Optimization of Plant Tissue Selection and Sampling Time for Reliable RT-PCR Detection of Pelamoviroid latenspruni, and the Influence of Climatic Conditions on Detection Efficiency

Abstract

Viroids are the smallest pathogens with no protein-coding properties, made up of a circular single-stranded RNA molecule, 246-401 nt length causing diseases in plants. PLMVd is the type member of the Pelamoviroid genus of the Avsunviroidae family. The aim of this thesis study was to find out the optimal sampling time and tissue in plants infected with PLMVd., The study was conducted on two persimmon plants number TH7 and TH9 with NCBI accession numbers MZ289071 and MZ289070, respectively, which had previously been shown to be infected with PLMVd. Between March 2021 and February 2022, sampling was performed monthly, and all available plant tissues were extracted and tested for TRNA using RT-PCR. The study concluded that the most reliable testing organs and times when there is a seasonal limitation are the flower bud, bark, and leaf tissue in April, flower, leaf, bark, and fruit tissue in May, and the bark, leaf, and fruit tissue in September. It has been concluded that bark, leaf, and fruit tissue samples provide consistent results regardless of season. The independent sample t test was used to estimate the likelihood that the PLMVd concentration in climatic data would yield positive or negative findings, as well as its significance. According to the study results, sampling is recommended between 14.40-20.90 °C, humidity rate 41.40-49.30%, mean soil temperature 7.35-11.875 °C, sunshine duration 223.10-345.00 hours, and sunshine intensity 223.56-313.33 cal÷cm². It was determined that sampling should be conducted in accordance with the viroid's biology, the host's phenological phase, and regional meteorological circumstances.

Keywords

• PLMVd
• persimmon
• suitable sampling time
• suitable tissue
• climatic conditions

ŞEFTALİ LATENT MOZAİK VİROİDİ (Peach Latent Mosaic Pelamoviroid-PLMVd)’NİN GÜVENİLİR TEŞHİSİ İÇİN UYGUN ZAMAN ve UYGUN BİTKİ DOKUSUNUN RT-PCR YÖNTEMİ ile BELİRLENMESİ ve İKLİM KOŞULLARININ VİROİD TEŞHİSİ ÜZERİNE ETKİSİ

Öz

Viroids are the smallest pathogens with no protein-coding properties, made up of a circular single-stranded RNA molecule, 246-401 nt length causing diseases in plants. PLMVd is the type member of the Pelamoviroid genus of the Avsunviroidae family. The aim of this thesis study was to find out the optimal sampling time and tissue in plants infected with PLMVd., The study was conducted on two persimmon plants number TH7 and TH9 with NCBI accession numbers MZ289071 and MZ289070, respectively, which had previously been shown to be infected with PLMVd. Between March 2021 and February 2022, sampling was performed monthly, and all available plant tissues were extracted and tested for TRNA using RT-PCR. The study concluded that the most reliable testing organs and times when there is a seasonal limitation are the flower bud, bark, and leaf tissue in April, flower, leaf, bark, and fruit tissue in May, and the bark, leaf, and fruit tissue in September. It has been concluded that bark, leaf, and fruit tissue samples provide consistent results regardless of season. The independent sample t test was used to estimate the likelihood that the PLMVd concentration in climatic data would yield positive or negative findings, as well as its significance. According to the study results, sampling is recommended between 14.40-20.90 °C, humidity rate 41.40-49.30%, mean soil temperature 7.35-11.875 °C, sunshine duration 223.10-345.00 hours, and sunshine intensity 223.56-313.33 cal÷cm². It was determined that sampling should be conducted in accordance with the viroid's biology, the host's phenological phase, and regional meteorological circumstances.

Anahtar Kelimeler

• PLMVd
• Trabzon hurması
• uygun örnekleme zamanı
• uygun doku
• iklim koşulları

