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Investigation of tomato ringspot virus (ToRSV) by Real-Time TaqMan RT-PCR in Hakkari province, Turkey

Year 2021, Volume: 27 Issue: 3, 335 - 340, 04.09.2021
https://doi.org/10.15832/ankutbd.677710

Abstract

Tomato ringspot virus (ToRSV) belongs to the Nepovirus genus in the family Secoviridae. It has a wide host range and is listed as a quarantine virus in Turkey. In this study, 80 leaf samples were collected from tomato, pepper, cucumber and grapevine cultivation sites located in three different parts of Hakkari province: Şemdinli, Çukurca and Center districts. Real-time TaqMan reverse transcription-polymerase chain reaction (RT-PCR) method was used for the detection of the virus. Amplification was carried out in reaction mix including QuantiNova Probe RT-PCR kit (Qiagen, Germany) using primers and TaqMan probe based on 3'-UTR (untranslated region) of virus, which amplified a 182 bp product of the genome. ToRSV was detected in 13 of the 80 samples and threshold cycle (CT) values ranged from 23.9 to 37.4. It was found that 16.25% of the samples collected from the districts of Hakkari province were found to be infected with ToRSV whereas no ToRSV was detected in the samples collected from the center of the city. The virus was detected on pepper and cucumber samples in Çukurca district, and it was also detected in tomato, pepper, cucumber and grapevine samples in Şemdinli district. To our knowledge, this study is the first report of molecular detection of ToRSV by real-time TaqMan RT-PCR in Turkey.

Supporting Institution

Hakkari University Scientific Research Projects Unit

Project Number

EF2015BAP4

Thanks

We are grateful to Dr. Stephan Winter, Dr. Wulf Menzel (Leibniz Institute DSMZ, German) and Farshad Rakhshandehroo (Islamic Azad University, Tehran, Iran) for providing us ToRSV isolate as positive control and support.

