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Use of secA Gene for Characterization of Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India

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Abstract

Surveys of commercial sugarcane varieties were conducted to the phytoplasma disease incidence in eight major sugarcane growing states of India (Uttarakhand, Uttar Pradesh, Maharashtra, Bihar, Assam, Chhattisgarh, Haryana and Tamil Nadu) during 2014–2015. Leaves from 24 symptomatic sugarcane plants of eight varieties showing grassy shoot and chlorosis symptoms, and of 8 non-symptomatic plants were collected and analyzed for phytoplasma presence using 16S rRNA and secA gene-specific primers. Amplification of 1.8- and 1.2-kb products using nested primers (P1/P7 and R16F2n/R16R2) of 16S rRNA gene and 880- and 480-bp products using secA gene-specific primer pairs (SecAfor1/SecArev3 and SecAfor2/SecArev3) was obtained for all the 24 symptomatic sugarcane samples. Pairwise sequence comparison, phylogenetic and in silico RFLP analysis of partial 16S rRNA and secA gene sequences of eight strains of sugarcane grassy shoot phytoplasma representative of the eight states confirmed the association of ‘Candidatus phytoplasma oryzae’-related strains (16SrXI-B) with symptomatic sugarcane varieties. The study confirmed that secA gene-specific primers could be employed for molecular characterization of phytoplasmas associated with sugarcane grassy shoot phytoplasmas belonging to 16SrXI group.

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References

  • Ahrens, U., and E. Seemüller. 1992. Detection of DNA of plantpathogenic mycoplasma-like organisms by a polymerase chain reaction that amplifies a sequence of the 16S rRNA gene. Phytopathology 82: 828–832.

    Article  CAS  Google Scholar 

  • Al-Abadi, S.Y., M.A. Al-Sadi, M. Dickinson, M.S. Al-Hammadi, R. Al-Shariqi, R.A. Al-Yahyai, E.A. Kazerooni, and A. Bertaccini. 2016. Population genetic analysis reveals a low level of genetic diversity of ‘Candidatus phytoplasma aurantifolia’ causing witches’ broom disease in lime. SpringerPlus 5 (1): 1701.

    Article  PubMed  PubMed Central  Google Scholar 

  • Bekele, B., S. Abeysinghe, T.X. Hoat, J. Hodgetts, and M. Dickinson. 2011. Development of specific secA-based diagnostics for the 16SrXI and 16SrXIV phytoplasmas of the Gramineae. Bulletin of Insectology 64: 15–16.

    Google Scholar 

  • Bila, J., A. Mondjana, B. Samils, and N. Högberg. 2015. High diversity, expanding populations and purifying selection in phytoplasmas causing coconut lethal yellowing in Mozambique. Plant Pathology 64 (3): 597–604.

    Article  CAS  Google Scholar 

  • Botti, S., and A. Bertaccini. 2003. Variability and functional role of chromosomal sequences in phytoplasmas of 16SrI-B subgroup (aster yellows and related strains). Journal of Applied Microbiology 94 (1): 103–110.

    Article  CAS  PubMed  Google Scholar 

  • Deng, S., and C. Hiruki. 1991. Amplification of 16SrRNA genes from culturable and non-culturable mollicutes. Journal of Microbiological Methods 14: 53–61.

    Article  CAS  Google Scholar 

  • Gundersen, D.E., and I.-M. Lee. 1996. Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia Mediterranea 35: 144–151.

    CAS  Google Scholar 

  • Hodgetts, J., N. Boonham, R. Mumford, N. Harrison, and M. Dickinson. 2008. Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution on candidate species of ‘Candidatus Phytoplasma’. International Journal of Systematic and Evolutionary Microbiology 58: 1826–1837.

    Article  CAS  PubMed  Google Scholar 

  • Lee, I.-M., D.E. Gundersen, R.E. Davis, and I.-M. Bartoszyk. 1998. Revised classification scheme of phytoplasmas based on RFLP analysis of 16S rRNA and ribosomal protein gene sequences. International Journal of Systematic Bacteriology 48: 1153–1169.

    Article  CAS  Google Scholar 

  • Lee, I.-M., Y. Zhao, and K.D. Bottner. 2006. SecY gene sequence analysis for finer differentiation of diverse strains in the aster yellows phytoplasma group. Molecular and Cellular Probes 20 (2): 87–91.