References

1. Al Rwahnih, M., Myrta, A., Abou-Ghanem, N., Di Terlizzi, B., & Savino, V. (2008). Viruses and viroids of stone fruits in Jordan. OEPP/EPPO Bulletin, 31 (1), 95–98.
2. Albanese, G., Giunchedi, L., La Rosa, L., & Poggi Pollini, C. (1992). Peach latent mosaic viroid in Italy. Acta Horticulturae, 309, 331–338.
3. Barba, M., Ragozzino, E., & Faggioli, F. (2007). Pollen transmission of Peach latent mosaic viroid. Journal of Plant Pathology, 89 (2), 287–289.
4. Boubourakas, I. N., Faggioli, F., Fucuta, S., Barba, M., & Kyriakopoulou, P. E. (2009). The presence of Peach latent mosaic (PLMVd) in Greece. Phytopathologia Mediterranea, 48 (2), 321.
5. Cho, I. S., Park, M. J., Kwon, S. J., Choi, G. S., Hammond, J., & Lim, H. S. (2016). First report of Persimmon cryptic virus and Persimmon virus A in Korea. Journal of Plant Pathology, 98 (3), 694.
6. Choueiri, E., Abou Ghanem-Sabanadzovic, N., Khazzaka, K., Sabanadzovic, S., Di Terlizzi, B., Jreijiri, F., & Savino, V. (2001). Identification of Peach latent mosaic viroid in Lebanon. Journal of Plant Pathology, 83 (2), 225–227.
7. Çiftçi, O., Yılmaz, F., & Çaplık, D. (2022). Elâzığ ve Mardin illerinde peach latent mosaic viroid (PLMVd)'nin durumu. Ulusal Meyvecilik Sempozyumu, Eğirdir, Isparta.
8. De La Torre-Almaráz, R., Pallás, V., & Sánchez-Navarro, J. A. (2015). First report of Peach latent mosaic viroid in peach trees from Mexico. Plant Disease, 99 (6), 899.

