Türkiye'nin Isparta ilinden elde edilen apple stem pitting virus izolatlarının yaygınlığı ve moleküler karakterizasyonu

Year 2022, Volume: 8 Issue: 3, 475 - 483, 15.12.2022

Ali Çelik

https://doi.org/10.24180/ijaws.1180101

Abstract

Türkiye, sahip olduğu iklim çeşitliliği ve coğrafi özellikler nedeniyle meyvecilik açısından dünyada oldukça önemli bir ülke konumundadır. Bu meyvelerden bir tanesi olan elma ülkemizde yoğun olarak yetiştiriciliği yapılan bir meyve olup özellikle Akdeniz Bölgesi elma tarımı ile ön plana çıkmaktadır. Günümüzde viral hastalıklar elma tarımı içerisinde önemli bir verim kayıp unsuru olarak ele alınmaktadır. Bu çalışmada Türkiye’nin önemli bir elma üreticisi konumunda olan Isparta ilinde apple stem pitting virus (ASPV)’nin yaygınlık durumu belirlenmişve moleküler karakterizasyonu gerçekleştirilmiştir. Toplanan 70 adet elma yaprağı örneğinden 7’sinde ASPV enfeksiyonu DAS-ELISA ve RT-PCR yöntemi ile belirlenmiştir. Virüsün kılıf protein bölgesinin kısmi dizi bilgisi elde edilerek GenBank erişim numaraları alınmıştır. Oluşturulan benzerlik matrisinde izolatların GenBank referans izolatları ile 79-93% oranında nükleotid düzeyinde benzerlik gösterdiği tespit edilmiştir. GenBank’ta yer alan ve ASPV’nin filogenetik ayrımında güvenilir olduğu değerlendirilen belirli sayıda izolat seçilerek elde edilen filogenetik ağaç 6 gruba ayrılmış ve bu çalışma kapsamında elde edilen izolatlar filogrup 1 içerinde yer almıştır. Bu çalışma ASPV’nin Isparta bölgesinde yaygınlık durumunun incelendiği ilk çalışma özelliğindedir. Araştırma sonuçlarının ASPV’nin Türkiye’deki durumunun daha iyi anlaşılmasına katkı sunacağı düşünülmektedir.

Keywords

ASPV, filogenetik ilişki, moleküler karakterizasyon

Incidence and coat protein characterization of apple stem pitting virus isolates from Isparta province of Turkey

Abstract

Turkey is one of the major countries in the world in terms of fruit growing due to its climate diversity and geographical features. Apple, which is one of these fruits, is grown intensively in Turkey, and especially the Mediterranean Region is important for apple agriculture. Today, viral diseases are considered as an important yield loss factor in apple farming. This study investigated the incidence and molecular characterization of apple stem pitting virus (ASPV) in Isparta province, a significant apple-producing region in Turkey. By using the DAS-ELISA and RT-PCR methods, ASPV infection was found in 7 out of 70 collected apple leaf samples. The partial nucleotid sequences of ASPV were obtained and registered in GenBank for accession numbers. The generated similarity matrix by using the representative isolates revealed that the new ASPV isolates shared 79–93% of their nucleotide sequences with GenBank reference acessions. The isolates collected in this research were clustered in group 1 of the phylogenetic tree that was created by selecting a specific number of isolates from GenBank and thought to be reliable in the phylogenetic differentiation of ASPV. This is the first study to examine the prevalence of ASPV in the Isparta region and its phylogeny. It is possible that the results of the research will contribute to a better understanding of the situation of ASPV in Turkey.

