Detection of Beet black scorch virus and other Associated Soil-borne Viruses and Determining some of their Molecular Aspects

Document Type : Research Article

Authors

1 Ferdowsi University of Mashhad

2 Agricultural Research, Education and Extension Organization )AREEO(, Karadj, Iran

Abstract

Introduction: Soil-borne sugar beet viruses are responsible for the destructive diseases of sugar beet. They can cause significant yield losses worldwide. Four of the soil-borne sugar beet viruses consisted of Beet necrotic yellow vein virus (BNYVV), Beet soil-borne mosaic virus (BSBMV), Beet soil-borne virus (BSBV) and Beet virus Q (BVQ) are transmitted by the protis Polymyxa betae, a common root infecting parasite which ensures the long-term persistence of the viruses in the soils and one consisted of Beet black scorch virus (BBSV), is transmitting by Olpidium brassicae. So far, four out of five aforementioned viruses have been reported (except for BSBMV) in Iran. BNYVV is the causal agent of the rhizomania disease which has been reported in mixed-infections with BSBV, BVQ and/or BBSV. In previous studies, BSBV, BVQ and BBSV have been found alongside the BNYVV in some root samples. Nevertheless, up to now, no field has been spotted with black scorch symptoms of sugar beet leaves. Recently, we observed symptoms of burns on leaves and similar signs of rhizomania disease in the roots of some sugar beet cultivars in the fields of Khorasan Razavi province. The purpose of this study was to detect soil-borne viruses of sugar beet and determine some of their molecular aspects.
Materials and Methods: In this study, sugar beet with bearded roots and black scorching of leaves symptoms were collected from Mashhad, Fariman, Chenaran, Jolge-Rokh, and Jovein sugar beet fields. Total RNA was extracted from 100 mg of rootlets using RNeasy Mini Kit (Qiagen-Germany) based on the manufacturer's protocol. The presence of three viruses of BSBV, BVQ and BNYVV were analyzed by multiplex reverse transcription-polymerase chain reaction (mRT-PCR). However, For BBSV detection, simplex RT-PCR was used to detect of the 3′-UTR of the genomic RNA. For the molecular characterization of the BNYVV isolates, the BNYVV type (A or B) was determined with duplex RT-PCR (dRT-PCR), using A/B-type-specific primers pairs for the triple gene block (TGB) gene in RNA-2 and the partial p25 gene of the RNA-3 segment of the virus. RT-PCR was done using the PrimeScript™ Reverse Transcriptase kits and the PrimeSTAR GXL DNA Polymerase (Takara, Japan). The PCR products were cloned in pGEM®-T Easy Vector (Promega-USA). The recombinant plasmids were extracted using PrimPrep Plasmid DNA isolation kit (GenetBio-Korea) and then sequenced (Macrogene, South Korea). Nucleotide sequences data were analyzed using Chromas (version 1.45) and MEGA7 softwares.
Results and Discussion: The results showed that in the three samples with bearded root symptoms (Mashhad, Jovein, and Jolge-rokh), only BNYVV (A-type) was present and there were no BSBV and BVQ in the tested samples. In addition, in the two samples (Fariman and Chenaran), none of the three viruses was detected. The results showed that the two BNYVV isolates had ‘ACHG’ (Mashhad and Jolge-Rokh isolates) or ‘AHHG’ (Jovein isolate) residues in the tetrad position. So that the amino acid cysteine (C) in a68 position was converted to histidine (H). Although this A-type tetrad has been previously reported by Mehrvar et al. (2009) in Khorasan Razavi and Northern Khorasan, Semnan, Qazvin, Zanjan, Ilam, Hamedan, and West Azarbaijan provinces. In this study, BBSV was detected in all samples. In Mashhad, Jolge-rokh, and Jovein samples, BNYVV was present accompanied by BBSV. However, BBSV was detected alone from Fariman (holding black scorching of the leaves and vascular necrosis of root symptoms) and Chenaran (black scorching of the leaves) samples. These results are consistent with the results of other researchers from Spain and the United States who reported the presence of rhizomnia symptoms in the BBSV infected roots.
Conclusion: While most of  the farmers in Khorasan province cultivate resistant cultivars of sugar beet carrying the Rz1 gene for successive years in a field, the breakdown of the resistance and emerging of new resistance breaking (RB) variant of the virus have occurred via amino acid changes. However, more research on BNYVV pathogenicity by the use of additional sources of resistance and alternative disease control majors is needed to have a suitable conclusion. In addition, the results of this study showed that the presence of both viruses (BBSV and BNYVV) together could exacerbate the Rhizomania syndrome symptoms while single infection by BBSV could just cause vascular necrosis in the root and black scorching symptoms of the leaves. This could be very important in symptoms based diagnosing of the disease and preventing errors in evaluating the resistance of sugar beet cultivars in the field.