9. Desvignes, J. C. (1986). Peach latent mosaic and its relation to peach mosaic and peach yellow mosaic virus diseases. Acta Horticulturae, 193, 51–58.
10. Di Serio, F., Malfitano, M., Flores, R., & Randles, J. W. (1999). Detection of peach latent mosaic viroid in Australia. Australasian Plant Pathology, 28 (1), 80–81.
11. Ding, X., Liu, X., & Chen, Z. (2013). The main diseases on Chinese persimmon tree. Acta Horticulturae, 996, 299–306.
12. El-Dougdoug, K. A., Rehab, D. A., Rezk, A. A., & Sofy, A. R. (2012). Incidence of fruit trees viroid diseases by tissue print hybridization in Egypt. International Journal of Virology, 8, 114–120. https://doi.org/10.3923/ijv.2012.114.120
13. EPPO. (2005). Data sheets on quarantine organisms, Tomato ringspot nepovirus. OEPP/EPPO Bulletin, 35, 313–318. https://doi.org/10.1111/j.1365-2338.2005.00831.x
14. EPPO. (2006). Data sheets on quarantine organisms, American plum line pattern virus (APLPV). OEPP/EPPO Bulletin, 36, 157–160. https://doi.org/10.1111/j.1365-2338.2006.00928.x
15. EPPO. (2013). Data sheets on quarantine organisms, Tomato infectious chlorosis virus. OEPP/EPPO Bulletin, 43, 462–470. https://doi.org/10.1111/epp.12062
16. EPPO. (2020). Data sheets on quarantine organisms, Candidatus Phytoplasma mali, Ca. P. pyri and Ca. P. prunorum. OEPP/EPPO Bulletin, 50, 69–85. https://doi.org/10.1111/epp.12612
17. EPPO. (2022). Data sheets on quarantine organisms, Begomovirüsler. OEPP/EPPO Bulletin, 52, 643–664. https://doi.org/10.1111/epp.12887
18. EPPO. (2023). Data sheets on quarantine organisms, Plum pox virus. OEPP/EPPO Bulletin, 53, 518–539. https://doi.org/10.1111/epp.12948
19. Faggioli, F., Loreti, S., & Barba, M. (1997). Occurrence of Peach latent mosaic viroid (PLMVd) on plum in Italy. Plant Disease, 81, 423.
20. Fiore, N., Abou Ghanem-Sabanadzovic, N., Infante, R., Myrta, A., & Pallás, V. (2003). Detection of Peach latent mosaic viroid in stone fruits from Chile. Options Méditerranéennes Série B, CIHEAM Bari (IT), 143–145.
21. Flores, R., Delgado, S., Gas, M. E., Carbonell, A., Molina, D., Gago, S., & De la Peña, M. (2004). Viroids: The minimal non-coding RNAs with autonomous replication. FEBS Letters, 567 (1), 42–48.
22. Flores, R., Di Serio, F., Hernandez, C., Barba, M., & Hadidi, A. (2011). Peach Latent Mosaic Viroid and its Diseases in Peach Trees. In Virus and Virus-Like Diseases of Pome and Stone Fruits. Springer, pp. 219-224.
23. Flores, R., Hernandez, C., Avinent, L., Llacer, G., Arregui, J. M., Hermoso, A., Juarez, J., Navarro, L., & Desvignes, J. C. (1992). Studies of the detection, transmission, and distribution of Peach latent mosaic viroid (PLMVd) in peach trees. Acta Horticulturae, 309, 325-330.
24. Flores, R., Hernández, C., Desvignes, J. C., & Llacer, G. (1990). Some properties of the viroid inducing peach latent mosaic disease. Research in Virology, 141 (1), 109-118.
25. Flores, R., Hernandez, C., Llácer, G., Shamloul, A. M., Gıunchedı, L., & Hadidi, A. (2003). Stone Fruit Viroids, Chapter 22, Peach latent mosaic viroid in peach. In Viruses, p. 156.
26. Foissac, X., Svanella-Duas, L., Dulucq, M. J., Candresse, T., & Gentit, P. (2001). Polyvalent detection of fruit tree tricho, capillo and foveaviruses by nested RT-PCR using (PDO RT-PCR). Acta Horticulturae, 550, 37-43.
27. Garland, J. A., & Cree, L. A. (1999). Plant health risk assessment: Review of distribution maps of quarantine pests for Europe (CABI/EPPO, 1998). PRA 99-39. Canadian Food Inspection Agency, Nepean, Canada.
28. Gazel, M., Ulubaş-Serçe, C., Çağlayan, K., Luigi, M., & Faggioli, F. (2008). Incidence and genetic diversity of Peach latent mosaic viroid isolates in Turkey. Journal of Plant Pathology, 90 (3), 495-503.
29. Gazel, M., Serçe, Ç. U., Öztürk, H., & Çağlayan, K. (2020). Detection of Candidatus Phytoplasma pyri in different pear tissues and sampling time by PCR-RFLP analyses. Mustafa Kemal Üniversitesi Tarım Bilimleri Dergisi, 25 (3), 406-412.
30. Hadidi, A., Giunchedi, L., Shamloul, A. M., Poggi-Pollini, C., & Amer, M. A. (1997). Occurrence of Peach latent mosaic viroid in stone fruits and its transmission with contaminated blades. Plant Disease, 81, 154–158.
31. Hassan, M., Gomez, G., Pallas, V., Myrta, A., & Rysanek, P. (2009). Simultaneous detection and genetic variability of stone fruit viroids in the Czech Republic. European Journal of Plant Pathology, 124 (2), 363–368.