    Article  CAS  PubMed  Google Scholar 

  • Madhupriya, G.P. Rao, A. Kumar, and V.K. Baranwal. 2015. Classification of sesame phytoplasma strain in India at 16Sr subgroup level. Journal of Plant Pathology 3:523–528.

    Google Scholar 

  • Marcone, C. 2002. Phytoplasma disease of sugarcane. Sugar Tech 4: 79–85.

    Article  Google Scholar 

  • Marcone, C., A. Ragozzino, I. Camele, G.L. Rana, and E. Seemüller. 2001. Updating and extending genetic characterization and classification of phytoplasmas from wild and cultivated plants in southern Italy. Journal of Plant Pathology 83 (2): 133–138.

    CAS  Google Scholar 

  • Mehdi, A., V.K. Baranwal, M. KochuBabu, and D. Praveena. 2011. Sequence analysis of 16S rRNA and secA genes confirms the association of 16SrI-B subgroup phytoplasma with oil palm (Elaeisguineensis Jacq.) stunting disease in India. Journal of Phytopathology 160: 6–12.

    Article  Google Scholar 

  • Nabi, S., D.K. Madhupriya, G.P. Dubey, V.K.Baranwal Rao, and P. Sharma. 2015. Characterization of phytoplasmas associated with sesame (Sesamum indicum) phyllody disease in North India utilizing multi locus genes and RFLP analysis. Indian Phytopathology 68 (1): 112–119.

    Google Scholar 

  • Nasare, K., A. Yadav, A.K. Singh, K.B. Shivasharanappa, Y.S. Nerkar, and V.S. Reddy. 2007. Molecular and symptom analysis reveal the presence of new phytoplasmas associated with sugarcane grassy shoot disease in India. Plant Disease 91: 1413–1418.

    Article  CAS  Google Scholar 

  • Ramaswamy, M., S. Nair, V.P. Soumya, and G.V. Thomas. 2013. Phylogenetic analysis identifies a ‘Candidatus phytoplasma oryzae’-related strain associated with yellow leaf disease of areca palm (Areca catechu L.) in India. International Journal of Systematic and Evolutionary Microbiology 63: 1376–1382.

    Article  PubMed  Google Scholar 

  • Rao, G.P., S. Srivastava, P.S. Gupta, A. Singh, M. Singh, and C. Marcone. 2008. Detection of sugarcane grassy shoot phytoplasma infecting sugarcane in India and its phylogenetic relationships to closely related phytoplasmas. Sugar Tech 10: 74–80.

    Article  CAS  Google Scholar 

  • Rao, G.P., S. Mall, and C. Marcone. 2012. Recent biotechnological approaches in diagnosis and management of sugarcane phytoplasma diseases. In Functional plant science and biotechnology, recent trends in biotechnology and microbiology, vol. 2, ed. A.R. Sundar, and R. Viswanathan, 19–29. New York: Global Science Books.

    Google Scholar 

  • Rao, G.P., A.K. Madhupriya, S.Kumar Tiwari, and V.K. Baranwal. 2014. Identification of sugarcane grassy shoot-associated phytoplasma and one of its putative vectors in India. Phytoparasitica 42: 349–354.

    Article  Google Scholar 

  • Rao, G.P., and M. Kumar. 2017. World status of phytoplasma diseases associated with eggplant. Crop Protection 96: 22–29.

    Article  Google Scholar 

  • Schneider, B.E., C.D.S. Seemüller, and B.C. Kirkpatrick. 1995. Phylogenetic classification of plant pathogenic mycoplasma like organisms or phytoplasmas. In Molecular and diagnostic procedures in mycoplasmology, vol. 2, ed. S. Raszin, and J.G. Tully, 369–380. New York: Academic Press.

    Chapter  Google Scholar 

  • Srivastava, S., V. Singh, P.S. Gupta, O.K. Sinha, and A. Baitha. 2006. Nested PCR assay for detection of sugarcane grassy shoot phytoplasma in the leafhopper vector Deltocephalus vulgaris: A first report. Plant Pathology 22: 25–32.

    Article  Google Scholar 

  • Shao, J., R. Jomantiene, E.L. Dally, Y. Zhao, I.-M. Lee, D.L. Nuss, and R.E. Davis. 2006. Phylogeny and characterization of phytoplasmal nusA and use of the nusA gene in detection of group 16SrI strains. Journal of Plant Pathology 88 (2): 193–201.

