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Journal of Integrative Agriculture  2021, Vol. 20 Issue (8): 2170-2179    DOI: 10.1016/S2095-3119(20)63335-4
Special Issue: 植物病理合辑Plant Protection—Plant Pathology 植物病毒合辑Plant Virus
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Robust molecular detection of the new Tomato brown rugose fruit virus in infected tomato and pepper plants from Turkey
Hakan FIDAN1, Pelin SARIKAYA1, Kubra YILDIZ2, Bengi TOPKAYA2, Gozde ERKIS3, Ozer CALIS1
1 Plant Protection Department, Faculty of Agriculture, Akdeniz University, The Campus, Konyaalti 07070, Antalya, Turkey
2 Plant Health Department, Bati Akdeniz Agricultural Research Institute (BATEM), Muratpasa 07050, Antalya, Turkey
3 Antalya Directorate of Agricultural Quarantine, Republic of Turkey Ministry of Agriculture and Forestry, Muratpasa 07050, Antalya, Turkey
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Tomato brown rugose fruit virus (ToBRFV) causes severe fruit loss in tomato (Solanum lycopersicum) and pepper (Capsicum annuum) plants.  It is an emerging Tobamovirus that is spreading globally.  The major challenge is to develop a reliable method for the detection of the virus, and to better characterize the symptoms it causes.  The aims of this study, therefore, were to characterize the symptom development on tomato and pepper plants, and to establish a reliable detection method for the virus.  Following infection of the tomato and pepper plants with ToBRFV, the leaves turned chlorotic, mosaic or mottled, while the fruit became rugose, necrotic and marbled, and showed discoloration with yellow or brown spots.  Transmission electron microscopy (TEM) revealed single rod-like virus particles characteristic of the Tobamoviruses.  Classical reverse transcription PCR (RT-PCR) and quantitative PCR (qPCR) with specific primers and probes confirmed that the virus is ToBRFV.  We found that the resistance genes from tomato, Tm-22, and pepper, L1, L2, L3 and L4, did not confer resistance to ToBRFV.  Here, we present a PCR-based method as a diagnostic test for detecting ToBRFV in infected seeds.  This method will help to prevent further spread of the virus in commercial seeds.
Keywords:   tomato        pepper        Tobamovirus        ToBRFV        resistance  
Received: 29 March 2020   Accepted:
Corresponding Authors:  Correspondence Ozer CALIS, Tel: +90-242-3106536, Fax: +90-242-3102479, E-mail:   
About author:  Hakan FIDAN, E-mail:;

Cite this article: 

Hakan FIDAN, Pelin SARIKAYA, Kubra YILDIZ, Bengi TOPKAYA, Gozde ERKIS, Ozer CALIS. 2021. Robust molecular detection of the new Tomato brown rugose fruit virus in infected tomato and pepper plants from Turkey. Journal of Integrative Agriculture, 20(8): 2170-2179.

