Molecular characterization and geographical distribution of Chickpea chlorotic dwarf virus in Iran

Bananej, Kaveh; Sokhansanj, Yalda; Rakhshandehroo, Farshad; Ahoonmanesh, Ali

doi:10.22092/jaep.2019.125722.1278

Document Type : Plant Pathology

Authors

¹ Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran.

² Faculty member

³ Foulad Institute Technology (FIT), Foulad-shahr, Isfahan-Iran.

https://doi.org/10.22092/jaep.2019.125722.1278

Abstract

Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is one of the most important viral agents which associated with yellowing symptom in the chickpea fields. During the surveys, 2015-2016, 248 chickpea and lentil plant samples showing yellowing symptom were collected from five provinces: Lorestan, Kermanshah, Zanjan, East and West Azarbaijan, in Iran. The samples were tested to CpCDV infection, using TBIA and positive samples in TBIA were tested by PCR. Total DNA of positive samples were extracted and enriched using rolling-circle amplification (RCA). RCA products were restricted using Xho I enzyme and yielding products of ~2.5-6 kb. These fragments were used for polymerase chain reaction (PCR), using specific primers for RepA protein of CpCDV. PCR amplicons with an expected size of ~960 bp were amplified, cloned and sequenced.TBIA and PCR results showed the presence of CpCDV infection in all surveyed provinces with the highest infection in chickpea plants. Nucleotide sequence comparisons showed that Iranian isolates shared the highest identity to strain A, D and F from India, Pakistan, and Yemen. Phylogenetic anlyses showed that Iranian CpCDV strains were grouped with Sudan, Morrocco, India, and Pakistan (strain D, group III), Sudan, Oman, Yemen, and Pakistan (starin F, GroupIV), and Tunesia, Egypt, Syria, and Turkey (strain A, group V).

Keywords

20.1001.1.10265007.1398.87.1.12.5

Full Text

AKHTAR, K. P., AHMAD, M., SHAH, T. M., ATTA, B. M. 2011. Transmission of Chickpea chlorotic dwarf virus in chickpea by the leafhopper Orosius albicinctus (Distant) in Pakistan. Plant Protect. Science, No. 47: 1–4.

AKHTAR, S., KHAN, A. J., BRIDDON, R. W. 2013. A distinct strain of Chickpea chlorotic dwarf virus infecting pepper in Oman. Plant Disease, No. 98: 286-286.

ANONYMOUS, 2017. Statistical annual report of Iranian agricultural crops. Ministry of Agriculture Jihad, NO. 40(1): 53.

FAHMY, I. F., TAHA, O., EL-ASHRY, A. N. 2015. First genome analysis and molecular characterization of

Chickpea chlorotic dwarf virus Egyptian isolate infecting squash. Virus Diseases, No. 26: 33–41.

FAOSTAT, 2014. Prunus production: National Agricultural statistics Service, USDA.

FAO, 2014. FAOSTAT Database results from FAO website. Food and Agriculture Organization of the United Nations.

FARZADFAR, S., POURRAHIM, R., GOLNARAGHI, A. R., AHOONMANESH, A. 2008. PCR detection and partial molecular characterization of Chickpea chlorotic dwarf virus in naturally infected sugar beet plants in Iran. Jouranl of Plant Pathology, No. 90: 247-251.

FIALLO-OLIVE, E., MOHAMMED, I. U., TURAKI, A. A., MUHAMMAD, A., NAVAS-CASTILLO, J. A. 2017.Novel Strain of the mastrevirus Chickpea chlorotic dwarf virus infecting papaya in Nigeria. Plant Disease, No. 101: 1684.

HAMZA, M., TAHIR, M. N., MUSTAFA, R., KAMAL, H., KHAN, M. Z., MANSOOR, S., BRODDON, R.W., AMIN, I. 2018. Identification of a dicot infecting mastrevirus along with alpha-and betasatellite associated with leaf curl disease of spinach (Spinacia oleracea) in Pakistan. Virus Research, No. 256: 174–182.

HORN, N. M., REDDY, S. V., REDDY, D. V. R. 1994. Virus-vector relationships of Chickpea chlorotic dwarf geminivirus and the leafhopper Orosius orientalis (Hemiptera: Cicadellidae). Ann. Appl. Biol., No. 124: 441–450.