Keywords

ASPV, phylogenetic relationship, molecular characterization

References

• Adams, M. J., Antoniw, J. F., Bar-Joseph, M., Brunt, A. A., Candresse, T., Foster, G. D., Martelli, G.P., Milne, R.G. & Fauquet, C. M. (2004). Virology Division News: The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Archives of virology, 149(5), 1045-1060. https://doi.org/10.1007/s00705-004-0304-0.
• Ji, Z., Zhao, X., Duan, H., Hu, T., Wang, S., Wang, Y., & Cao, K. (2013). Multiplex RT-PCR detection and distribution of four apple viruses in China. Acta virologica, 57(4), 435-441. https://doi.org/10.4149/av_2013_04_435.
• Birişik, N, & Baloğlu, S. (2011). Yumuşak çekirdekli meyve ağaçlarında dokusunda zararlı viral etmenlerin saptanması ve dağılım oranlarının belirlenmesi. Bitki Koruma Bülteni, 51(3), 287-299.
• Birişik, N., Myrta, A., Hassan, M., & Baloğlu, S. (2006, May). A preliminary account on apple viruses in Mediterranean region of Turkey. In XX International Symposium on Virus and Virus-Like Diseases of Temperate Fruit Crops-Fruit Tree Diseases 781 (pp. 125-130). https://doi.org/10.17660/ActaHortic.2008.781.18.
• Clark, M. F., & Adams, A. N. (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. Journal of general virology, 34(3), 475-483. https://doi.org/10.1099/0022-1317-34-3-475.
• Constable, F. E., Joyce, P. A., & Rodoni, B. C. (2007). A survey of key Australian pome fruit growing districts for exotic and endemic pathogens. Australasian Plant Pathology, 36(2), 165-172. https://doi.org/10.1071/AP07003.
• Dhir, S., Tomar, M., Thakur, P. D., Ram, R., Hallan, V., & Zaidi, A. A. (2010). Molecular evidence for Apple stem pitting virus infection in India. Plant pathology, 59(2). https://doi.org/10.1111/j.1365-3059.2009.02164.x.
• Dhir, S., Lakshmi, V., & Hallan, V. (2021). Development of immunodiagnostics for Apple stem pitting virus and Apple mosaic virus infecting apple in India. Indian Phytopathology, 74(1), 189-199. https://doi.org/10.1007/s42360-020-00305-z.
• Claude, M., & Fauquet, M. (2004). Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. Elsevier Science & Technology.
• Holmes, E. C. (2009). The evolution and emergence of RNA viruses. Oxford University Press.
• Hu, G. J., Dong, Y. F., Zhang, Z. P., Fan, X. D., Ren, F., & Li, Z. (2017). Occurrence and genetic diversity analysis of apple stem pitting virus isolated from apples in China. Archives of virology, 162(8), 2397-2402. https://doi.org/10.1007/s00705-017-3384-3.
• İlbagi, H., Katsiani, A., Uzunogullari, N., Katis, N., & Çitir, A. (2013). First report of apple stem pitting virus on pear and quince orchards in northern Turkey. Journal of Plant Pathology, 95(2). http://dx.doi.org/10.4454/JPP.V95I2.034.
• Jelkmann, W. (1994). Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex-and carlaviruses. Journal of General Virology, 75(7), 1535-1542. https://doi.org/10.1099/0022-1317-75-7-1535.
• Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111-120. https://doi.org/10.1007/BF01731581.
• Klerks, M. M., Leone, G., Lindner, J. L., Schoen, C. D., & Van den Heuvel, J. F. J. M. (2001). Rapid and sensitive detection of Apple stem pitting virus in apple trees through RNA amplification and probing with fluorescent molecular beacons. Phytopathology, 91(11), 1085-1091. https://doi.org/10.1094/PHYTO.2001.91.11.1085.
• Komorowska, B., Malinowski, T., & Michalczuk, L. (2010). Evaluation of several RT-PCR primer pairs for the detection of Apple stem pitting virus. Journal of Virological Methods, 168(1-2), 242-247. https://doi.org/10.1016/j.jviromet.2010.04.024.
• Komorowska, B., Siedlecki, P., Kaczanowski, S., Hasiów-Jaroszewska, B., & Malinowski, T. (2011). Sequence diversity and potential recombination events in the coat protein gene of Apple stem pitting virus. Virus research, 158(1-2), 263-267. https://doi.org/10.1016/j.virusres.2011.03.003.
• 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. https://doi.org/10.1093/molbev/msy096.
• Liu, N., Niu, J., & Zhao, Y. (2012). Complete genomic sequence analyses of Apple stem pitting virus isolates from China. Virus Genes, 44(1), 124-130. https://doi.org/10.1007/s11262-011-0666-9.
