Türkiye’de Şeker Pancarı Üretim Alanlarında Enfeksiyon Oluşturan Beet Necrotic Yellow Vein Virus İzolatlarının P31 Geninin Moleküler Karakterizasyonu

Year 2022, Volume: 37 Issue: 3, 505 - 524, 31.10.2022

Murat Güngör Ebru Erkan , Nazlı Kutluk Yılmaz

https://doi.org/10.7161/omuanajas.1051610

Abstract

Vektör Polymyxa betae ile taşınan ve “rhizomania” olarak da adlandırılan hastalığa yol açan Beet necrotic yellow vein virus (BNYVV), Türkiye’de ve dünyada şeker pancarı üretim alanlarında sıklıkla rastlanan en tahripkar virüs hastalığıdır. Bu çalışmada, Türkiye’nin farklı coğrafik bölgelerinden elde edilen BNYVV izolatlarının, p31 geninin moleküler olarak karakterize edilmesi hedeflenmiştir. Bu
amaçla, BNYVV ile bulaşık olduğu bilinen 17 toprak örneği kullanılmıştır. Öncelikle, tuzak bitki testi yöntemine göre BNYVV izolatlarının yeniden çoğaltımı sağlanmıştır. BNYVV RNA-4’ü tarafından kodlanan p31 proteini, virüsün vektörle etkili olarak taşınması ve virülensi ile ilişkilidir. Bu çalışmada, 12 farklı izolatın p31 gen bölgesinin nükleotit dizileri elde edilmiştir. Bu izolatların dünya izolatları ile
BLAST analizi ve elde edilen filogenetik ağaç, izolatları; Grup II ve Grup III olmak üzere iki farklı p31 grubuna ayrılmıştır. Grup II’de IGR-6, IGR-9 ve ERC-52 izolatları yer almış, Kas2 izolatı (Kazakistan) ile yüksek nükleotit benzerliğine (% 99.76-% 99.88) sahip olduğu belirlenmiştir. GZP-27, ELZ-44, SMS-61, EDR-125, BRS-148, CNK-150, KAS-281, KYS-524 ve ANK-617 izolatları ise Grup III’de yer almış, IV4  izolatı (İtalya) ile en yüksek benzerlik (% 99.88-% 100) göstermişlerdir. Yürütülen bu çalışma sonucunda, BNYVV izolatlarının p31 genom bölgesine göre genetik ilişkileri ortaya konulmuştur.

Keywords

Bnyvv, P. Betae, Rhizomania, Rna-4, Sekans Analizi

Supporting Institution

Ondokuz Mayıs Üniversitesi BAP (PYO.ZRT.1904.12.015)

Project Number

TÜBİTAK (TOVAG: 110O188) projesi

Thanks

Bu çalışmanın bir parçası, Ondokuz Mayıs Üniversitesi BAP (PYO.ZRT.1904.12.015) komisyonu tarafından desteklenmiş olup, çalışmada kullanılan toprak örnekleri TÜBİTAK (TOVAG: 110O188) projesi kapsamında toplanmıştır.

Molecular Characterization of P31 Gene of Beet Necrotic Yellow Vein Virus İsolates in Sugar Beet Production Areas of Turkey

Abstract

Beet necrotic yellow vein virus (BNYVV), which is known as “the agent of rhizomania disease” and transmitted by Polymyxa betae, is the most destructive and prevalent virus species in sugar beet fields in Turkey and in the world. The objective of this study was to molecularly characterize BNYVV isolates, obtained from different geographical locations of Turkey, based the p31 gene of them. For this purpose, 17 soil samples known to be infested with BNYVV were used. Firstly, BNYVV was propogated as bait plant technique. P31 protein encoded by BNYVV RNA-4 is associated with efficient vector transmission and virulence. In this study, nucleotide sequences of p31 coding region of 12 different isolates were obtained. The BLAST and phylogenetic analysis divided BNYVV isolates into two different p31 groups as Group II and Group III. The Group II consisted of IGR-6, IGR-9 and ERC-52 isolates and found to have high nucleotide identity with Kas2 isolate (99.76%-99.88%). Also, GZP-27, ELZ-44, SMS-61, EDR-125, BRS-148, CNK-150, KAS-281, KYS-524 and ANK-617 which were divided into Group III had the highest similarity (99.88%-100%) with IV4 isolate (Italy). As a result of this study, genetic relationship among BNYVV isolates according to the p31 genome region were revealed.