    CAS  Google Scholar 

  • Streten, C., and K.S. Gibb. 2005. Genetic variation in ‘Candidatus phytoplasma australiense’. Plant Pathology 54: 8–14.

    Article  CAS  Google Scholar 

  • Tamura, K., G. Stecher, D. Peterson, A. Filipski, and S. Kumar. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725–2729.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thompson, J.D., D.G. Higgins, and T.J. Gibson. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties, and weight matrix choice. Nucleic Acids Research 22: 4673–4680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tiwari, A.K., S.K. Vishwakarma, and G.P. Rao. 2012. Increasing incidence of sugarcane grassy shoot disease in Uttar Pradesh, India and its impact on yield and quality of sugarcane. Phytopathogenic Mollicutes 2: 63–67.

    Article  Google Scholar 

  • Tiwari, A.K., V.K. Madhupriya, K.P. Srivastava, B.L.Sharma Pandey, and G.P. Rao. 2016. Detection of sugarcane grassy shoot phytoplasma (16SrXI-B subgroup) in Pyrilla perpusilla Walker in Uttar Pradesh, India. Phytopathogenic Mollicutes 6 (1): 56–59.

    Article  Google Scholar 

  • Tiwari, A.K., S. Kumar, S. Mall, V. Jadon, and G.P. Rao. 2017. New efficient natural leafhopper vectors of sugarcane grassy shoot phytoplasma in India. SugarTech 9 (2): 191–197.

    Google Scholar 

  • Valiunas, D., R. Jomantiene, A. Ivanauskas, I. Urbonaite, D. Sneideris, and R.E. Davis. 2015. Molecular identification of phytoplasmas infecting diseased pine trees in the UNESCO-protected curonian spit of Lithuania. Forests 6: 2469–2483.

    Article  Google Scholar 

  • Viswanathan, R., C. Chinnaraja, R. Karuppaiah, K.V. Ganesh, R.J.J. Jenshi, and P. Malathi. 2011. Genetic diversity of sugarcane grassy shoot (SCGS)-phytoplasmas causing grassy shoot disease in India. Sugar Tech 13: 220–228.

    Article  CAS  Google Scholar 

  • Wongkaew, P., Y. Hanboonsong, P. Sirithorn, C. Choosai, S. Boonkrong, T. Tinnangwattana, R. Kitchareonpanya, and S. Damak. 1997. Differentiation of phytoplasmas associated with sugarcane and gramineous weed white leaf disease and sugarcane grassy shoot disease by RFLP and sequencing. Theoretical and Applied Genetics 95: 660–663.

    Article  CAS  Google Scholar 

  • Wei, W., R.E. Davis, I.-M. Lee, and Y. Zhao. 2007. Computer simulated RFLP analysis of 16S rRNA genes: Identification of ten new phytoplasma groups. International Journal of Systematic and Evolutionary Microbiology 57: 1855–1867.

    Article  CAS  PubMed  Google Scholar 

  • Yadav, A., V. Thorat, S. Deokule, Y. Shouche, and D.T. Prasad. 2016. New Subgroup 16SrXI-F phytoplasma strain associated with sugarcane grassy shoot (SCGS) disease in India. International Journal of Systematic and Evolutionary Microbiology. doi:10.1099/ijsem.0.001635.

    PubMed  Google Scholar 

  • Zhang, R.Y., W.F. Li, Y.K. Huang, X.Y. Wang, H.L. Shan, Z.M. Luo, and J. Yin. 2016. Group 16SrXI phytoplasma strains, including subgroup 16SrXI-B and a new subgroup, 16SrXI-D, are associated with sugar cane white leaf. International Journal of Systematic and Evolutionary Microbiology 66: 487–491.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India

    Shailender Kumar & G. P. Rao

  2. Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh Post Graduate Institute of Biomedical Science and Research, Balawala, Dehradun, Uttarakhand, 248161, India

    Vikas Singh Jadon

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  1. Shailender Kumar
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  2. Vikas Singh Jadon
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  3. G. P. Rao
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Correspondence to Shailender Kumar.

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Kumar, S., Jadon, V.S. & Rao, G.P. Use of secA Gene for Characterization of Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India. Sugar Tech 19, 632–637 (2017). https://doi.org/10.1007/s12355-017-0541-7

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