32. Hassen, I. F., Roussel, S., Kummert, J., Fakhfakh, H., Marrakchi, M., & Jijakli, M. H. (2005). Detection and epidemiological characteristics of Peach latent mosaic viroid in Tunisia. Communications in Agricultural and Applied Biological Sciences, 70 (3), 115–128.
33. Howell, W. E., Skrzeczkowski, L. J., Mink, G. I., Nunez, A., & Wessels, T. (1997). Non-transmission of Apple Scar Skin Viroid and Peach Latent Mosaic Viroid Through Seed. XVII International Symposium Virus and Virus-Like Diseases of Temperate Fruit Crops, 1 November 1998, Bethesda, MD, USA, pp. 635–640.
34. Ismaeil, F., Abou Ghanem-Sabanadzovic, N., Myrta, A., Di Terlizzi, B., & Savino, V. (2001). First record of Peach latent mosaic viroid and Hop stunt viroid in Syria. Journal of Plant Pathology, 83 (3), 225–227.
35. Jawhar, J., Di Terlizzi, B., Turturro, C., Khoury, W., & Savino, V. (1997). Virus and Virus-Like Diseases of Stone Fruits in Lebanon. Abstract of a paper presented at the 6th Arab Congress of Plant Protection, 1997-10-27/31, Beirut (LB), p. 214.
36. Jawhari, M., Abrahamian, P., Sater, A. A., Sobh, H., Tawidian, P., & Abou-Jawdah, Y. (2015). Specific PCR and real-time PCR assays for detection and quantitation of ‘Candidatus Phytoplasma phoenicium’. Molecular and Cellular Probes, 29 (1), 63–70.
37. Jevremovic, D., & Paunovic, S. (2008). Detection of Peach latent mosaic viroid on peach in Serbia. Acta Horticulturae, 781, 557–560.
38. Jo, Y., Choi, H., Cho, J. K., Yoon, J. Y., Choi, S. K., & Cho, W. K. (2016). First report of Peach latent mosaic viroid in peach trees in Korea. Plant Disease, 100 (1), 234.
39. Kwon, J. H., & Park, C. S. (2003). Sooty mold of persimmon (Diospyros kaki) caused by Cladosporium cladosporioides. The Plant Pathology Journal, 19 (5), 266-268.
40. Kyriakopoulou, P. E., Giunchedi, L., & Hadidi, A. (2001). Peach latent mosaic viroid and pome fruit viroids in naturally infected cultivated pear Pyrus communis and wild pear P. amygdaliformis: Implications on possible origin of these viroids in the Mediterranean region. Journal of Plant Pathology, 83, 51-62.
41. Kyriakopoulou, P. E., Giunchedi, L., Barba, M., Boubourakas, N., Kaponi, M. S., & Hadidi, A. (2017). Peach Latent Mosaic Viroid in Temperate Fruit Trees Other Than Peach. In Viroids and Satellites. Chapter 30, pp. 317-329. https://doi.org/10.1016/B978-0-12-801498-1.00030-9
42. Loreti, S., Faggioli, F., Cardoni, M., Mordenti, G., Babini, A. R., Poggi Pollini, C., & Barba, M. (1999). Comparison of different diagnostic methods for detection of Peach latent mosaic viroid. EPPO Bulletin, 29 (4), 433–438.
43. Martínez-García, B., Marco, C. F., Goytia, E., López-Abella, D., Serra, M. T., Aranda, M. A., & López-Moya, J. J. (2004). Development and use of detection methods specific for Cucumber vein yellowing virus (CVYV). European Journal of Plant Pathology, 110, 811–821.
44. Mavrič Pleško, I., Viršček Marn, M., Miladinović, Z., & Zindović, J. (2012). First report of Peach latent mosaic viroid in peach trees in Montenegro. Plant Disease, 96 (1), 150.
45. Nakaune, R., & Nakano, M. (2008). Identification of a new Apscaviroid from Japanese persimmon. Archives of Virology, 153, 969–972. https://doi.org/10.1007/s00705-008-0073-2
46. Nieto, A. M., Di Feo, L., & Nome, C. F. (2008). First report of Peach latent mosaic viroid in peach trees in Argentina. Plant Disease, 92 (7), 1137.
47. Oksal, H. D., Aydın, S., Baran, M., Emir, C., Karanfil, A., Bozdoğan, O., & Sipahioğlu, H. M. (2021). Persimmon (Diospyros kaki L.) and johnsongrass [Sorghum halepense (L.) Pers.] are new natural hosts of Peach latent mosaic viroid. Applied Ecology and Environmental Research, 19 (6), 4629–4639. http://dx.doi.org/10.15666/aeer/1906_46294639
48. Osaki, H., Yamamuchi, Y., Sato, Y., Tomita, Y., Kawai, Y., Miyamoto, Y., & Ohtsu, Y. (1999). Peach latent mosaic viroid isolated from stone fruits in Japan. Annals of the Phytopathological Society of Japan, 65, 3–8.
49. Paduch-Cichal, E., & Skrzeczkowski, J. L. (2001). Occurrence of peach latent mosaic viroid in Polish orchards. Phytopathologia Polonica, 22, 137–143.
50. Palou, L., Montesinos-Herrero, C., Tarazona, I., Besada, C., & Taberner, V. (2015). Incidence and etiology of postharvest fungal diseases of persimmon (Diospyros kaki Thunb. cv. Rojo Brillante) in Spain. Plant Disease, 99 (10), 1416–1425.
