Üftade GÜNER, Hikmet Murat SİPAHİOĞLU, Mustafa USTA

Incidence and genetic stability of Potato spindle tuber pospiviroid in potato in Turkey

The prevalence of Potato spindle tuber pospiviroid (PSTVd) infection in randomly selected potato tubers was determined via nonisotopic dot blot hybridization and reverse transcriptase polymerase chain reaction (RT-PCR). In January and February of 2010, 168 seedling tubers of Solanum tuberosum, representing 27 cultivars, were received from different seedling potato producers in Turkey. Digoxigenin-labeled RNA probes of PSTVd were synthesized from the cloned PCR products and applied in dot blot hybridization to detect viroids in RNA extracts isolated from dormant potato tubers. PSTVd was found in 7 samples and 6 cultivars (Innovator, Lady Jo, Russet Burbank, Agria, Provento and Konsül). Some RNA samples, although positive by RT-PCR test, did not give a hybridization signal by dot blot assay. The complete genome of a selected isolate (PSTVd-TR) was cloned and sequenced. Primary and secondary structure analysis showed that the RNA genome of the PSTVd-TR isolate (GenBank Accession No. HQ456944) differed from other compared isolates by only a few nucleotides. The highest identity (99%) was in a PSTVd isolate that was identified in Solanum spp. in Italy (Accession No. EF459700). The infectivity of PSTVd-TR isolate was shown 2 weeks after the mechanical inoculation of sap extracts onto seedlings of tomato cultivar Joker. The PSTVd infections were proven by RT-PCR assay in symptomless tomato seedlings.

Anahtar Kelimeler:

Key words: Dot blot hybridization, molecular characterization, potato, PSTVd

Incidence and genetic stability of Potato spindle tuber pospiviroid in potato in Turkey

Keywords:

