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Development of a Reverse Transcription-Recombinase Polymerase Amplification Assay for Detection of Sugarcane Yellow Leaf Virus

  • Xiao-Yan Feng
  • Lin-Bo Shen
  • Wen-Zhi Wang
  • Jun-Gang Wang
  • Zheng-Ying Cao
  • Cui-Lian Feng
  • Ting-Ting Zhao
  • Shu-Zhen Zhang
Research Article
  • 38 Downloads

Abstract

Sugarcane yellow leaf virus (SCYLV, genus Polerovirus) is a harmful agent that causes sugarcane yellow leaf disease. Current methods for SCYLV detection present some limitations. In this study, a novel isothermal amplification assay, namely reverse transcription-recombinase polymerase amplification (RT-RPA), was developed to promote SCYLV detection for disease management. The assay was evaluated in terms of specificity, sensitivity, reliability, temperature limit, and time limit. The developed RT-RPA assay was highly specific and non-cross-reactive with Potato leafroll virus, which is a type of species in Polerovirus. This assay can also detect at least 103-fold diluted cDNA from a SCYLV-infected sugarcane leaf, and its sensitivity is tenfold lower than that of RT-polymerase chain reaction (PCR). The reliability of the proposed assay was examined by detecting field sugarcane samples via RT-RPA and RT-PCR assays. The RT-RPA assay showed the same results as those of RT-PCR assay, indicating that the former was highly reliable for SCYLV detection. Analysis of the temperature and time limits revealed a wide operating temperature range from 27 to 45 °C, which was easily reached, and a rapid assay duration of 20 min. In summary, the developed RT-RPA assay was rapid, specific, and reliable with acceptable sensitivity and easily reachable operating temperature and thus could be a promising tool for SCYLV diagnosis in sugarcane.

Keywords

Recombinase polymerase amplification Sugarcane Sugarcane yellow leaf virus Yellow leaf disease 

Abbreviations

CP

Coat protein

LAMP

Loop-mediated isothermal amplification

MBP

Molecular-beacon probe

NASBA

Nucleic acid sequence-based amplification

PCR

Polymerase chain reaction

PLRV

Potato leafroll virus

RPA

Recombinase polymerase amplification

RT

Reverse transcription

SCYLV

Sugarcane yellow leaf virus

YL

Yellow leaf

Notes

Acknowledgements

This study was funded by the National Natural Science Foundation of China (31771865) and Sugar Crop Research System (CARS-170301). The authors would like to thank Professor Cheng-Gui Han from China Agricultural University for generously donating PLRV-infected N. benthamiana leaves for the cross-reactivity study.

Author Contributions

Shu-Zhen Zhang devised the experiments. Xiao-Yan Feng operated the experiments, analyzed the results, and wrote the manuscript. Lin-Bo Shen collected field sugarcane samples. Wen-Zhi Wang, Jun-Gang Wang, Zheng-Ying Cao, Cui-Lian Feng, and Ting-Ting Zhao revised the manuscript. All authors have read and approved the manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12355_2018_602_MOESM1_ESM.pdf (278 kb)
Supplementary material 1 (PDF 278 kb)

