 100 rpm. Plasmid mini-preparation 
was done from the culture by alkaline lysis method as described by 
Sambrook and Russel (2001).  

After confirmation of the presence of inserted DNA, the clone 
was named as pTZ57R+CP and the isolates were named based on 
the geographical location from which it was collected. 

 

Sequencing of the cloned insert 
 
After successful confirmation of the presence of expected insert in 
the clone, the plasmid DNA was isolated in large scale using 
plasmid extraction kit (QIAGEN GmbH, Hilden, Germany) and 
sequenced using the automated sequencing facility at Microsynth, 
Switzerland. Sequencing was done in both directions using M 13 
forward and reverse primers in an ABI Prism 377 DNA sequencer 
(MWG Biotech Limited). 
 
 
Sequence analysis 

 
The complete coat protein sequences of ToLCV isolates from 
various geographical locations were obtained from NCBI (Table 1). 
For sequence comparison, published nucleotide and amino acid 
sequences from related viruses of gemini group were used. 
Genebank (Benson et al., 1996) searches were done using the 
BLAST program (Altschul et al., 1990). The nucleotide sequences 
were translated to amino acid sequences using the bioedit program 
and the open reading frame (ORF) was also determined using 
bioedit program. Dendrogram and phylogenetic analysis was 



3 

 

 
 
 

 
Table 1. Reference geminivirus sequences and their GenBank accession numbers.  

 
 Designation Region/country GeneBank source 

 TLCGV-Kelloo Gujarath, India AF449999 

 ToLCGV-Nepal Gujarath, India AY234383 

 TLCGV-Varnasi Varnasi, India AY190290 

 ToLCGV-Vadodara Vadodara, India AF413671 

 ToLCV19.Patna Patna, India AJ810358 

 ToLCV17.Nasik Nasik, India AJ810356 

 ToLCCV-G18  AJ558119 

 ToLCV18.Malvastrum.Pa  AJ810357 

 CrYVMV  AJ507777 

 SiYVV-Madurai Madurai, India AM259382 

 ToLCNDV-Severe New Delhi, India U15015 

 SYLCV  AJ620187 

 ToLCNDV-PkT1/8 New Delhi, India AF448059 

 TLCNDV-Lucknow Lucknow, India Y16421 

 ToLCNDV-PkT5/6 New Delhi, India AF448058 

 ToLCNDV-Mild New Delhi, India U15016 

 ToLCNDV-Potato New Delhi, India AY286316 

 ToLCNDV-AVT1 New Delhi, India AY428769 

 ToLCNDV-S[Jessore] New Delhi, India AJ875157 

 TLCNDV-Luffa New Delhi, India AF102276 

 SqLCCV-[Pumpkin_Coimb Coimbatore, India AY184487 

 ToLCV-32.Tirupati Tirupati, India AJ810371 

 ToLCV2.Assam Assam, India AJ810341 

 ToLCV-9.Tomato.Calcut Calcutta, India AJ810348 

 LoYMV  AF509739 

 ToLCBV-Bangalore Bangalore, India Z48182 

 ToLCV27.Thrissur.Kera Thrisur, India AJ810366 

 VS228.Haveri Haveri, India  

 ToLCBV-TNAU1 Tamil Nadu, India DQ358098 

 ToLCV24.Ranibennur Ranebennuru, India AJ810363 

 ToLCV7.Belgaum Belgaum,India AJ810346 

 VS229.Belgaum1 Belgaum,India  

 VS226.Dharwad Dharwad, India  

 VS230.Belgaum2 Belgaum,India  

 ToLCBV-TNAU2 Tamil Nadu, India DQ358099 

 ToLCBV-Kolar Kolar, India AF428255 

 ToLCBV-AVT1  AY428770 

 ToLCV-30.Maderahalli. Maderahalli, India AJ810369 

 ToLCV-Ban5 Bangalore, India AF295401 

 ToLCBV-Cotton Bangalore, India AY456684 

 ToLCV-Ban4 Bangalore, India AF165098 

 ToLCSLV Srilanka AF274349 

 |ToLCKV-Ban2 Bangalore, India U38239 

 ToLCKV.Arskeri Arsikeri, India AY753203 

 ToLCV3.Aurangabad Aurangabad, India AJ810342 

 ToLCV-Tagetes  DQ339120 

 TbLCV-Kar1  AY007615 

 ChLCV-[Multan] Pakistan AF336806 

 ToLCND-PRM  DQ629103 

 CLCuBV  AY705380 

 MaYVV-[Y47]  AJ457824 



4 

 

 
 
 

 
Table 1. Contd.  