Keywords

BNYVV, P. betae, Rhizomania, RNA-4, Sequencing

Project Number

TÜBİTAK (TOVAG: 110O188) projesi

References

• Asher, M.J.C., Henry, C.M., 1993. Research to contain beet Rhizomania in the UK. In: Ebbels, D. (Ed.). Plant Health and the European Single Market. British Crop Protection UK. pp.111-122.
• Biancardi, E., Lewellen, R. T., 2016. Introduction. In: Biancardi, E., Tamada, T. (Eds.). Rhizomania. Springer International Publishing Switzerland. pp. 3-28.
• Bouzoubaa, S., Ziegler, V., Beck, D., Guilley, H., Richards, K., Jonard, G., 1986. Nucleotide sequence of Beet necrotic yellow vein virus RNA-2. Journal of General Virology, 67, 1689-1700. https://doi.org/10.1099/0022-1317-67-8-1689
• Camelo-García, V.M., Edwards Molina, J.P., Nagata, T., Rezende, J.A.M., Silva, J.M.F., 2019. Effect of rhizomania on red table-beet biomass production and molecular characterization of an isolate of Beet necrotic yellow vein virus from Brazil. European Journal of Plant Pathology, 154, 1021-1028. https://doi.org/10.1007/s10658-019-01722-1
• Chiba, S., Miyanishi, M., Andika, I.B., Kondo, H., Tamada, T., 2008. Identification of amino acids of Beet necrotic yellow vein virus p25 protein required for induction of the resistance responce in leaves of Beta vulgaris plants. Journal of General Virology, 89: 1314-1323. doi: 10.1099/vir.0.83624-0.
• Chiba, S., Kondo, H., Miyanishi, M., Andika, I.B., Han, C., Tamada, T., 2011. The evolutionary history of Beet necrotic yellow vein virus deduced from genetic variation, geographic origin and spread, and the breaking of host resistance. Molecular Plant Microbe Interactions, 24 (2): 207-218. doi: 10.1094/MPMI-10-10-0241
• Dehnen-Schmutz, K., Di Serio, F., Gonthier, P., Jacques, M.A., Miret, J.A.J., Justesen, A.F., Macleod, A., Magnusson, C.S., Milonas, P., Navas-Cortes, J.A., Parnell, S., Potting, R., Reignault, P.L., Thulke, H., Van der Werf, W., Civera, A.V., Yuen, J., Zappalà, L., Candresse, T., Chatzivassiliou, E., Winter, S., Maiorano, A., Delbianco, A., Bragard, C., 2020. Pest categorization of beet necrotic yellow vein virus. EFSA Journal, 18 (12): 6360. doi:10.2903/j.efsa.2020.6360
• Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum lilelihood approach. Journal of Molecular Evolution, 17 (6): 368-376. https://doi.org/10.1007/BF01734359
• Gilmer, D., Bouzoubaa, S., Hehn, A., Guilley, H., Richards, K., Jonard, G., 1992. Efficent cell-to-cell movement of Beet necrotic yellow vein virus requires 3’proximal genes located on RNA 2. Virology, 189: 40-47. doi: 10.1016/0042-6822(92)90679-j
• Gilmer, D., Ratti, C., ICTV Report Consortium, 2017. ICTV Virus Taxonomy Profile: Benyviridae. Journal of General Virology, 98 (7): 1571-1572. doi:10.1099/jgv.0.000864
• Kaya, R., 2009. Distribution of rhizomania disease in sugar beet growing areas of Turkey. Tarım Bilimleri Dergisi, 15 (4): 332-340. doi: 10.7161/anajas.2012.273.144
• Keskin, B., 1964. Polymyxa betae n.sp. ein parasit in den wurzein von Beta vulgaris Tournefort, besonders wahrendden jugendent wicklung den zuckerrübe. Archives of Microbiology, 49: 348-374. doi: 10.1007/BF00406857
• Koch, F., 1987. Bericht über eine in verschiedene zuckerrübenanbaugebiete der Turkseker in Anatolien und Thrazien zum stadium von wurzelerkrankungen. KWS Kleinwanzlebener Saatzucht, AG, Einbeck, Germany.
• Koenig, R., Haeberle, A.M., Commandeur, U., 1997. Detection and characterization of a distinct type of Beet necrotic yellow vein virus RNA-5 in sugar beet growing area in Europe. Archives of Virology, 142:1499-1504. doi: 10.1007/s007050050176
• Koenig, R., Lennefors, B.L., 2000. Moleculer analyses of European A, B and P type sources of Beet necrotic yellow vein virus and detection of the rare P type in Kazakhstan. Archives of Virology, 145: 1561- 1570. doi: 10.1007/s007050070076
