Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye

Filiz Randa Zelyüt; Ali Karanfil; Adyatma Irawan Santosa

doi:10.31015/jaefs.2024.4.7

EN

Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye

Abstract

In this study, the status of infections caused by viruses and phytoplasmas in tomato production areas of Bilecik province was determined using conventional molecular methods. During the 2022 tomato production season, 93 plants exhibiting symptoms such as mosaic, leaf and fruit deformations, flower anomalies, and necrotic spots were collected. Viral agents such as tomato spotted wilt virus (TSWV), cucumber mosaic virus (CMV), southern tomato virus (STV), tobamoviruses, and potyviruses were screened by RT-PCR, while phytoplasmas were detected by nested-PCR. Single, double, and triple infections were detected in 50 of the 93 plants. 17, 5, and 21 plants were infected by a single pathogen for TSWV, STV, and phytoplasmas, respectively. 1, 3, and 2 plants were infected by two pathogens for STV+TSWV, STV+phytoplasma, and TSWV+phytoplasma, respectively. Only one plant detected a triple infection caused by STV, TSWV, and phytoplasmas. The phytoplasma genetic group was determined as 16Sr XII-A by PCR RFLP in-silico and in-vitro methods. Sequencing studies revealed that TSWV had high nucleotide sequence similarity with other Türkiye isolates for the NSs partial gene and STV entire CP gene region. For phytoplasmas, sequencing studies showed that the obtained tomato strains overlapped one-to-one with stolbur strains. Phylogenetic analyses applied with global isolates for TSWV NSs and STV CP gene regions showed the existence of 2 main groups (Clade I and Clade II). TSWV and STV isolates obtained from this study clustered in large main branches (Clade I).

Keywords

Bilecik, Tomato, Virus, Phytoplasma, PCR, Sequencing

Supporting Institution

Bilecik Şeyh Edebali University, The Scientific Research Coordination Unit

Project Number

2022-01.BŞEÜ.06-0

References

Abadkhah, M., Koolivand, D. & Eini O. A. (2018). New Distinct Clade for Iranian Tomato spotted wilt virus Isolates Based on the Polymerase, Nucleocapsid, and Non-structural Genes. Plant Pathology Journal, 34(6):514-531. https://doi.org/10.5423/PPJ.OA.04.2018.0062
Akdura, N., & Çulal Kılıç, H. (2022). Hakkari İli Domates ve Biber Üretim Alanlarında Yonca Mozaik Virüsü ve Domates Lekeli Solgunluk Virüsü’nün Belirlenmesi. Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 26(3), 435-440. https://doi.org/10.19113/sdufenbed.1082948
Bozdoğan, V. & Kamberoglu, M. A. (2016). Incidence and Distribution of Tomato Spotted Wilt Tospovirus (TSWV) in Vegetable Crops in Antalya Province of Türkiye. The Journal of Turkish Phytopathology, 44(1-2-3), 39-49.
Çağlayan, K. (2023). Diversity, distribution, and status of phytoplasmas diseases in Türkiye. In Diversity, Distribution, and Current Status (pp. 249-267). Academic Press. https://doi.org/10.1016/B978-0-323-91896-1.00012-X
Çağlar, B.K. & Şimşek, E. (2022). Detection and Multigene Typing of 'Candidatus Phytoplasma solani'-Related Strains Infecting Tomato and Potato Plants in Different Regions of Türkiye. Pathogens, 11;11(9):1031. https://doi.org/10.3390/pathogens11091031
Ember, I., Bodor, P., Zsófi, Z., Palfi, X., Villango, S., Pálfi, Z., ... & Bisztray, G. D. (2016, March). Impact of Bois Noir disease on grapevine performance and wine quality of Vitis Vinifera L. Cv.'Chardonnay'in Hungary. in tagungsbeiträge anlässlich des 4. european bois noir workshop 9.-11. märz, 2016, klosterneuburg österreich.
Fidan, H., Karacaoğlu, M. & Çağlar, B.K. (2019). Tomato Yellow Leaf Curl Virus (Tylcv) Strains And Epidemiological Role Of Bemisia Tabaci (Hemiptera: Aleyrodidae) Biotypes On Tomato Agroecology In Türkiye. Applied Ecology And Environmental Research, 17:4, 9131-9144. http://dx.doi.org/10.15666/aeer/1704_91319144
Güller, A. & Usta M. (2020). Stolbur and Clover Proliferation Phytoplasma Infections in Tomato from Bingöl province Türkiye. Turkish Journal of Agricultural and Natural Sciences,7:4. 855–866. https://doi.org/10.30910/turkjans.727892
Güller, A., Usta, M., & Randa-Zelyüt, F. (2023). Genetic diversity and population structure of tomato brown rugose fruit virus (ToBRFV) variants from Antalya province, Türkiye. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51(3), 13356. https://doi.org/10.15835/nbha51313356
Güneş, N., Türkseven, S. G., ÖZSARI, P., Gümüş, M., & Sivritepe, D. B. (2022). Incidence and possible sources of Tomato spotted wilt virus in tobacco grown in Denizli Province, Türkiye. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 50(2), 12529-12529. https://doi.org/10.15835/nbha50212529