References

  • Arlı-Sökmen M, Şevik M A (2006). Viruses infecting field-grown tomatoes in Samsun province. Turkey Archives of Phytopathology and Plant Protection 39 (4): 283-288.
  • Azeri T & Çiçek Y (1997). Detection of virus diseases affecting almond nursery trees in western Anatolia (Turkey). EPPO Bulletin 27 (4): 547-550.
  • Bitterlin M W, Gonsalves D & Scorza R (1987). Improved mechanical transmission of tomato ringspot virus to Prunus seedlings. Phytopathology 77: 560-563.
  • Digiaro M, Elbeaino T & Martelli G P (2007). Development of degenerate and species-specific primers for the differential and simultaneous RT-PCR detection of grapevine-infecting nepoviruses of subgroups A, B and C. Journal of Virological Methods 141: 34-40.
  • Fidan Ü (1995). Virus diseases of vegetables in greenhouses in İzmir and Muğla. Journal of Turkish Phytopathology 24(1): 7-14.
  • Fuchs M, Abawi G S, Marsella-Herrick P, Cox R, Cox K D, Carroll J E & Martin R R (2010). Occurrence of tomato ringspot virus and tobacco ringspot virus in highbush blueberry in Newyork state. Journal of Plant Pathology 92 (2): 451-459.
  • Griesbach J A (1995). Detection of Tomato Ringspot virus by polymerase chain reaction. Plant Disease 79: 10.
  • Moini A A (2010). Identification of Tomato ringspot virus (ToRSV) on apple in Iran. Australasian Plant Disease Notes 5:105-106.
  • Msikita W (2007). Issues with Tomato Ringspot Virus (ToRSV) Detection, WERA 020 Annual Report.
  • OEPP/EPPO (2005). Tomato ringspot nepovirus. Bulletin OEPP/EPPO Bulletin 35: 313-318.
  • OEPP/EPPO (2013). PM 3/32 (2) Tomato ringspot virus in fruit trees and grapevine: inspection. Phytosanitary procedures. Bulletin OEPP/EPPO Bulletin 43(3):397.
  • Osman F, Leutenegger C, Golino D & Rowhani A (2008). Comparison of low-density arrays, RT-PCR and real-time TaqMan® RT-PCR in detection of grapevine viruses. Journal of Virological Methods 149:292-299.
  • Pinkerton J N, Kraus J, Martin R R & Schreiner R P (2008). Epidemiology of Xiphinema americanum and Tomato ringspot virus on red raspberry, Rubus idaeus. Plant Disease 92:364-371.
  • Riviera L, Zamorano A & Fior N (2016). Genetic divergence of tomato ringspot virus. Archieve Virology 161(5):1395-9. https://doi.org/10.1007/s00705-016-2775-1.
  • Roberts J M K, Ireland K B, Tay W T & Paini D, (2018). Honey bee-assisted surveillance for early plant virus detection. Annals Applied Biology 173, 285–293.
  • Rott M E, Tremaine J H, Rochan D M (1991). Nucleotide sequence of tomatoringspot virus RNA-2. Journal of General Virology 72: 1505-1514.
  • Rott M E, Gilchrist A, Lee L & Rochon D M (1995). Nucleotide sequence of tomato ringspot virus RNA-1. Journal of General Virology 76: 465-473.
  • Samuitiene M, Zitikaite I, Navalinskiene M & Valiunas D (2003). Identification of tomato ringspot nepovirus by RT-PCR. Biologija 4: 35-38.
  • Sanfaçon H, Zhang G, Chisholm J, Jafarpour B & Jovel J (2006). In: Teixcira daSilva, J. (Ed.), Molecular Biology of Tomato Ringspot Nepovirus, a Pathogen of Ornamentals, Small Fruits and Fruit Trees. Global Science Books, London. 540-546.
  • Sanfaçon H, Wellink S, Le Gall O, Karasev A, van de Vlugt R A A & Wetzel T (2009). Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Archives of Virology 154: 899-907.
  • Sertkaya G (2010). Tomato ringspot nepovirus (ToRSV) in wild blackberry (Rubus fruticosus L.) in Hatay province of Turkey. Julius- Kühn Archiv 427.
  • Sneideris D, Zitikaite I, Zizyte M & Grigaliünaite B (2012). Identification of nepoviruses in tomato (Lycopersicon esculentum Mill.). Žemdirbystė=Agriculture 99(2):173-178.
  • Sokhansanj Y & Rakhshandehroo F (2012). First Report of Tomato ringspot virus Infecting Pepper in Iran. Disease Notes 96(12):1828.
  • Stewart E L, Qu X S, Overton B E, Gildow F E, Wenner N G & Grove D S (2007). Development of a real-time RT-PCR SYBR Green assay for Tomato ring spot virus in grape. Plant Diseases 91: 1083-1088.
  • Tang J, Khan S, Delmiglio C & Ward L I (2014). Sensitive detection of Tomato ringspot virus by real-time TaqMan RT-PCR targeting the highly conserved 3-UTR region. Journal of Virological Methods 201:38-43.
  • Tzanetakis I E, Martin R R (2013). Expanding Field of Strawberry Viruses Which Are Important in North America. International Journal of Fruit Science 13:184-195.
  • Yeşilçöllü S, Gümüş M, Paylan I. C. (2011). Studies on the Detection of Viruses in Strawberry Growing Areas in Aegean Region. The Journal of Turkish Phytopathology 40( 1-3):13-20.
  • Zindovic J, Marn V M, Plesko I M (2014). Phytosanitary status of grapevine in Montenegro. EPPO Bulletin 44(1):60-64.
Year 2021, Volume: 27 Issue: 3, 335 - 340, 04.09.2021
https://doi.org/10.15832/ankutbd.677710