Keywords


1- Asher MJC. 1993. Rhizomania. In: Cooke DA, Scott RK (eds) The sugar beet crop: science into practice. Chapman & Hall, London, pp 311–346.
2- Borodynko N., Hasiow-Jaroszewska B., and Pospieszny H. 2009. Evidence for the presence of Beet necrotic yellow vein virus types A and B in Poland. Journal of Plant Diseases and Protection 116(3): 106-108.
3- Bornemann K., and Varrelmann M. 2009. The variability of Beet necrotic yellow vein virus p25 pathogenicity factor previously allocated to geographically distinct isolates can be retrieved in single representative A- and B-type soils. Institute of Sugar Beet Research (IFZ) In DPG AK Pflanzenvirologie.
4- Canova A. 1959. Appunti di patologia della barbabietola. Informatore Fitopatologico 9(20): 390–396.
5- Cao Y., Cai Z., Ding Q., Li D., Han C., Yu J., and Liu Y. 2002. The complete nucleotide sequence of Beet black scorch virus (BBSV), a new member of the genus Necrovirus. Archives of Virology 147(12): 2431-2435.
6- Chiba S., Kondo H., Miyanishi M., Andika I.B., Han C., and Tamada T. 2011. The evolutionary history of Beet necrotic yellow vein virus deduced from genetic variation, geographical origin and spread, and the breaking of host resistance. Molecular Plant-Microbe Interactions 24(2): 207-218.
7- Crutzen F., and Bragard C. 2010. Pomoviruses associated with the rhizomania syndrome: a reverse genetic approach of the genome and multiplication requirements in planta. Thèse de doctorat à l’Universite catholique de Louvain. Belgique.
8- Cui X. 1988. An icosahedral virus found in sugar beet. J Xinjiang Shihezi Agric College 10: 73-78.
9- Farzadfar S., Pourrahim R., Golnaraghi A.R., and Shahraeen N. 2002. First report of Beet soil-borne virus in Iran. Plant Disease 86: 187.
10- Farzadfar S., Pourrahim R., Golnaraghi A.R., and Ahoonmanesh A. 2005. First report of Beet virus Q in sugar beet in Iran. Plant Disease. 88: 1359.
11- Fujisawa I., and Sugimoto T. 1977. Transmission of Beet necrotic yellow vein virus by Polymyxa betae. Japanese Journal of Phytopathology 43(5): 583-586.
12- Galein Y. 2013. The epidemiology of rhizomania in the Pithiviers region of France (Doctoral dissertation, UCL-Universite Catholique de Louvain).
13- Gonzalez-Vazquez M., Ayala J., Garcia-Arenal F., and Fraile A. 2009. Occurrence of Beet black scorch virus infecting sugar beet in Europe. Plant Disease 93(1): 21-24.
14- Guo L.H., Cao Y.H., Li D.W., Niu S.N., Cai Z.N., Han C.G., Zhai Y.F., and Yu J.L. 2005. Analysis of nucleotide sequences and multimeric forms of a novel satellite RNA associated with Beet black scorch virus. Journal of Virology 79(6): 3664-3674.
15- Henry C. 1996. British Sugar beet review. British Sugar Beet Review (Vol. 64). I.J. Schapringer.
16- Heijbroek W., Musters P.M.S., and Schoone A.H.L. 1999. Variation in pathogenicity and multiplication of Beet necrotic yellow vein virus (BNYVV) in relation to the resistance of sugar-beet cultivars. European Journal of Plant Pathology 105(4): 397-405.
17- Izadpanah, K., Hashemi, P., Kamran, R., Pakniat, M., Sahandpour, A. and Masumi, M., 1996. Widespread occurrence of rhizomania-like disease of sugarbeet in Fars.Iranian Journal of Plant Pathology 32(3/4): 200-206. (In Persian)
18- Ivanovic M., Macfarlane I., and Woods R.D. 1983. Viruses of sugar beet associated with Polymyxa betae. Annual Report of Rothamsted Experimental Station for, 1982: 189-190.