References

  1. Abd, E.W.A., P. Patel, O. Faye, S. Thaloengsok, D. Heidenreich, P. Matangkasombut, K. Manopwisedjaroen, A. Sakuntabhai, A.A. Sall, and F.T. Hufert. 2015. Recombinase polymerase amplification assay for rapid diagnostics of dengue infection. PLoS ONE 10 (6): e0129682.CrossRefGoogle Scholar
  2. Ahmad, Y.A., L. Rassaby, M. Royer, Z. Borg, K.S. Braithwaite, T.E. Mirkov, M.S. Irey, X. Perrier, G.R. Smith, and P. Rott. 2006. Yellow leaf of sugarcane is caused by at least three different genotypes of Sugarcane yellow leaf virus, one of which predominates on the Island of Reunion. Archives of Virology 151 (7): 1355–1371.CrossRefPubMedGoogle Scholar
  3. Ahmed, A., L.H. der Van, and R.A. Hartskeerl. 2014. Development of a recombinase polymerase amplification assay for the detection of pathogenic Leptospira. International Journal of Environmental Research and Public Health 11 (5): 4953–4964.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Aljanabi, S.M., Y. Parmessur, Y. Moutia, S. Saumtally, and A. Dookun. 2001. Further evidence of the association of a phytoplasma and a virus with yellow leaf syndrome in sugarcane. Plant Pathology 50 (5): 628–636.CrossRefGoogle Scholar
  5. Amata, R.L., E. Fernandez, D. Filloux, D.P. Martin, P. Rott, and P. Roumagnac. 2015. Prevalence of Sugarcane yellow leaf virus in sugarcane producing regions in Kenya revealed by reverse transcription loop-mediated isothermal amplification method. Plant Disease 100 (2): 260–268.CrossRefGoogle Scholar
  6. Amer, H.M., E.W.A. Abd, M.A. Shalaby, F.N. Almajhdi, F.T. Hufert, and M. Weidmann. 2013. A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay. Journal of Virological Methods 193 (2): 337–340.CrossRefPubMedGoogle Scholar
  7. Babu, B., B.K. Washburn, S.H. Miller, K. Poduch, T. Sarigul, G.W. Knox, F.M. Ochoa-Corona, and M.L. Paret. 2016. A rapid assay for detection of Rose rosette virus using reverse transcription-recombinase polymerase amplification using multiple gene targets. Journal of Virological Methods 240: 78–98.CrossRefPubMedGoogle Scholar
  8. Boyle, D.S., D.A. Lehman, L. Lillis, D. Peterson, M. Singhal, N. Armes, M. Parker, O. Piepenburg, and J. Overbaugh. 2013. Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. Mbio 4 (2): 49–52.CrossRefGoogle Scholar
  9. Chinnaraja, C., and R. Viswanathan. 2015. Quantification of Sugarcane yellow leaf virus in sugarcane following transmission through aphid vector, Melanaphis sacchari. VirusDisease 26 (4): 237–242.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Chinnaraja, C., R. Viswanathan, R. Karuppaiah, K. Bagyalakshmi, P. Malathi, and B. Parameswari. 2013. Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination. European Journal of Plant Pathology 135 (2): 335–349.CrossRefGoogle Scholar
  11. Comstock, J.C., and J.D. Miller. 2004. Yield comparisons: Disease-free tissue-culture versus bud-propagated sugarcane plants and healthy versus yellow leaf infected plants. Journal American Society Sugar Cane Technologists 24: 31–40.Google Scholar
  12. Comstock, J.C., M.S. Irey, and B.E.L. Lockhart. 1998. Incidence of yellow leaf syndrome in CP cultivars based on polymerase chain reaction and serological techniques. Sugar Cane 4: 21–24.Google Scholar
  13. Crannell, Z.A., B. Rohrman, and R. Richards-Kortum. 2014. Equipment-free incubation of recombinase polymerase amplification reactions using body heat. PLoS ONE 9 (11): e112146.CrossRefPubMedPubMedCentralGoogle Scholar
  14. ElSayed, A.I., A.R. Weig, and E. Komor. 2011. Molecular characterization of Hawaiian Sugarcane yellow leaf virus genotypes and their phylogenetic relationship to strains from other sugarcane-growing countries. European Journal of Plant Pathology 129 (3): 399–412.CrossRefGoogle Scholar
  15. ElSayed, A.I., E. Komor, M. Boulila, R. Viswanathan, and D.C. Odero. 2015. Biology and management of Sugarcane yellow leaf virus: an historical overview. Archives of Virology 160 (12): 2921–2934.CrossRefPubMedGoogle Scholar