HORN, N. M., REDDY, S. V., REDDY, D. V. R. 1995. Assessment of yield losses caused by Chickpea chlorotic dwarf geminivires in chickpea (Cicer arientinum) in India. European Journal of Plant Pathology, No. 101: 221-224.

HORN, N. M., REDDY, S. V., ROBERTS, I. M., REDDY, D. V. R. 1993. Chickpea chlorotic dwarf virus, a new leafhopper-transmitted geminivirus of chickpea in India. Ann. Appl. Biol., No. 122: 467-479.

HORN, N. M., REDDY, S. V., van den Huevel, J. F. J. M., and REDDY, D. V. R. 1996. Survey of chickpea (Cicer arietinum L.) for chickpea stunt disease and associated viruses in India and Pakistan. Plant Disease, NO.80: 286-290.

KANAKALA, S., KURIA, P. 2019. Chickpea chlorotic dwarf virus: An Emerging Monopartite Dicot Infecting Mastrevirus. Viruses, No. 11(1): 5-20.

KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, No. 16:111-120.

KRABERGER, S., HARKINS, G. W., KUMARI, S.G., THOMAS, J. E., SCHWINGHAMER, M. W., SHARMAN, M., COLLINGS, D. A., BRIDDON, R.W., MARTIN, D. P., VARSANI, A. 2013. Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East. Virology, NO.444: 282-291.

KRABERGER, S., KUMARI, S. G., HAMED, A. A., GRONENBORN, B., THOMAS, J. E., SHARMAN, M., HARKINS, G. W., MUHIRE, B. M., MARTIN, D. P., VARSANI, A. 2015. Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains. Infection, Genetics and Evolution, No. 29: 203-215.

KUMARI, S. G., MAKKOUK, K. M., ATTAR, N., GHULAM, W. 2004. First report of Chickpea chlorotic dwarf virus infecting spring chickpea in Syria. Plant Disease, No. 88: 424.

MAKKOUK, K. M., COMEAUE, A. 1994. Evaluation of various methods for the detection of Barley yellow dwarf luteovirus by the tissueblot immunoassay and its use for BYDV detection in cereals inoculated at different growth stages. Europian Journal of Plant Pathololigy , No. 100: 71-80.

MAKKOUK, K. M., FAZLALI, Y., KUMARI, S. G., and FARZADFAR, S. 2002. First record of Beet western yellows virus, Chickpea chlorotic dwarf virus, Faba bean necrotic yellows virus and Soybean dwarf virus infecting chickpea and lentil crops in Iran. Plant Pathology, No. 51: 387-387.

MAKKOUK, K. M., KUMARI, S. G., SHAHRAEEN, N., FAZLALI, Y., FARZADFAR, S., GHOTBI, T., MANSOURI, A. R. 2002. Identification and seasonal variation of viral diseases of chickpea and lentil in Iran. Journal of Plant Diseases and Protection, No. 110(2): 157–169.

MUMTAZ, H., KUMARI, S. G., MANSOOR, S., MARTIN, D. P., BRIDDON, R.W. 2011. Analysis of the sequence of a dicot-infecting mastrevirus (Family Geminiviridae) originating from Syria. Viris Genes, No. 42: 422-428.

NAHID, N., AMIN, I., MANSOOR, S., RYBICKI, E. P., VAN DER WALT, E., BRIDDON, R. W. 2008. Two dicot-infecting mastreviruses (family Geminiviridae) occur in Pakistan. Archive of Virology, No. 153: 1441-1451.

SAITOU, N., NEI, M., 1987. The neighbour-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. No. 4: 406-425.

TAMURA, K., STECHER, G., PETERSON, D., FILIPSKI, A., KUMAR, S., 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution. No. 30(12): 2725-2729.

OUATTARA, A., TIENDREBEOGO, F., LEFEUVRE, P., HOAREAU, M., CLAVERIE, S., TRAORE, E. V., BARRO, N., TRAORE, O., VARSANI, A., LETT, J. M. 2017. New strains of Chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso. Archive of Virology, No. 162: 1791–1794.

OWOR, B. E., SHEPHERD, D. N., TAYLOR, N. J., EDEMA, R., MONJANE, A. L., THOMSON, J. A., MARTIN, D. P., VARSANI, A. 2007. Successful application of FTA® Classic Card technology and use of bacteriophage φ29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes. Journal of Virological Methods, No. 140: 100–105.

References