19- Junxi J., Jingfeng Z., Shaochen C., Dajin Y., Jialin Y., Zhunan C., and Yi L. 1999. Transmission of Beet black scorch virus by Olpidium brassicae. Acta Agriculturae Universitatis Jiangxiensis. 21(4): 525-528.
20- Kobs G. 1997. Cloning blunt-end DNA fragments into the pGEM®-T Vector Systems. Promega Notes, 62, pp.15-18.
21- Koenig R., and Loss S. 1997. Beet soil-borne virus RNA1: genetic analysis enabled by a starting sequence generated with primers to highly conserved helicase-encoding domains. J. gen.Virol. 78: 3161-3165.
22- Koenig R., Pleij C.W., Beier C., and Commandeur U. 1998. Genome properties of Beet virus Q, a new furo-like virus from sugarbeet, determined from unpurified virus. Journal of General Virology 79(8): 2027-2036.
23- Koenig R., and Valizadeh J. 2008a. Molecular and serological characterization of an Iranian isolate of Beet black scorch virus. Archives of Virology 153(7): 1397-1400.
24- Koenig R., Kastirr U., Hotschulte B., Deml G., and Varrelmann M. 2008b. 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.
25- Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35(6): 1547-1549.
26- Kutluk-Yilmaz N.D. 2016. Identification of strain types of some Beet necrotic yellow vein virus isolates determined in Northern and Central Parts of Turkey. Eurasian Journal Soil Science 5(3): 241-248.
27- Kutluk-Yilmaz N.D.K., Arli-Sokmen M., and Kaya R. 2018. p25 pathogenicity factor deletion mutants of Beet necrotic yellow vein virus occurring in sugar beet fields in Turkey. Journal of Plant Diseases and Protection 125(1): 89-98.
28- Kruse M., Koenig R., Hoffmann A., Kaufmann A., Commandeur U., Solovyev A.G., Savenkov I., and Burgermeister W. 1994. Restriction fragment length polymorphism analysis of reverse transcription-PCR products reveals the existence of two major strain groups of Beet necrotic yellow vein. Journal of General Virology 75(8): 1835-1842.
29- Lennefors B.L. 2006. Molecular breeding for resistance to rhizomania in sugar beets. Doctoral thesis. Swedish University of Agricultural Sciences.Uppsala 2006. Acta Universitatis Agriculturae Sueciae. ISSN 1652-6880.
30- Li M., Liu T., Wang B., Han C., Li D., and Yu J. 2008. Phylogenetic analysis of Beet necrotic yellow vein virus isolates from China. Virus Genes 36(2): 429-432.
31- Liu H.Y., and Duffus J.E. 1988. The occurrence of a complex of viruses associated with rhizomania of sugarbeet.Phytopathology, 78, p.1583.
32- Liu J., and Xian H. 1995. Preliminary report on Beet black scorch virus.China Sugar Beet 3: 30-31.
33- Liu, H.Y., Sears, J.L. and Lewellen, R.T., 2005. Occurrence of resistance-breaking Beet necrotic yellow vein virus of sugar beet. Plant Disease 89(5): 464-468.
34- Mehrvar M., and Bragard C. 2011. Iranian diversity of Beet black scorch virus and satellite. In Proceedings of the Eighth Symposium of the International Working Group on Plant Viruses with Fungal Vectors, Louvain-La-Neuve, Belgium, 6-8 July, 2011(pp. 41-46). International Working Group on Plant Viruses with Fungal Vectors.
35- Mehrvar M., Valizadeh J., Koenig R., and 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(3): 501-506.
36- Meunier A., Schmit J.F., Stas A., Kutluk N., and Bragard C. 2003. Multiplex reverse transcription-PCR 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.Appl. Environ. Microbiology 69(4): 2356-2360.