Gundersen, D. E., & Lee, I. M. (1996). Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia mediterranea, 144-151. https://www.jstor.org/stable/42685262
Hanson, P., Lu, S., Wang, J., Chen, W., Kenyon, L., Tan, C., Tee, K.L., Wang, Y., Hsu, Y., Schafleitner, R., Ledesma, D. & Yang, R. (2016). Conventional and molecular marker-assisted selection and pyramiding of genes for multiple disease resistance in tomato. Scientia Horticulturae, 201:346–354. https://doi.org/10.1016/j.scienta.2016.02.020
Hogenhout, S. A., Oshima, K., Ammar, E. D., Kakizawa, S., Kingdom, H. N., & Namba, S. (2008). Phytoplasmas: bacteria that manipulate plants and insects. Molecular Plant Pathology, 9(4), 403-423. https://doi.org/10.1111/j.1364-3703.2008.00472.x
Karanfil A. & Korkmaz S. (2017). Detection and molecular characterization based on coat protein gene of Cucumber mosaic virus (CMV) from cowpea production fields of Çanakkale province in Turkey. Plant Protection Bulletin, 57 (3), 293-304. https://doi.org/10.16955/bitkorb.340046
Karanfil, A. (2021). Prevalence and molecular characterization of Cucumber mosaic virus isolates infecting tomato plants in Marmara region of Türkiye. Plant Protection Bulletin, 61(4), 19-25. https://doi.org/10.16955/bitkorb.981093
Kumari, S., Nagendran, K., Rai, A. B., Singh, B., Rao, G. P. & Bertaccini, A. (2019). Global status of phytoplasma diseases in vegetable crops. Frontiers in Microbiology, 10, 1349. https://doi.org/10.3389/fmicb.2019.01349
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 35(6), 1547-1549. https://doi.org/10.1093/molbev/msy096
Lee, I. M., Hammond, R. W., Davis, R. E., & Gundersen, D. E. (1993). Universal amplification and analysis of pathogen 16S rDNA for classification and identification of mycoplasmalike organisms. Phytopathology, 83(8), 834-842.
Li, R., Mock, R., Huang, Q., Abad, J., Hartung, J. & Kinard,G. (2008). A reliable and inexpensive method of nucleic acid extraction for the PCR-based detectionof diverse plant pathogens. Journal of Virological Methods, 154(1-2): 48-55. https://doi.org/10.1016/j.jviromet.2008.09.008
Li, Y., Tan, G., Lan, P., Zhang, A., Liu, Y., Li, R. & Li, F. (2018). Detection of tobamoviruses by RT-PCR using a novel pair of degenerate primers. Journal of Virological Methods, 259:122-128. https://doi.org/10.1016/j.jviromet.2018.06.012
Morca, A. F., Çelik, A., Coşkan, S., Santosa, A. I., & Akbaş, B. (2022). Population analysis on tomato spotted wilt virus isolates inducing various symptoms on tomato, pepper, and Chenopodium album in Türkiye. Physiological and Molecular Plant Pathology, 118, 101786. https://doi.org/10.1016/j.pmpp.2022.101786
Navas-Castillo, J., Fiallo-Olive, E. & Sanchez-Campos, S. (2011). Emerging virus diseases transmitted by whiteflies. Annual Review Phytopathology, 49:219–248. https://doi.org/10.1146/annurev-phyto-072910-095235
Navrátil, M., Válová, P., Fialová, R., Lauterer, P., Šafářová, D., & Starý, M. (2009). The incidence of stolbur disease and associated yield losses in vegetable crops in South Moravia (Czech Republic). Crop Protection, 28(10), 898-904. https://doi.org/10.1016/j.cropro.2009.05.008
Oladokun, J.O., Halabi, M.H., Barua, P. & Nath, P.D. (2019). Tomato brown rugose fruit disease: current distribution, knowledge and future prospects. Plant Pathology, 68:1579–1586. https://doi.org/10.1111/ppa.13096
Panno, S., Davino, S., Caruso, A.G., Bertacca, S., Crnogorac, A., Mandić, A., Noris, E. & Matić, S. (2021). A Review of the Most Common and Economically Important Diseases That Undermine the Cultivation of Tomato Crop in the Mediterranean Basin. Agronomy, 11:2188. https://doi.org/10.3390/agronomy11112188
Quaglino, F., Sanna, F., Moussa, A., Faccincani, M., Passera, A., Casati, P., ... & Mori, N. (2019). Identification and ecology of alternative insect vectors of ‘Candidatus Phytoplasma solani’to grapevine. Scientific Reports, 9(1), 19522. https://doi.org/10.1038/s41598-019-56076-9