Adams M J, Antoniw J F, Kreuze J. 2009. Virgaviridae: A new family of rod-shaped plant viruses. Archives of Virology, 154, 1967–1972.
Agarwal S, Rao A V. 2000. Tomato lycopene and its role in human health and chronic diseases. Canadian Medical Association Journal, 163, 739–744.
Antignus Y, Lachman O, Pearlsman M, Maslenin L, Rosner A. 2008. A new pathotype of Pepper mild mottle virus (PMMoV) overcomes the L4 resistance genotype of pepper cultivars. Plant Disease, 92, 1033–1037.
Cambrón-Crisantos J M, Rodríguez-Mendoza J, Valencia-Luna J B, Alcasio-Rangel S, García-Ávila C J, López-Buenfil J A, Ochoa-Martínez D L. 2018. First report of Tomato brown rugose fruit virus (ToBRFV) in Michoacan, Mexico. Revista Mexicana de Fitopatología, 37, 1–8.
De Ronde D, Butterbach P, Kormelink R. 2014. Dominant resistance against plant viruses. Frontiers in Plant Science, 5, 307.
Dombrovsky A, Smith E. 2017. Seed transmission of Tobamoviruses: Aspects of global disease distribution. In: Jimenez-Lopez J C, ed., Seed Biology. IntechOpen, UK. pp. 234–260.
Doyle J J, Doyle J I. 1990. Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.
EPPO. 2019. European and Mediterranean Plant Protection Organization. [2020-8-18].
FAO (Food and Agriculture Organization of the United Nations). 2019. Food and agriculture organization of the united nations. [2020-7-17].
Fidan H, Sarikaya P, Calis O. 2019. First report of Tomato brown rugose fruit virus on tomato in Turkey. New Disease Reports, 39, 18.
Fidan H, Barut M. 2019. Screening of L4 resistance status to pepper mild mottle virus (PMMoV) and characterization by molecular methods. Mediterranean Agricultural Sciences, 32, 297–305. (in Turkish)
Genda Y, Kanda A, Hamada H, Sato K, Ohnishi J, Tsuda S. 2007. Two amino acid substitutions in the coat protein of Pepper mild mottle virus are responsible for overcoming the L(4) gene-mediated resistance in Capsicum spp. Phytopathology, 97, 787–793.
Gilardi P, Garcia-Luque I, Serra M T. 2004. The coat protein of tobamovirus acts as elicitor of both L2 and L4 gene-mediated resistance in Capsicum. Journal of General Virology, 85, 2077–2085.
Hamada H, Takeuchi S, Kiba A, Tsuda S, Hikichi Y, Okuno T. 2002. Amino acid changes in Pepper mild mottle virus coat protein that affect L3 gene-mediated resistance in pepper. Journal of General Plant Pathology, 68, 155–162.
Hanssen I M. Lapidot M, Thomma B P H J. 2010. Emerging viral diseases of tomato crops. Molecular Plant Microbe Interactions, 23, 539–548.
Lanfermeijer F C, Warmink J, Hille J. 2005. The products of the broken Tm-2 and the durable Tm-22 resistance genes from tomato differ in four amino acids. Journal of Experimental Botany, 56, 2925–2933.
Liu H J, Jian L, Xu J, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, Yang X, Li Z, Zhang M, Sun J, Bai M, et al. 2020. High-throughput CRISPR/Cas9 mutagenesis streamlines trait gene identification in maize. The Plant Cell, 32, 1397–1413.
Luria N, Smith E, Reingold V, Bekelman I, Lapidot M, Levin I, Elad N, Tam Y, Sela N, Abu-Ras A, Ezra N, Haberman A, Yitzhak L, Lachman O, Dombrovsky A. 2017. A new israeli Tobamovirus isolate infects tomato plants harboring Tm-22 resistance genes. PLoS ONE, 12, e0170429.
Matsumoto K, Sawada H, Matsumoto K, Hamada H, Yoshimoto E, Ito T, Takeuchi S, Tsuda S, Suzuki K, Kobayashi K, Kiba A, Okuno T, Hikichi Y, Suzuki K, Kobayashi K. 2008. The coat protein gene of tobamovirus P(0) pathotype is a determinant for activation of temperature-insensitive L (1a)-gene-mediated resistance in Capsicum plants. Archives of Virology, 153, 645–650.
Menzel W, Knierim D, Winter S, Hamacher J, Heupel M. 2019. First report of Tomato brown rugose fruit virus infecting tomato in Germany. New Disease Reports, 39, 1.
Meshi T, Motoyoshi F, Maeda T, Yoshiwoka S, Watanabe H, Okada Y. 1989. Mutations in the tobacco mosaic-virus 30-kD protein gene overcome Tm-2 resistance in tomato. The Plant Cell, 1, 515–522.
Palevitch D, Craker L E. 2012. Nutritional and medical importance of red pepper (Capsicum spp.). Journal of Herbs, Spices and Medicinal Plants, 3, 55–83.
Salem N, Mansour A, Ciuffo M, Falk B W, Turina M. 2016. A new tobamovirus infecting tomato crops in Jordan. Archives of Virology, 161, 503–506.
Skelton A, Buxton-Kirk A, Ward R, Harju V, Frew L, Fowkes A, Long M, Negus A, Forde S, Adams I P, Pufal H, McGreig S, Weekes R, Fox A. 2019. First report of Tomato brown rugose fruit virus in tomato in the United Kingdom. New Disease Reports, 40, 12.
Smith E, Dombrovsky A. 2019. Aspects in Tobamovirus Management in Intensive Agriculture.  IntechOpen, London.
Story E N, Kopec R E, Schwartz S J, Harris G H, 2010. An update on the health effects of tomato lycopene. Annual Review of Food Science and Technology, 1, 189–210.
Tomita R, Sekine K T, Mizumoto H, Sakamoto M, Murai J, Kiba A, Hikichi Y, Suzuki K, Kobayashi K. 2011. Genetic basis for the hierarchical interaction between Tobamovirus spp. and L resistance gene alleles from different pepper species. Molecular Plant Microbe Interactions, 24, 108–117.
Tripodi P, Kumar S. 2019. The Capsicum crop: An introduction. In: Ramchiary N, Kole C, eds., The Capsicum Genome.Compendium of Plant Genomes, Springer Nature, Switzerland. pp. 1–8.
Xu C, Sun X, Taylor A, Jiao C, Xu Y, Cai X, Wang X, Ge C, Pan G, Wang Q, Fei Z, Wang Q. 2017. Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing. Journal of Virology, 91, e00173–e00192.
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