• Ma, B. G., Niu, J. X., Morley-Bunker, M., Pan, L. Z., Zhang, H. P., & Zhang, L. X. (2008). Detection of three pear viruses by multiplex RT-PCR assays with co-amplification of an internal control. Australasian Plant Pathology, 37(2), 117-122. https://doi.org/10.1071/AP07081.
• Ma, X., Hong, N., Moffett, P., & Wang, G. (2016). Genetic diversity and evolution of Apple stem pitting virus isolates from pear in China. Canadian Journal of Plant Pathology, 38(2), 218-230. https://doi.org/10.1080/07060661.2016.1158741.
• Ma, X., Hong, N., Moffett, P., Zhou, Y., & Wang, G. (2019). Functional analysis of apple stem pitting virus coat protein variants. Virology journal, 16(1), 1-13. https://doi.org/10.1186/s12985-019-1126-8.
• Mathioudakis, M. M., Maliogka, V. I., Dovas, C. I., Vasilakakis, M., & Katis, N. I. (2006). First record of the Apple stem pitting virus(ASPV) in quince in Greece. Journal of Plant Pathology, 88(2), 225. http://dx.doi.org/10.4454/jpp.v88i2.867.
• Mathioudakis, M. M., Maliogka, V. I., Dovas, C. I., Paunović, S., & Katis, N. I. (2009). Reliable RT‐PCR detection of Apple stem pitting virus in pome fruits and its association with quince fruit deformation disease. Plant pathology, 58(2), 228-236. https://doi.org/10.1111/j.1365-3059.2008.01952.x.
• Mathioudakis, M. M., Maliogka, V. I., Katsiani, A. T., & Katis, N. I. (2010). Incidence and molecular variability of apple stem pitting ano Apple chlorotic leaf spot viruses in apple and pear orchards in greece. Journal of Plant Pathology, 139-147. http://dx.doi.org/10.4454/jpp.v92i1.23.
• Mathioudakis, M. M., Candresse, T., Barone, M., Ragozzino, A., & Katis, N. I. (2012). Cydonia japonica, Pyrus calleryana and P. amygdaliformis: three new ornamental or wild hosts of Apple stem pitting virus. Virus Genes, 44(2), 319-322. https://doi.org/10.1007/s11262-011-0682-9.
• Mathioudakis, M. M., Maliogka, V. I., Candresse, T., Nickel, O., Fajardo, T. V. M., Budzyńska, D., ... & Katis, N. I. (2021). Molecular characterization of the coat protein gene of greek apple stem pitting virus isolates: Evolution through deletions, insertions, and recombination events. Plants, 10(5), 917. https://doi.org/10.3390/plants10050917.
• Morán, F., Canales, C., Olmos, A., & Ruiz-García, A. B. (2020). Loquat (Eriobotrya japonica) is a new natural host of apple stem pitting virus. Plants, 9(11), 1560. https://doi.org/10.3390/plants9111560.
• Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS one, 9(9), e108277. https://doi.org/10.1371/journal.pone.0108277.
• Nadeem, M. A., Yeken, M. Z., Tekin, M., Mustafa, Z., Hatipoğlu, R., Aktaş, H., ... & Baloch, F. S. (2021). Contribution of Landraces in Wheat Breeding. In Wheat Landraces (pp. 215-258). Springer, Cham.
• Németh, M. V. (1984). Virus, mycoplasma, and rickettsia diseases of fruit trees. M. Nijhoff/Dr. W. Junk.
• Stouffer, R. F. (1989). Apple stem pitting. Virus and viruslike diseases of pome fruits and simulating noninfectious disorders. Cooperative Extension College of Agriculture and Home Economics. Washington State University.
• Tekin, M., Emiralioğlu, O., Yeken, M. Z., Nadeem, M. A., Çiftçi, V., & Baloch, F. S. (2022). Wild Relatives and Their Contributions to Wheat Breeding. In Ancient Wheats (pp. 197-233). Springer, Cham.
• Wu, Z. B., Ku, H. M., Su, C. C., Chen, I. Z., & Jan, F. J. (2010). Molecular and biological characterization of an isolate of apple stem pitting virus causing pear vein yellows disease in Taiwan. Journal of Plant Pathology, 721-728. http://dx.doi.org/10.4454/jpp.v92i3.318.
• Yang, H. Y., Liu, Z. J., Luo, S., & Li, L. L. (2017). First report of apple stem pitting virus infecting Nanking cherry in China. Plant Disease, 101(6), 1067. https://doi.org/10.1094/PDIS-11-16-1664-PDN.
• Yeken, M. Z., Emiralioğlu, O., Çiftçi, V., Bayraktar, H., Palacioğlu, G., & Özer, G. (2022). Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers. Molecular Biology Reports, 1-9.https://doi.org/10.1007/s11033-022-07229-z
• Yoon, J. Y., Joa, J. H., San Choi, K., Do, K. S., Lim, H. C., & Chung, B. N. (2014). Genetic diversity of a natural population of Apple stem pitting virus isolated from apple in Korea. The plant pathology journal, 30(2), 195. https://doi.org/10.5423/PPJ.NT.02.2014.0015.