Randa-Zelyüt, F., Santosa, A. I., & Karanfil, A. (2022). ‘Candidatus Phytoplasma solani’ (Subgroup 16SrXII-A) Associated with Nicotiana tabacum Leaf Abnormality in Türkiye. Tekirdağ Ziraat Fakültesi Dergisi, 19(3), 571-581. https://doi.org/10.33462/jotaf.1028263
Randa-Zelyüt, F, Fox A. & Karanfil A (2023). Population genetic dynamics of southern tomato virus from Türkiye. Journal of Plant Pathology, 105:211-224. https://doi.org/10.1007/s42161-022-01263-3
Roselló, S., Díez, M.J. & Nuez, F. (1996). Viral diseases causing the greatest economic losses to the tomato crop. I. The Tomato spotted wilt virus—a review. Scientia Horticulturae, 67:117–150. https://doi.org/10.1016/S0304-4238(96)00946-6
Sajid, Q.U.A. & Elçi, E. (2024). A comprehensive study on the molecular characterization of tomato spotted wilt orthotospovirus isolates and resistance genes in pepper and tomato. Turkish Journal of Botany, Vol. 48: No. 1, Article 3. https://doi.org/10.55730/1300-008X.2791
Van der Vlugt, R.A., Verbeek, M., Dullemans, A.M., Wintermantel, W.M., Cuellar, W.J., Fox, A. & Thompson, J.R. (2015). Torradoviruses. Annual Review of Phytopathology, 53:485–512. https://doi.org/10.1146/annurev-phyto-080614-120021
Weisburg, W.G., Tully, J.G., Rose, D.L., Petzel, J.P., Oyaizu, H., Yang, D., Mandelco, L., Sechrest, J., Lawrence, T.G. & Van Etten, J. (1989). A phylogenetic analysis of the mycoplasmas: basis for their classification. Journal of Bacteriology, 171(12): 6455–6467. https://doi.org/10.1128/jb.171.12.6455-6467.1989
Usta, M., Güller, A., & Demirel, S. (2021). Molecular identification of ‘Candidatus Phytoplasma solani’using SecY and Vmp1 Genes in Tomato Plants from Van province Van’dan Domates Bitkilerinde SecY ve Vmp1 Genlerini Kullanarak ‘Candidatus Phytoplasma solani’nin Moleküler Tanımlanması. Yuzuncu Yil University Journal of Agricultural Sciences, 31(4). https://doi.org/10.29133/yyutbd.950047
Usta, M., Güller, A. & Sipahioğlu H.M. (2018). Molecular Analysis Of Candidatus Phytoplasma Trifolii And Candidatus Phytoplasma Solani Associated With Phytoplasma Diseases Of Tomato Pdt İn Türkiye. International Journal of Agriculture and Biology, 20: 9. 1991–1996.
Usta, M. & Güller A. (2020). Detection and Molecular Characterization of Candidatus Phytoplasma trifolii a Member of the Clover Proliferation Grup Infecting Tomato Plants from Iğdır Province in Türkiye. Türk Tarım - Gıda Bilim ve Teknoloji Dergisi, 8:12. 2533–2540. https://doi.org/10.24925/turjaf.v8i12.2533-2540.3592
Usta, M., Güller A., Demirel S., Korkmaz G., & Kurt Z. (2023). New insights into tomato spotted wilt orthotospovirus TSWV infections in Türkiye Molecular detection phylogenetic analysis and in silico docking study. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 51:3, 1–22. https://doi.org/10.15835/nbha51313245
Yeşilyurt, N. & Çevik, B. (2019). Genetic diversity and phylogenetic analyses of tomato chlorosis virus isolates using the coat protein gene sequences. Journal of Plant Pathology, 101, 1143–1150. https://doi.org/10.1007/s42161-019-00297-4
Zelyüt, F. R. (2023). Genetic diversity and molecular variability of ’Candidatus Phytoplasma solani’based on multilocus sequence typing analysis in tomato plantations of western Türkiye. Physiological and Molecular Plant Pathology, 127, 102120. https://doi.org/10.1016/j.pmpp.2023.102120
Zhao, Y, Wei W., Lee, I.M., Shao, J., Suo, X. & Davis, R.E. (2013).The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment. Methods Molecular Biology, 938:329-38. https://doi.org/10.1007/978-1-62703-089-2_28
Zheng, L., Rodoni, B. C., Gibbs, M. J., & Gibbs, A. J. (2010). A novel pair of universal primers for the detection of potyviruses. Plant Pathology, 59(2), 211-220. https://doi.org/10.1111/j.1365-3059.2009.02201.x