51. Tarım ve Orman Bakanlığı Gıda Kontrol Genel Müdürlüğü. (2021). PLMVd Survey Talimatı. https://tarimorman.gov.tr/GKGM/Belgeler/DB_Bitki_Sagligi/Survey/45-PLMVd_Survey_Talimati_2021.pdf (Erişim Tarihi: 16 Ocak 2024)
52. Roenhorst, J. W., & Verhoeven, J. T. J. (1997). Virology. In Verslagen en Mededelingen van de Plantenziektenkundige Dienst 186 (Annual Report Diagnostic Centre 1996), 92–106.
53. Scortichini, M., D'Ascenzo, D., & Silvestro, D. D. (1998). Leaf necrosis and twig dieback of sweet persimmon (Diospyros kaki L.) caused by Pseudomonas syringae pv. syringae in Italy. European Journal of Plant Pathology, 104, 625-627. https://doi.org/10.1023/A:1008681317727
54. Škoric, D., Al-Rwahnih, M., & Myrta, A. (2008). First record of Peach latent mosaic viroid in Croatia. Acta Horticulturae, 781, 535–539.
55. Skrzeczkowski, L. J., Howell, W. E., & Mink, G. I. (1996). Occurrence of peach latent mosaic viroid in commercial peach and nectarine cultivars in the U.S. Plant Disease, 80, 823.
56. Susuri, L. R., Dida, L., Matić, S., Susuri, H. S., & Myrta, A. (2006). First record of Peach latent mosaic viroid and Hop stunt viroid in Kosova. Journal of Plant Pathology, 88 (3), 339.
57. Torres, H., Gómez, G., Pallás, V., Stamo, B., Shalaby, A., Aouane, B., Gavriel, I., Kominek, P., Caglayan, K., Sipahioglu, M., Michelutti, R., Myrta, A., & Fiore, N. (2004). Detection by tissue printing of stone fruit viroids, from Europe, the Mediterranean and North and South America. Acta Horticulturae, 657, 379-383.
58. Tuncel, F., Tekkaş, N., Türk, G., Oksal, H. D., & Sipahioğlu, H. M. (2020). First detection and molecular characterization of Peach latent mosaic viroid in a new natural host: Walnut (Juglans regia L.). Alinteri Journal of Agriculture Sciences, 35 (2), 37–44. https://doi.org/10.47059/alinteri/V35I2/AJAS20073
59. Turturo, C., Minafra, A., Ni, H., Wang, G., Di Terlizzi, B., & Savino, V. (1998). Occurrence of Peach latent mosaic viroid in China and development of an improved detection method. Journal of Plant Pathology, 80 (2), 165-169.
60. Tuzcu, Ö., & Yıldırım, B. (2000). Trabzon Hurması (Diospyros kaki L.) ve Yetiştiriciliği. Ankara; Tübitak Tarp Yayınları.
61. TÜİK. (2023). Türkiye, Ortadoğu Anadolu, Malatya illerinde Trabzon Hurması Bitkisine Ait Üretim Bilgileri. https://biruni.tuik.gov.tr/medas/?kn=92&locale=tr (Erişim Tarihi: 27.06.2023)
62. Veerakone, S., Tang, J. Z., Ward, L. I., Liefting, L. W., Perez-Egusquiza, Z., Lebas, B. S. M., Delmiglio, C., Fletcher, J. D., & Guy, P. L. (2015). A review of the plant virus, viroid, liberibacter and phytoplasma records for New Zealand. Australasian Plant Pathology, 44 (5), 463–514. https://doi.org/10.1007/s13313-015-0366-3
63. Verhoeven, J. T. J., Jansen, C. C. C., & Roenhorst, J. W. (2008). First report of pospiviroids infecting ornamentals in the Netherlands: Citrus exocortis viroid in Verbena sp., Potato spindle tuber viroid in Brugmansia suaveolens and Solanum jasminoides, and Tomato apical stunt viroid in Cestrum sp. Plant Pathology, 57 (2), 399.
64. Verhoeven, J. T. J., Westenberg, M., Van Ede, E. P. M., Visser, K., & Roenhorst, J. W. (2016). Identification and eradication of potato spindle tuber viroid in dahlia in the Netherlands. European Journal of Plant Pathology, 146 (2), 443–447.
65. Wang, J., Gao, R., Yu, X. M., An, M., Qin, Z. H., Liu, J., & Ai, C. X. (2015). Identification of ‘Candidatus phytoplasma ziziphi’ associated with persimmon (Diospyros kaki Thunb.) fasciation in China. Forest Pathology, 45 (4), 342–345. https://doi.org/10.1111/efp.12180
66. Xie, L., Zhang, J. Z., Cai, L., & Hyde, K. D. (2010). Biology of Colletotrichum horii, the causal agent of persimmon anthracnose. Mycology, 1 (4), 242–253.
67. Yamamoto, J., Tanaka, K., Ohtaka, N., & Sato, T. (2012). Black leaf spot of Japanese persimmon (Diospyros kaki), a new disease caused by Adisciso kaki sp. nov. Journal of General Plant Pathology, 78, 99–105.
68. Yazarlou, A., Jafarpour, B., Tarighi, S., Habili, N., & Randles, J. W. (2011). New Iranian and Australian peach latent mosaic viroid variants and evidence for rapid sequence evolution. Archives of Virology, 157 (2), 343–347.
69. Yılmaz, F. (2024). Güneydoğu Anadolu Bölgesi ceviz ve Antep fıstığındaki bazı virüs ve viroid hastalıklarının araştırılması ve moleküler karakterizasyonu.Doktora tezi, Malatya Turgut Özal Üniversitesi, Malatya, Türkiye.