 
SLCMV-TN6  AJ890228 

ICMV-Mah Maharastra, India AJ314739 

ToLCV28.Ageratum.Ke  AJ810367 

ToLCBdV.Bd2 Bangalore, India AF188481 

PaLCV-PD  DQ376036 

ToLCJoV  AJ875159 

PepLCBV Bangalore, India AF314531 

EuLCV-[G35]  AJ558121 

CLCuKV-Dabawali Kokhran AY456683 

BYVMV-[Madurai] India AF241479 

CLCuAV-[802a] Alababad AJ002455 

CLCuMV-[Bhatinda_05]  DQ191160 

CLCuRV [India_Abohar] India AY795606 

ToLCV-Taiwan  U88692 

MYMIV-[Cowpea]  AF481865 

MSV-A  Mastrevirus 
 

 
Table 2. District wise distribution of disease (ToLCV) incidence during 2005-06.  

 
 

S/N District 
 Percent (%) disease incidence  

 

 

Minimum Maximum Average 
 

   
 

 Rabi-05     
 

 1 Belgaum 4.00 75.00 25.83 
 

 2 Dharwad 5.00 60.00 45.00 
 

 3 Gadag 8.00 20.00 16.00 
 

 4 Haveri 8.00 100.00 33.43 
 

 Summer-06     
 

 1 Belgaum 60 100 80 
 

 2 Dharwad 90 100 95 
 

 3 Gadag 60 90 75 
 

 4 Haveri 75 90 87 
 

 
 
 
constructed by neighbour joining method using the Tree View 
program. 
 

 

RESULTS 

 

Detection of tomato leaf curl (begomo) virus in field 
samples of tomato incidence 

 
 
 
summer reveals that ToLCV was present in severe form 
ranging from 60-100% in almost all the major tomato 
fields surveyed. 
 
 
Distribution of TLCBs in North Karnataka (PCR 
detection) 
 

 

The survey data of the rabi season revealed that the 
ToLCV was present in almost all parts of Belgaum, 
Dharwad, Gadag and Haveri. Disease incidence ranged 
from 4-100% and was maximum in Hiremathuru (100.0%) 
of Haveri taluk, UAS campus (100.0%), Sidenur (70.0%) 
of Byadgi taluk, Itagi (60.0%) of Ranebennur taluk of 
Haveri district and Hulikppa (60.0%), Kalaghattagi taluk of 
Dharwad district (Table 2). While the survey data on 

 
All the five symptomatic representative samples collected 
from the different regions of North-Karnataka were found 
positive for PCR amplification with specific primers for 
DNA; a component of ToLCBV. These primers amplified 

a  1040 bp product. These primers produced expected 
results on the five samples for which CP sequences had 
been obtained. Table 3 shows the PCR amplification 
results of the five representative samples used for 
screening using ToLCBV primers of DNA-A. 



5 

 

 
 
 

 
Table 3. PCR detection of ToLCV in the tomato samples collected from different regions of North Karnataka.  

 
S/N Place Variety/hybrid Date of collection PCR detection 

1 UAS campus (Dharwad) Megha 6-12-05 + 

2 Honnihalli (Hukkeri Tq) (Belagao) Hy 2535 5-12-05 + 

3 Hattaragi (Hukkeri Tq) (Belagao) Utsav 5-12-05 + 

4 Hiremuttur (Hirekerur Tq) (Haveri) Sungro seeds 12-12-05 + 

5 Bikadakatti (Gadag Tq) (Gadag) Sungro seeds 3-12-05 + 
 
 

 

Cloning and sequencing of coat protein gene of 
tomato leaf curl virus isolates 

 
The coat protein gene was amplified by PCR and 
amplified product was eluted from the gel and ligated to 
pTZ57R/T of size 2.4 kb with T-overhang. Transformation 

of E.coli strain DH5 α was done with ligation mixture. The 
bacterial clones carrying the recombinant DNA molecules 
were colorless and could easily be distinguished from the 
non-recombinant blue colonies.  

Further, the clones carrying the coat protein gene were 
analyzed and confirmed by colony PCR, which produced 
about 1.0 kb product as resolved and analyzed by gel 
electrophoresis. The clones were sequenced using M13 
universal forward and reverse primers. 
 