• Koenig, R., Kastirr, U., Holtschulte, B., Deml, G., Varrelmann, M., 2008. Distribution of various types and P25 subtypes of Beet necrotic yellow vein virus in Germany and other European countries. Archives of Virology, 153: 2139-2144. doi: 10.1007/s00705-008-0234-3.
• Kruse, M., Koenig, R., Hoffman, A., Kaufmann, A., Commandeur, U., Solevyev, A.G., Savenkov, I., Burgermeister, W., 1994. Restriction fragment length polymorphism analysis of reverse transcription-PCR products reveals the existance of two major strain groups of beet necrotic yellow vein virus. Journal of General Virology, 75: 1835-1842. doi: 10.1099/0022-1317-75-8-1835.
• Kutluk Yılmaz, N.D., Meunier, A., Schmit, J.F., Stas, A., Bragard, C., 2007. Partial nucleotide sequence analysis of Turkish isolates of Beet necrotic yellow vein virus (BNYVV) RNA-3. Plant Patholology, 56: 311-316. doi:10.1111/j.1365-3059.2006.01493.x
• Kutluk Yılmaz, N.D., Arlı Sokmen, M., 2010. Occurrence of soilborne sugar beet viruses transmitted by Polymyxa betae northern and central parts of Turkey. Journal of Plant Pathology, 92 (2): 497-500. doi: http://dx.doi.org/10.4454/jpp.v92i2.196
• Kutluk Yılmaz N.D., Arlı-Sokmen, M., Kaya, R., Sevik M. A., Tunali, B., Demirtas, S., 2016a. The widespread occurrences of Beet soil borne virus and RNA-5 containing Beet necrotic yellow vein virus isolates in sugar beet production areas in Turkey. European Journal of Plant Pathology, 144 (2): 443-455. doi:10.1007/s10658-015-0780-y
• Kutluk Yılmaz, N.D., 2016b. Identification of strain types of some Beet necrotic yellow vein virus isolates determined in northern and central parts of Turkey. Eurasion Journal of Soil Science, 5 (3): 241-248. doi:10.18393/EJSS.2016.3.241-248
• Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870-1874. doi: 10.1093/molbev/msw054
• Li, M., Liu, T., Wang, B., Han, C.G., Li, D.W., Yu, J.L., 2008. Phylogenetic analysis of Beet necrotic yellow vein virus isolates from China. Virus Genes, 36: 429-432. doi: 10.1007/s11262-008-0202-8.
• Mehrvar, M., Valizadeh, J., Koenig, R., Bragard, C.G., 2009. Iranian Beet necrotic yellow vein virus (BNYVV): pronounced diversity of the P25 coding region in A-type BNYVV and identification of P-type BNYVV lacking a fifth RNA species. Archives of Virology, 154: 501-506. doi: 10.1007/s00705-009-0322-z
• Meunier, A., Schmit, J.F., Stas, A., Kutluk, N., Bragard, C., 2003. Multiplex reverse transcription for simultaneous detection of beet necrotic yellow vein virus, beet soilborne virus, and beet virus Q and their vector Polymyxa betae KESKIN on sugar beet. Applied and Environmental Microbiology, 2356-2360. doi: 10.1128/AEM.69.4.2356–2360.2003.
• Miyanishi, M., Kusume, T., Saito, M., Tamada, T., 1999. Evidence for three groups of sequence variants of beet necrotic yellow vein virus RNA 5. Archives of Virology, 144: 879-892. https://doi.org/10.1007/s007050050553
• Özer, G., Ertunç F., 2005. Detection of rhizomania disease in sugar beet plantations of Amasya sugar refinery. Journal of Agricultural Sciences, 11 (3): 339-343.
• Özdemir, H., 2014. Trakya Bölgesi şeker pancarı üretim alanlarında Beet necrotic yellow vein virus (BNYVV), Beet western yellows virus (BWYV) ve Beet yellows virus (BYV) hastalıklarının saptanması üzerine araştırmalar. Yüksek Lisans Tezi. Namık Kemal Üniversitesi, Fen Bilimleri Enstitüsü, 42s, Tekirdağ.
• Özgür, O.E., 2003. Türkiye Şeker Pancarı Hastalıkları. Türkiye Şeker Fabrikaları A. Ş. Genel Müdürlüğü Yayınları, 192s, Ankara.
• Özmen, C.Y., Khabbazi, S.D., Khabbazi, A.D., Gürel, S., Kaya, R., Oğuz, M.Ç., Turan, F., Rezaei, F., Kibar, U., Ergül, A., 2020. Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace. Nature Scientific Reports, 10, 4129. doi: 10.1038/s41598-020-61091-2