Details

Primary Language

English

Subjects

Plant Pathology

Journal Section

Research Article

Authors

Filiz Randa Zelyüt ^*
0000-0002-1366-4389
Türkiye

Ali Karanfil
0000-0002-4503-6344
Türkiye

Adyatma Irawan Santosa
0000-0002-2826-5444
Indonesia

Early Pub Date

December 9, 2024

Publication Date

December 28, 2024

Submission Date

September 9, 2024

Acceptance Date

November 1, 2024

Published in Issue

Year 2024 Volume: 8 Number: 4

DOI

https://doi.org/10.31015/jaefs.2024.4.7

IZ

https://izlik.org/JA99SU62NW

APA

Randa Zelyüt, F., Karanfil, A., & Santosa, A. I. (2024). Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye. International Journal of Agriculture Environment and Food Sciences, 8(4), 786-796. https://doi.org/10.31015/jaefs.2024.4.7

AMA

1.Randa Zelyüt F, Karanfil A, Santosa AI. Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye. int. j. agric. environ. food sci. 2024;8(4):786-796. doi:10.31015/jaefs.2024.4.7

Chicago

Randa Zelyüt, Filiz, Ali Karanfil, and Adyatma Irawan Santosa. 2024. “Investigation of Viruses and Phytoplasma Infections in Tomato Plantations in Bilecik Province, Türkiye”. International Journal of Agriculture Environment and Food Sciences 8 (4): 786-96. https://doi.org/10.31015/jaefs.2024.4.7.

EndNote

Randa Zelyüt F, Karanfil A, Santosa AI (December 1, 2024) Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye. International Journal of Agriculture Environment and Food Sciences 8 4 786–796.

IEEE

[1]F. Randa Zelyüt, A. Karanfil, and A. I. Santosa, “Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye”, int. j. agric. environ. food sci., vol. 8, no. 4, pp. 786–796, Dec. 2024, doi: 10.31015/jaefs.2024.4.7.

ISNAD

Randa Zelyüt, Filiz - Karanfil, Ali - Santosa, Adyatma Irawan. “Investigation of Viruses and Phytoplasma Infections in Tomato Plantations in Bilecik Province, Türkiye”. International Journal of Agriculture Environment and Food Sciences 8/4 (December 1, 2024): 786-796. https://doi.org/10.31015/jaefs.2024.4.7.

JAMA

1.Randa Zelyüt F, Karanfil A, Santosa AI. Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye. int. j. agric. environ. food sci. 2024;8:786–796.

MLA

Randa Zelyüt, Filiz, et al. “Investigation of Viruses and Phytoplasma Infections in Tomato Plantations in Bilecik Province, Türkiye”. International Journal of Agriculture Environment and Food Sciences, vol. 8, no. 4, Dec. 2024, pp. 786-9, doi:10.31015/jaefs.2024.4.7.

Vancouver

1.Filiz Randa Zelyüt, Ali Karanfil, Adyatma Irawan Santosa. Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye. int. j. agric. environ. food sci. 2024 Dec. 1;8(4):786-9. doi:10.31015/jaefs.2024.4.7

Cited By

Determination of Viral Diseases in Tomato and Pepper Production Areas of Kırşehir Province, Türkiye

Tekirdağ Ziraat Fakültesi Dergisi

https://doi.org/10.33462/jotaf.1655541

Abstracting & Indexing Services

Google Scholar | Crossref DOI Registry

All content published in this journal is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).
Authors retain copyright of their work and grant the journal a non-exclusive right to publish, reproduce, and distribute the articles within an open-access framework.

Web: dergipark.org.tr/jaefs E-mail: editorialoffice@jaefs.com Phone / WhatsApp: +90 850 309 59 27

Abstract

Project Number

Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye

Abstract

Keywords

Supporting Institution

Project Number

References

Details

Primary Language

Subjects

Journal Section

Authors

Early Pub Date

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

Cite

Cited By

Determination of Viral Diseases in Tomato and Pepper Production Areas of Kırşehir Province, Türkiye

Abstracting & Indexing Services

© International Journal of Agriculture, Environment and Food Sciences