 

Sequence analysis and phylogenetics 

 

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 tree was constructed using Clustal-W multiple 
alignments programme (Figure 1). The isolates under 
study clustered into two groups. The Dharwad isolate and 
Belgaum- 2 isolate were closely related (99.4% 
nucleotide similarity) and formed into one cluster (Figure  
1) and Haveri and Belgaum-1 isolates had comparatively 
less homology (97.30% nucleotide homology) between 
themselves and clustered into another sub group (Figure  
1). The isolates under study had lowest nucleotide 
sequence homology of 53.50-53.90% with ToLCV  
19.Patna(AJ810358)followedbyToLCV 
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).  

However, within the isolates under study, Haveri isolate 
(VS 228) had highest nucleotide sequence homology 

(97.30%) with Belgaum-1 (VS 229) and had lowest 
homology (95.1%) with Belgaum-2 (VS-230) isolate. The 
Belgaum –1 (VS 229) had highest homology (97.30%) 
with Haveri isolate (VS 228) and lowest (96.30%) 
homology with the Belgaum-2 (VS230).  

The Dharwad isolate had highest homology of 99.40% 
with Belgaum-2 (VS-230) isolate and had lowest 

 
 

 

homology of 95.60% with the Haveri isolate (VS 228), 
while the Belgaum-2 (VS230) isolate had lowest 
homology of 95.10% with Haveri isolate (VS 228).  

From Figure 1, it could be concluded that all the 
isolates under study, collected from North Karnataka 
were entirely distinct from the North Indian (Gen Bank 
Accessions) (TLCGV-Varnasi (AY190290)- average of 
69.20% homology, ToLCV19.Patna (AJ810358)- average 
of 53.60% homology and ToLCV18.Malvastrum.Pa 
(AJ810357) – average of 53.80% homology), North 
Eastern (ToLCV 2.Assam (AJ810341) - average of 
57.00% homology) and North Western Indian (ToLCGV-
Vadodara (AF413671) average of 69.0% homology) 
isolates. However, the isolates under study had less 
homology with only few South Indian isolates (ToLCV-
30.Maderahalli (AJ810369) average of 72.15% homology 
and ToLCV-24. Ranebennur (AJ810363) average of 
71.97% homology). But these had highest homology of  
96.00% with the South Indian isolate, ToLCBV-AVT1 
(AY428770). The homology with South Indian begomo 
viruses was ranging from 63.90% with ToLCKV. Arsikeri 
(AY753203) isolate to 96.00% with ToLCBV-AVT-1  
(AY428770) isolate. However, they have got more than 
90% homology with majority of the South Indian isolates. 
 

 

Genetic relationship of ToLCV based on amino acid 
sequence 

 

To look at the functional diversity of the CPs, their 
nucleotide sequences were translated into amino acid 
sequences. Amino acid sequence similarity identity 
reveals that all the isolates under study had highest 
amino acid homology 97.60-99.60% with ToLCV Ban-5 
(AF295401) and ToLCBV-Cotton (AY456684) followed by 
ToLCV 27 Thrissur. Kerala (AJ810366). While the lowest 
homology of 42.90-43.30% was found with SiYVV-
Madurai isolate (AF259382) followed by ToLCCV-G18 
(AJ558119) with 71.2-71.9% homology. 
 

 

DISCUSSION 

 

The tests on the samples collected during survey 
revealed that the ToLCV was present in all the fields 
visited based on the symptoms in the field and also by 



6 

 

  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Figure 1. Dendrogram showing clustering pattern of nucleotide sequences of 
ToLCV coat protein gene from different geographical locations. 

 

 

PCR amplification in the laboratory.  
CP genes represent the most conserved gene in the 

family Geminiviridae and CP sequences can be used as 
preliminary virus identification or to infer geographic and 
vector relationships (Brown et al., 2001). The 
phylogenetic analysis of the four CP sequences obtained 
from North Karnataka samples showed that they are all 
closely related to the isolates from South India (Ban-04, 
Ban-05, ToLCBV-cotton and ToLCBV-TNAU 2). 
However, there is only slight variation among the isolates 
under study and there is greater variation when 
compared with the isolates/accessions (GenBank) from 
North India, North Eastern India and also of North 
Western India. Percentage identity figures for members 
within each cluster were in agreement with the criteria of 

 
 

 

<90% CP nucleotide identity representative in general of 
different geminivirus species (Faquet and Stanley, 2003). 
However, recently recombination between begomovirus 
DNA-A molecules has been reported to be a frequent 
occurrence (Fondong et al., 2000; Kirthi et al., 2002; 
Zhou et al., 1997). Although the sequencing of the full 
length DNA-A component is desirable, a partial sequence 
approach based on CPs was adopted to enable a wider 
scale study to be conducted on Indian TLCBs 
diversityand phylogeography.  