Abstract

Project Number

EF2015BAP4

References

  • Arlı-Sökmen M, Şevik M A (2006). Viruses infecting field-grown tomatoes in Samsun province. Turkey Archives of Phytopathology and Plant Protection 39 (4): 283-288.
  • Azeri T & Çiçek Y (1997). Detection of virus diseases affecting almond nursery trees in western Anatolia (Turkey). EPPO Bulletin 27 (4): 547-550.
  • Bitterlin M W, Gonsalves D & Scorza R (1987). Improved mechanical transmission of tomato ringspot virus to Prunus seedlings. Phytopathology 77: 560-563.
  • Digiaro M, Elbeaino T & Martelli G P (2007). Development of degenerate and species-specific primers for the differential and simultaneous RT-PCR detection of grapevine-infecting nepoviruses of subgroups A, B and C. Journal of Virological Methods 141: 34-40.
  • Fidan Ü (1995). Virus diseases of vegetables in greenhouses in İzmir and Muğla. Journal of Turkish Phytopathology 24(1): 7-14.
  • Fuchs M, Abawi G S, Marsella-Herrick P, Cox R, Cox K D, Carroll J E & Martin R R (2010). Occurrence of tomato ringspot virus and tobacco ringspot virus in highbush blueberry in Newyork state. Journal of Plant Pathology 92 (2): 451-459.
  • Griesbach J A (1995). Detection of Tomato Ringspot virus by polymerase chain reaction. Plant Disease 79: 10.
  • Moini A A (2010). Identification of Tomato ringspot virus (ToRSV) on apple in Iran. Australasian Plant Disease Notes 5:105-106.
  • Msikita W (2007). Issues with Tomato Ringspot Virus (ToRSV) Detection, WERA 020 Annual Report.
  • OEPP/EPPO (2005). Tomato ringspot nepovirus. Bulletin OEPP/EPPO Bulletin 35: 313-318.
  • OEPP/EPPO (2013). PM 3/32 (2) Tomato ringspot virus in fruit trees and grapevine: inspection. Phytosanitary procedures. Bulletin OEPP/EPPO Bulletin 43(3):397.
  • Osman F, Leutenegger C, Golino D & Rowhani A (2008). Comparison of low-density arrays, RT-PCR and real-time TaqMan® RT-PCR in detection of grapevine viruses. Journal of Virological Methods 149:292-299.
  • Pinkerton J N, Kraus J, Martin R R & Schreiner R P (2008). Epidemiology of Xiphinema americanum and Tomato ringspot virus on red raspberry, Rubus idaeus. Plant Disease 92:364-371.
  • Riviera L, Zamorano A & Fior N (2016). Genetic divergence of tomato ringspot virus. Archieve Virology 161(5):1395-9. https://doi.org/10.1007/s00705-016-2775-1.
  • Roberts J M K, Ireland K B, Tay W T & Paini D, (2018). Honey bee-assisted surveillance for early plant virus detection. Annals Applied Biology 173, 285–293.
  • Rott M E, Tremaine J H, Rochan D M (1991). Nucleotide sequence of tomatoringspot virus RNA-2. Journal of General Virology 72: 1505-1514.
  • Rott M E, Gilchrist A, Lee L & Rochon D M (1995). Nucleotide sequence of tomato ringspot virus RNA-1. Journal of General Virology 76: 465-473.
  • Samuitiene M, Zitikaite I, Navalinskiene M & Valiunas D (2003). Identification of tomato ringspot nepovirus by RT-PCR. Biologija 4: 35-38.
  • Sanfaçon H, Zhang G, Chisholm J, Jafarpour B & Jovel J (2006). In: Teixcira daSilva, J. (Ed.), Molecular Biology of Tomato Ringspot Nepovirus, a Pathogen of Ornamentals, Small Fruits and Fruit Trees. Global Science Books, London. 540-546.
  • Sanfaçon H, Wellink S, Le Gall O, Karasev A, van de Vlugt R A A & Wetzel T (2009). Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Archives of Virology 154: 899-907.
  • Sertkaya G (2010). Tomato ringspot nepovirus (ToRSV) in wild blackberry (Rubus fruticosus L.) in Hatay province of Turkey. Julius- Kühn Archiv 427.
  • Sneideris D, Zitikaite I, Zizyte M & Grigaliünaite B (2012). Identification of nepoviruses in tomato (Lycopersicon esculentum Mill.). Žemdirbystė=Agriculture 99(2):173-178.
  • Sokhansanj Y & Rakhshandehroo F (2012). First Report of Tomato ringspot virus Infecting Pepper in Iran. Disease Notes 96(12):1828.
  • Stewart E L, Qu X S, Overton B E, Gildow F E, Wenner N G & Grove D S (2007). Development of a real-time RT-PCR SYBR Green assay for Tomato ring spot virus in grape. Plant Diseases 91: 1083-1088.
  • Tang J, Khan S, Delmiglio C & Ward L I (2014). Sensitive detection of Tomato ringspot virus by real-time TaqMan RT-PCR targeting the highly conserved 3-UTR region. Journal of Virological Methods 201:38-43.
  • Tzanetakis I E, Martin R R (2013). Expanding Field of Strawberry Viruses Which Are Important in North America. International Journal of Fruit Science 13:184-195.
  • Yeşilçöllü S, Gümüş M, Paylan I. C. (2011). Studies on the Detection of Viruses in Strawberry Growing Areas in Aegean Region. The Journal of Turkish Phytopathology 40( 1-3):13-20.
  • Zindovic J, Marn V M, Plesko I M (2014). Phytosanitary status of grapevine in Montenegro. EPPO Bulletin 44(1):60-64.
There are 28 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Makaleler
Authors

Nevin Akdura 0000-0001-6162-0500

Murat Şevik 0000-0002-9604-3341

Project Number EF2015BAP4
Publication Date September 4, 2021
Submission Date January 20, 2020
Acceptance Date April 30, 2020
Published in Issue Year 2021 Volume: 27 Issue: 3

Cite

APA Akdura, N., & Şevik, M. (2021). Investigation of tomato ringspot virus (ToRSV) by Real-Time TaqMan RT-PCR in Hakkari province, Turkey. Journal of Agricultural Sciences, 27(3), 335-340. https://doi.org/10.15832/ankutbd.677710

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