  16. ElSayed, A.I., M. Boulila, and P. Rott. 2014. Molecular evolutionary history of Sugarcane yellow leaf virus based on sequence analysis of RNA-dependent RNA polymerase and putative aphid transmission factor-coding genes. Journal of Molecular Evolution 78 (6): 349–365.CrossRefPubMedGoogle Scholar
  17. Euler, M., Y.J. Wang, D. Heidenreich, P. Patel, O. Strohmeier, S. Hakenberg, M. Niedrig, F.T. Hufert, and M. Weidmann. 2013. Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents. Journal of Clinical Microbiology 51 (4): 1110–1117.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Gao, S.J., Y.H. Lin, Y.B. Pan, M.B. Damaj, Q.N. Wang, T.E. Mirkov, and R.K. Chen. 2012. Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China. Virus Genes 45 (2): 340–349.CrossRefPubMedGoogle Scholar
  19. Goncalves, M.C., M.M. Klerks, M. Verbeek, J. Vega, and H. Jfjmvanden. 2002. The use of molecular beacons combined with NASBA for the sensitive detection of Sugarcane yellow leaf virus. European Journal of Plant Pathology 108 (5): 401–407.CrossRefGoogle Scholar
  20. Grisham, M.P., R.M. Johnson, and P.V. Zimba. 2010. Detecting Sugarcane yellow leaf virus infection in asymptomatic leaves with hyperspectral remote sensing and associated leaf pigment changes. Journal of Virological Methods 167 (2): 140–145.CrossRefPubMedGoogle Scholar
  21. Grisham, M.P., Y.B. Pan, B.L. Legendre, M.A. Godshall, G. Eggleston, and D.M. Hogarth. 2001. Effect of Sugarcane yellow leaf virus on sugarcane yield and juice quality. Proceedings-International Society of Sugar Cane Technology 24: 434–438.Google Scholar
  22. Lehrer, A.T., and E. Komor. 2008. Symptom expression of yellow leaf disease in sugarcane cultivars with different degrees of infection by Sugarcane yellow leaf virus. Plant Pathology 57 (1): 178–189.Google Scholar
  23. Lehrer, A.T., A. Kusalwong, and E. Komor. 2008. High incidence of Sugarcane yellow leaf virus (SCYLV) in sugar plantations and germplasm collections in Thailand. Australasian Plant Disease Notes 3 (1): 89–92.CrossRefGoogle Scholar
  24. Li, R., R. Mock, Q. Huang, J. Abad, J. Hartung, and G. Kinard. 2008. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of Virological Methods 154: 48–55.CrossRefPubMedGoogle Scholar
  25. Lin, Y.H., S.J. Gao, M.B. Damaj, H.Y. Fu, R.K. Chen, and T.E. Mirkov. 2014. Genome characterization of Sugarcane yellow leaf virus from China reveals a novel recombinant genotype. Archives of Virology 159 (6): 1421–1429.CrossRefPubMedGoogle Scholar
  26. Londoño, M.A., C.L. Harmon, and J.E. Polston. 2016. Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics. Virology Journal 13 (1): 1–9.CrossRefGoogle Scholar
  27. Mekuria, T.A., S.L. Zhang, and K.C. Eastwell. 2014. Rapid and sensitive detection of Little cherry virus 2 using isothermal reverse transcription-recombinase polymerase amplification. Journal of Virological Methods 205: 24–30.CrossRefPubMedGoogle Scholar
  28. Mondal, D., P. Ghosh, M.A.A. Khan, F. Hossain, S. Böhlkenfascher, G. Matlashewski, A. Kroeger, P. Olliaro, and A.A.E. Wahed. 2016. Mobile suitcase laboratory for rapid detection of Leishmania donovani using recombinase polymerase amplification assay. Parasites & Vectors 9 (1): 281–288.CrossRefGoogle Scholar
  29. Moonan, F., and T.E. Mirkov. 2002. Analyses of genotypic diversity among North, South, and Central American isolates of Sugarcane yellow leaf virus: Evidence for Colombian origins and for intraspecific spatial phylogenetic variation. Journal of Virology 76 (3): 1339–1348.CrossRefPubMedPubMedCentralGoogle Scholar
  30. Moonan, F., J. Molina, and T.E. Mirkov. 2000. Sugarcane yellow leaf virus: An emerging virus that has evolved by recombination between luteoviral and poleroviral ancestors. Virology 269 (1): 156–171.CrossRefPubMedGoogle Scholar