• Rahim, M.D., Andika, I.B., Han, C., Kondo, H., Tamada, T., 2007. RNA4-encoded P31 of Beet necrotic yellow vein virus is involved in efficient vector transmission, symptom severity and silencing suppression in roots. Journal of General Virology, 88: 1611-1619. doi: 10.1099/vir.0.82720-0
• Rush C.M., 2003. Ecology and Epidemiolgy of Benyviruses and Plasmodiophorid Vectors. Annu. Rev. Phytopathol. 41, 567-92.
• Schirmer, A., Link, D., Cognat, V., Moury, B., Beuve, M., Meunier, A., Bragard, C., Gilmer, D., Lemaire, O., 2005. Phylogenetic analysis of isolates of Beet necrotic yellow vein virus collected wordwide. Journal of General Virology, 86: 2897-2911. doi:10.1099/vir.0.81167-0
• Scholten, O.E., Lange, W., 2000. Breeding for resistance to rhizomania in sugar beet: a review. Euphytica, 112: 219-231. doi: 10.1023/A:1003988003165
• Tamada, T., Baba, T., 1973. Beet necrotic yellow vein virus from rhizomania affected sugar beet in Japan. Ann. Phytopathol. Soc. Jpn., 39: 325-332.
• Tamada, T., Abe, H., 1989. Evidence that beet necrotic yellow vein virus RNA-4 is essential for efficient transmission by the fungus Polymyxa betae. Journal of General Virology, 70: 3391-3398. https://doi.org/10.1099/0022-1317-70-12-3391
• Tamada, T., Abe, H., Saito, M., Kiguchi, T., Harada, T., 1989. Production and pathogenicity of isolates of Beet necrotic yellow vein virus with different numbers of RNA components. Journal of General Virology, 70: 3399-3409. https://doi.org/10.1099/0022-1317-70-12-3399
• Tamada, T., Saito, M., Kiguchi, T., Kusume, T., 1990. Effect of isolates of Beet necrotic yellow vein virus with different of RNA components on the development of rhizomania symtoms. Proc. Ist Symp. Int. Work. Group. Plant Viruses Fungal Vectors, 41-44, 21-24 Ağustos, Braunscweig, Germany.
• Tamada, T., Kusume, T., Uchino, H., Kiguchi, T., Saito, M., 1996. Evidence that Beet necrotic yellow vein virus RNA 5 is involved in symtom development of sugar beet roots. Proc. 3rd Symp. Int. Work. Group Plant Viruses Fungal Vectors, 49-52, 6-7 Ağustos, Dundee, Scotland.
• Tamada, T., Uchino, H., Kusume, T., Saito, M., 1999. RNA-3 deletion mutants of beet necrotic yellow vein virus do not cause rhizomania disease in sugar beets. Phytopathology, 89: 1000-1006. https://doi.org/10.1094/phyto.1999.89.11.100
• Tamada, T., 2016. General features of Beet necrotic yellow vein virus. In: Biancardi, E., Tamada, T. (Eds.). Rhizomania. Springer International Publishing Switzerland. pp. 55-83.
• Tamada, T., Kondo, H., Chiba, S., 2016. Genetic diversity of Beet necrotic yellow vein virus. In: Biancardi, E., Tamada, T. (Eds.). Rhizomania. Springer International Publishing Switzerland. pp. 109-131.
• Tamura, K., Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526. doi: 10.1093/oxfordjournals.molbev.a040023
• Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. Clustal W: Improving the sensitivity of proggosive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680. doi: 10.1093/nar/22.22.4673
• Yardımcı, N., Çulal Kılıç, H., 2011. Identification of Beet necrotic yellow vein virus in lakes district: A major beet growing area in Turkey. Indian Journal of Virology, 22 (2): 127-130. doi: 10.1007/s13337-011-0047-y
• Wang, Y., Fan, H., Wang, X-B., Li, M., Li, D., Yu, J., 2011. Detection and characterization of spontaneous internal deletion mutants of Beet necrotic yellow vein virus RNA3 from systemic host Nicotiana benthamiana. Virology Journal, 8: 335. doi: 10.1186/1743-422X-8-335
• Ward, L., Koenig, R., Budge, G., Garrido, C., McGrath, C., Stubbey, H., Boonham, N., 2007. Occurrence of two different types of RNA-5 containing beet necrotic yellow vein virus in the UK. Archives of Virology, 152: 59-73. doi:10.1007/s00705-006-0832-x
• Zhuo, N., Jiang, N., Zhang, C., Zhang, Z.Y., Zhang, G.Z., Han, C.G., Wang, Y., 2015. Genetic diversity and population structure of Beet necrotic yellow vein virus in China. Virus Research, 205: 54-62. doi: 10.1016/j.virusres.2015.05.009