Key words: Dot blot hybridization, molecular characterization, potato, PSTVd,

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Alabdullah A, Elbeaino T, Minafra A, Gigiaro M, Martelli GP (2009) Detection and variability of Olive latent virus 3 in the Mediterranean region. Journal of Plant Pathology 91: 521-525.
Behjatnia SAA, Dry IB, Krake LR, Conde BD, Connelly MI, Randles JW, Rezaian MA (1996) New potato spindle tuber viroid and tomato leaf curl geminivirus strains from a wild Solanum sp. Phytopathology 86: 880-886.
Bostan H, Gazel M, Elibuyuk IO, Cağlayan K (2010) Occurrence of pospiviroid in potato, tomato and some ornamental plants in Turkey. African Journal of Biotechnology 9: 2613-2617.
Bussière F, Lafontaine D, Perreault JP (1996) Compilation and analysis of viroid and viroid-like RNA sequences. Nucleic Acids Research 24: 1793-1798.
Di Serio F (2007) Identifi cation and characterization of Potato spindle tuber viroid infecting Solanum jasminoides and S. rantonnetii in Italy. Journal of Plant Pathology 89: 297-300.
Diener TO (1971) Potato spindle tuber ‘virus’: IV. A replicating, low molecular weight RNA. Virology 45: 411-428.
Diener TO (1987) Potato spindle tuber. In: Th e Viroids (Ed. TO Diener). Plenum Press, New York, pp. 221-233.
Diener TO (1993) Th e viroid: big punch in a small package. Trends in Microbiology 1: 289-294.
Flores R, Randles JW, Bar-Joseph M, Diener TO (1998) A proposed scheme for viroid classifi cation and nomenclature. Archives of Virology 143: 623-629.
Foissac X, Savalle-Dumas L, Gentit P, Dulucq MJ, Candresse T (2001) Polyvalent detection of fruit tree Tricho, Capillo, and Faveaviruses by nested RT-PCR using degenerated and inosine containing primers (PDO RT-PCR). Acta Horticulturae 357: 52-59.
Gandía M, Palacio A, Duran-Vila N (2000) Variability of Citrus exocortis viroid (CEVd). In: Proceedings, XIV Conference of the International Organization of Citrus Virologists, pp. 265- 272.
Gora A, Candresse T, Zagorski W (1994) Analysis of the population structure of three phenotypically distinct PSTVd isolates. Archives of Virology 138: 233-245.
Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sanger HL (1978) Nucleotide sequence and secondary structure of Potato spindle tuber viroid. Nature 273: 203-208.
Hadidi A, Flores R, Randles JW, Semancik JS (2003) Viroids. CSIRO Publishing, Collingwood, Australia.
Herold T, Haas B, Singh RP, Boucher A, Sanger HL (1992) Sequence analysis of fi ve new fi eld isolates demonstrates that the chain length of Potato spindle tuber viroid (PSTVd) is not strictly conserved but is variable as in other viroids. Plant Molecular Biology 19: 329-333.
Lakshman DK, Tavantzis SM (1993) Primary and secondary structure of a 360-nucleotide isolate of Potato spindle tuber viroid. Archives of Virology 128: 319-331.
Önelge N, Bozan O (2005) Investigation of Potato spindle tuber viroid (PSTVd) in potato seeds. In: Proceedings, Second Seed Congress of Turkey, Adana, Turkey, p. 378.
Owens RA, Cress DE (1980) Molecular cloning and characterization of Potato spindle tuber viroid cDNA sequences. Proc Natl Acad Sci USA 77: 5302-5306.
Pallás V, Más P, Sánchez-Navarro JA (1998) Detection of plant RNA viruses by non-isotopic dot-blot hybridization. In: Plant Virus Protocols: From Virus Isolation to Transgenic Resistance (Eds. G Foster and S Taylor). Humana Press, Totowa, New Jersey, pp. 461-468.
Pfannenstiel MA, Slack SA (1980) Response of potato cultivars to infection by the Potato spindle tuber viroid. Phytopathology 70: 922-926.
Puchta H, Herold T, Verhoeven K, Roenhorst A, Ramm K, Schmidt- Puchta W, Sanger HL (1990) A new strain of Potato spindle tuber viroid (PSTVd-N) exhibits major sequence diff erences as compared to all other strains sequenced so far. Plant Molecular Biology 15: 509-511.
Riesner D, Gross HJ (1985) Viroids. Annual Review of Biochemistry 54: 531-564.
Sanchez-Navarro JA, Aparicio F, Rowhani A, Pallás V (1998) Comparative analysis of ELISA, nonradioactive molecular hybridization and PCR for the detection of Prunus necrotic ringspot virus in herbaceous and Prunus hosts. Plant Pathology 47: 780-786.
Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK (1976) Viroids are single-stranded covalently closed circular RNA molecules existing as a highly base-paired structure. Proc Natl Acad Sci USA 73: 3852-3856.
Schnölzer M, Haas B, Ramm K, Hofmann H, Sanger HL (1985) Correlation between structure and pathogenicity of Potato spindle tuber viroid (PSTV). EMBO Journal 4: 2181-2190.
Semancik JS, Conejero, V (1987) Viroid pathogenesis and expression of biological activity. In: Viroids and Viroid-like Pathogens (Ed. JS Semancik). CRC Press, Boca Raton, Florida, pp. 71-126.
Shamloul AM, Hadidi A, Zhu SF, Singh RP, Sagredo B (1997) Sensitive detection of Potato spindle tuber viroid using RT-PCR and identifi cation of a viroid variant naturally infecting pepino plants. Canadian Journal of Plant Pathology 19: 89-96.
Singh RP (1998) Viroids twenty-fi ve years later: personal refl ections. In: Topics in Tropical Virology (Eds. DN Black, DD Shukla, N Rishi). Malhotra Publishing House, New Delhi, pp. 131-152.
Singh RP (1999) Development of the molecular methods for potato virus and viroid detection and prevention. Genome 42: 592- 604.
Singh RP, Clark MC (1971) Infectious low-molecular weight ribonucleic acid from tomato. Biochemical and Biophysical Research Communications 44: 1077-1083.
Singh RP, Dhar AK (1998) Detection and management of plant viroids. In: Plant Virus Disease Control (Eds. A Hadidi, RK Khetarpal, H Koganezawa). APS Press, St. Paul, Minnesota, pp. 428-477.
Singh RP, Finnie RE, Bagnall RH (1970) Relative prevalence of mild and severe strains of potato spindle tuber virus in eastern Canada. Am Potato J 47: 289-293.
Singh RP, Nie X, Singh M (1999) Tomato chlorotic dwarf viroid: an evolutionary link in the origin of pospiviroids. Journal of General Virology 80: 2823-2828.
Sipahioglu HM, Usta M, Ocak M (2006) Use of dried high-phenolic laden host leaves for virus and viroid preservation and detection by PCR methods. Journal of Virological Methods 137: 120-124.
Verhoeven JTHJ, Botermans M, Roenhorst JW, Westerhof J, Meekes ETM (2009) First report of Potato spindle tuber viroid in cape gooseberry (Physalis peruviana) from Turkey and Germany. Plant Disease 93: 316.
Visvader JE, Symons RH (1985) Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic Acids Research 13: 2907-2920.
Wassenegger M, Heimes S, Sanger HL (1994) An infectious viroid RNA replicon evolved from an in vitro-generated non- infectious viroid deletion mutant via a complementary deletion in vivo. EMBO Journal 13: 6172-6177.