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Pcr-based Detection and Characterisation of Tomato Leaf Curl and Other Related Geminiviruses in Bangladesh (2016-2017)

M. A. Y. Akhond
Biotechnology Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur-1701, Bangladesh

M. R. Kabir
Biotechnology Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur-1701, Bangladesh

Abstract/ Executive Summary:

The experiment was conducted with a view to characterise Geminivirus strains in different crops beginning with tomato. In the present experiment, genomic DNA was extracted from the 58 leaf samples of 12 cucurbit crops showing virus like symptoms collected from 5 districts of the country. Isothermal amplification method followed by restriction digestion was used for initial detection of the virus. Results of the pairwise sequence comparison of the virus coat-protein gene showed the presence of two tomato infecting Geminiviruses where only a single species (Tomato leaf curl New Delhi virus) was identified from 29 of the 30 samples. A phylogenetic tree was constructed and analyses of the sequences confirmed the above findings and show the ability of tomato leaf curl viruses to infect a wide host range.

Keywords: Tomato variety, Fertilizer recommendations, Tomato grown, Geminivirus, Emphasis to tomato, Leaf curl

Location: Biotechnology Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur, Bangladesh

Start Date: 00-00-2016

End Date: 00-00-2017

Program Area: Pest Management

Commodity: Fungal Disease

Objectives:

To characterise geminivirus strains in different crops with emphasis to tomato.

Methodology:

Genomic DNA was extracted from the 58 leaf samples of 12 cucurbit crops showing virus like symptoms collected from 5 districts of the country. Isothermal amplification method followed by restriction digestion was used for initial detection of the virus. Geminivirus-specific universal primers were designed and used for the PCR amplification of the Coat protein sequence (AV1) from the ‘A’ genome of the viruses. Amplification products from 30 samples were sequenced and the obtained sequences from both strands were assembled in computer using ‘Geneious V10’ software. Identities of the isolates were confirmed by using pairwise identitiy analysis. All the sequences were aligned using the ‘Muscle’ software and a phylogenetic tree was constructed for comparison. Sequence alignment and the tree construction using Maximum likelihood method were carried out from within the sequence analysis software (MEGA6) based on the Tamura-Nei model (1993).

Source of Information: Annual Research Report 2016-2017, Biotechnology Division, BARI, Joydebpur, Gazipur, Bangladesh

Article Link (Online Journal):

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

Molecular analyses of the 58 cucurbit samples from 5 districts of Bangladesh revealed the presence of Geminivirus in 36 samples (62%). Coat-protein (AV1) sequenceses were obtained from 30 isolates and paiwise sequence comparisons were carried out using using an additional 22 various Geminivirus sequences from published NCBI database. Results of the pairwise sequence comparison showed the presence of two tomato infecting Geminiviruses where only a single species (Tomato leaf curl New Delhi virus) was identified from 29 of the 30 samples. Phylogenetic trees were constructed and analyses of the sequences confirmed the above findings and show the ability of tomato leaf curl viruses to infect a wide host range. Further analyses of the whole virus genomes will be carried out to confirm the present results.

Knowledge Management: Report/Proceedings