  31. Rohrman, B.A., and R.R. Richards-Kortum. 2012. A paper and plastic device for performing recombinase polymerase amplification of HIV DNA. Lab on a Chip 12 (17): 3082–3088.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Rosser, A., D. Rollinson, M. Forrest, and B.L. Webster. 2015. Isothermal recombinase polymerase amplification (RPA) of Schistosoma haematobium DNA and oligochromatographic lateral flow detection. Parasites & Vectors 8 (1): 446–450.CrossRefGoogle Scholar
  33. Rott, P., T.E. Mirkov, S. Schenck, and J.C. Girard. 2007. Recent advances in research on Sugarcane yellow leaf virus, the causal agent of sugarcane yellow leaf. Proceedings-International Society of Sugar Cane Technology 26: 968–977.Google Scholar
  34. Schenck, S., and A.T. Lehrer. 2007. Factors affecting the transmission and spread of Sugarcane yellow leaf virus. Plant Disease 84 (10): 1085–1088.CrossRefGoogle Scholar
  35. Silva, G., M. Bömer, C. Nkere, P.L. Kumar, and S.E. Seal. 2015. Rapid and specific detection of Yam mosaic virus by reverse-transcription recombinase polymerase amplification. Journal of Virological Methods 222: 138–144.CrossRefPubMedGoogle Scholar
  36. Tew, T.L., and R.M. Cobill. 2008. Genetic improvement of sugarcane (Saccharum spp.) as an energy crop. In Genetic improvement of bioenergy crops, ed. W. Vermerris, 273–294. New York: Springer.CrossRefGoogle Scholar
  37. Viswanathan, R., M. Balamuralikrishnan, and R. Karuppaiah. 2008. Identification of three genotypes of Sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization. Virus Genes 37 (3): 368–379.CrossRefPubMedGoogle Scholar
  38. Wang, M.Q., and G.H. Zhou. 2010. A near-complete genome sequence of a distinct isolate of Sugarcane yellow leaf virus from China, representing a sixth new genotype. Virus Genes 41 (2): 268–272.CrossRefPubMedGoogle Scholar
  39. Wang, M.Q., D.L. Xu, R. Li, and G.H. Zhou. 2012. Genotype identification and genetic diversity of Sugarcane yellow leaf virus in China. Plant Pathology 61 (5): 986–993.CrossRefGoogle Scholar
  40. Xu, C., L. Li, W.J. Jin, and Y.S. Wan. 2014. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops. International Journal of Molecular Sciences 15: 18197–18205.CrossRefPubMedPubMedCentralGoogle Scholar
  41. Xu, D.L., G.H. Zhou, X.P. Ren, Q.H. Shao, and S.H. Wu. 2005. Molecular identification of Sugarcane yellow leaf virus occurred at a sugarcane resources collecting station in Guangdong. Acta Phytopathologica Sinica 35 (5): 466–468. (in Chinese).Google Scholar
  42. Zhang, S.L., M. Ravelonandro, P. Russell, N. Mcowen, P. Briard, S. Bohannon, and A. Vrient. 2014. Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP® using reverse transcription-recombinase polymerase amplification. Journal of Virological Methods 207 (3): 114–120.CrossRefPubMedGoogle Scholar
  43. Zhou, D.G., C.F. Wang, Z. Li, Y. Chen, S.W. Gao, J.L. Guo, W.Y. Lu, Y.C. Su, L.P. Xu, and Y.X. Que. 2016. Detection of Bar transgenic sugarcane with a rapid and visual loop-mediated isothermal amplification assay. Frontiers in Plant Science 7: 279–289.PubMedPubMedCentralGoogle Scholar
  44. Zhou, G.H., J.G. Li, D.L. Xu, W.K. Shen, and H.H. Deng. 2006. Occurrence of Sugarcane yellow leaf virus in South China and its transmission by the sugarcane-colonizing aphid, Ceratovacuna lanigera. Scientia Agricultura Sinica 39 (10): 2023–2027. (in Chinese).Google Scholar
  45. Zhu, Y.J., H. Mccafferty, G. Osterman, S. Lim, R. Agbayani, A. Lehrer, S. Schenck, and E. Komor. 2011. Genetic transformation with untranslatable coat protein gene of Sugarcane yellow leaf virus reduces virus titers in sugarcane. Transgenic Research 20 (3): 503–512.CrossRefPubMedGoogle Scholar

Copyright information

© Society for Sugar Research & Promotion 2018

Authors and Affiliations

  • Xiao-Yan Feng
    • 1
  • Lin-Bo Shen
    • 1
  • Wen-Zhi Wang
    • 1
  • Jun-Gang Wang
    • 1
  • Zheng-Ying Cao
    • 1
  • Cui-Lian Feng
    • 1
  • Ting-Ting Zhao
    • 1
  • Shu-Zhen Zhang
    • 1
  1. 1.Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina

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