The isolates under study had very close (95.10-99.6%) 
homology among themselves with respect to nucleotide 
sequence, they belonged to one group and they show 
very wide variation of up to 46.50% divergence with 
respect to nucleotide sequence with some of the North 



7 

 

 
 
 

 

Indian ToLCV 17. Nasik (AJ 810356), ToLCV 19.Patna 
(AJ 810358) isolates and only with few south Indian 
isolates like ToLCV-30.Maderahalli (AJ810369), ToLCKV. 
Arsikeri (AY 753203) and ToLCV3.Aurangabad (AJ 
810342). And high amino acid homology of 96.8-99.6% 
among themselves and up to 57.10% with SiYVV-
Madurai (AM259382) amino acid sequence diversity with 
the other North Indian isolates of begomo viruses and up 
to 29.00% diversity with tomato isolate ToLCCV-G18 (AJ 
558119). Similar results were reported by few workers 
(Padidam et al., 1995), where he sequenced the 
genomes of two isolates of tomato leaf curl geminivirus 
from India (ToLCNDV-Mild and ToLCNDV-severe). The 
ToLCV-Indian isolate contains A and B components and 
the two isolates have 94% sequence identity. Srivastava 
et al. (1993) compared the amino acid sequence of the 
putative coat protein product of ToLCNDV- Lucknow with 
some other mono and bipartite gemini viruses and 
revealed a maximum of 86% homology with Indian 
cassava mosaic virus. Similarly, few authors (Shimizu 
and Ikegami, 1999) reported that in total nucleotide 
sequence comparisons with other gemini viruses, tomato 
leaf curl virus was most closely related to tomato leaf curl 
virus from Taiwan (TwToLCV) (76% identity), tomato leaf 
curl virus from Bangalore (ToLCV-Ban) (74%) and 
ageratum yellow vein virus (AYVV) (74%), all possessing 
a monopartite genome.  

The full length 2759 nucleotide long DNA-A like viral 
genome was sequenced and sequence comparisons 
indicated that ToLCV-Ban4 is similar to the other three 
isolates from Bangalore previously sequenced and is 
closely related to ToLCV-Ban2 (approximately 91% 
nucleotide sequence identity). Phylogenetic analysis 
showed that the ToLCV isolates from Bangalore 
constitute a group of viruses separated from those of 
Northern India (Muniyappa et al., 2000).  

The diversity and distribution of begomo viruses in 
tomato in Northern Karnataka determined in this study 
are therefore are likely to only represent general trends 
and understands true situation. A CP sequence 
represents the most conserved region of the begomo 
virus genome and hence there is least diversity among 
the isolates studied. However, when we compared these 
isolates with the other ToLCV isolates from Kolar district 
(AJ810369|ToLCV-30.Maderahalli), which is a highly 
potential area for commercial cultivation of tomato and 
also the area of first report of B-biotype in India, it has got 
only around 72.00% nucleotide homology. This indicates 
that there is diversity among the gemini viruses infecting 
tomato with in the state.  

Breeders working towards the incorporation of 
begomovirus resistance genes into tomato must take into 
account the high degree of genetic diversity among 
tomato leaf curl viruses in Karnataka. A given resistance 
gene might be extremely effective against a particular 
begomovirus species and totally ineffective against 
distinct unrelated species. Also, the rate of evolution of  
begomoviruses  seems to be quite fast (Padidam et al., 

 
 

 
 

 

1999), leading to the quick emergence of new strains or 
species that might overcome resistance genes. The 
durability of resistance based on a single gene is 
therefore questionable. The genetic diversity of 
begomoviruses present in a region must be taken into 
consideration, in order to orient breeding programs 
towards resistance to the species prevalent in each 
region. 

 

ACKNOWLEDGEMENTS 
 

Authors wish to thank Mr. Salil Jalali (Technical officer), 
Ms. P. Swarnalatha, Senior Research Fellow at Indian 
Institute of Horticulture Research, Bangalore for their 
assistance in carrying out this piece of work. 

 
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