37- Pavli O., Prins M., Goldbach R., and Skaracis G.N. 2011. Efficiency of Rz1-based rhizomania resistance and molecular studies on BNYVV isolates from sugar beet cultivation in Greece. European Journal of Plant Pathology 130(2): 133-142.
38- Pferdmenges F. 2007. Occurrence, spread and pathogenicity of different Beet necrotic yellow vein virus (BNYVV) isolates (Vol. 23). Cuvillier Verlag.
39- Russo M., Martelli G.P., and Di Franco A. 1981.The fine structure of local lesions of Beet necrotic yellow vein virus in Chenopodium amaranticolor. Physiological Plan Pathology 19(2): 237-IN11.
40- Ratti C., Clover G.R., Autonell C.R., Harju V.A., and Henry C.M. 2005. A multiplex RT-PCR assay capable of distinguishing Beet necrotic yellow vein virus types A and B. Journal of Virological Methods 124(1-2): 41-47.
41- Rush C.M. 2003.Ecology and epidemiology of Benyviruses and plasmodiophorid vectors. Annual review of Phytopathology 41(1): 567-592.
42- Rush C.M., Liu H.Y., Lewellen R.T., and Acosta-Leal R. 2006. The continuing saga of rhizomania of sugar beets in the United States. Plant Disease 90(1): 4-15.
43- Samiei A., Mehrvar M., and Zakiaghl M. 2017. Genetic diversity and distribution of Beet black scorch virus in some provinces of Iran, 20(4): 540–547.(In Persian with English abstract)
44- Schirmer A., Link D., Cognat V., Moury B., Beuve M., Meunier A., Bragard C., Gilmer D., and Lemaire O. 2005. Phylogenetic analysis of isolates of Beet necrotic yellow vein virus collected worldwide. Journal of General Virology 86(10): 2897-2911.
45- Shen R., and Miller W.A. 2007. Structures required for poly (A) tail-independent translation overlap with, but are distinct from, cap-independent translation and RNA replication signals at the 3′ end of Tobacco necrosis virus RNA. Virology 358(2): 448-458.
46- Sohi H., and Maleki M. 2004. Evidence for presence of types A and B of Beet necrotic yellow vein virus (BNYVV) in Iran. Virus Genes 29(3): 353-358.
47- Tamada T. 1975. Beet necrotic yellow vein virus. CMI/AAB Descriptions of plant viruses, 144(4).
48- Tamada T., Shirako Y., Abe H., Saito M., Kiguchi T., and 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(12): 3399-3409.
49- Wang X., Zhang Y., Xu J., Shi L., Fan H., Han C., Li D., and Yu J. 2012. The R-rich motif of Beet black scorch virus P7a movement protein is important for the nuclear localization, nucleolar targeting, and viral infectivity. Virus Research 167(2): 207-218.
50- Webb K.M., Wintermantel W.M., Kaur N., Prenni J.E., Broccardo C.J., Wolfe L.M., and Hladky L.L. 2015. Differential abundance of proteins in response to Beet necrotic yellow vein virus during compatible and incompatible interactions in sugar beet containing Rz1 or Rz2. Physiological and Molecular Plant Pathology 91: 96-105.
51- Weiland J.J., Van Winkle D., Edwards M.C., Larson R.L., Shelver W.L., Freeman T.P., and Liu H.Y. 2007. Characterization of a US isolate of Beet black scorch virus. Phytopathology 97(10): 1245-1254.
52- Zhang Y., Zhang X., Niu S., Han C., Yu J., and Li D. 2011. Nuclear localization of Beet black scorch virus capsid protein and its interaction with importin α. Virus Research 155(1): 307-315.
53- Zhuo N., Jiang N., Zhang C., Zhang Z.Y., Zhang G.Z., Han C.G., and Wang Y. 2015. Genetic diversity and population structure of Beet necrotic yellow vein virus in China. Virus Research 205: 54-62.
CAPTCHA Image