Research in Plant Disease (식물병연구)

The Korean Society of Plant Pathology (한국식물병리학회)
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Detection of Apple Scar Skin Viroid by Reverse Transcription Recombinase Polymerase Amplification Assay

  • Kim, Na-Kyeong (Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Lee, Hyo-Jeong (Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Ryu, Tae-Ho (Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University) ;
  • Cho, In-Sook (Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Ju, Ho-Jong (Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University) ;
  • Jeong, Rae-Dong (Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University)
  • Received : 2021.06.17
  • Accepted : 2021.06.29
  • Published : 2021.06.30
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Abstract

The aim of the present study was to develop a sensitive and specific detection method for the rapid detection of apple scar skin viroid (ASSVd) in apple leaves. The resulting reverse transcription recombinase polymerase amplification (RT-RPA) assay can be completed in 10 min at 42℃, is 10 times more sensitive than conventional reverse transcription polymerase chain reaction, and can specifically amplify ASSVd without any cross-reactivity with other common apple viruses, including apple stem grooving virus, apple stem pitting virus, and apple chlorotic leaf spot virus. The reliability of the RT-RPA assay was assessed, and the findings suggested that it can be successfully utilized to detect ASSVd in field-collected samples. The RT-RPA assay developed in the present study provides a potentially valuable means for improving the detection of ASSVd in viroid-free certification programs, especially in resource-limited conditions.

Keywords

Acknowledgement

This work was carried out with the support of Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ014947032021) Rural Development Administration, Republic of Korea.

References

  1. Diener, T. O. 2001. The viroid: biological oddity or evolutionary fossil? Adv. Virus Res. 57: 137-184. https://doi.org/10.1016/S0065-3527(01)57003-7
  2. Hadidi, A., Huang, C., Hammond, R. W. and Hashimoto, J. 1990. Homology of the agent associated with dapple apple disease to apple scar skin viroid and molecular detection of these viroids. Phytopathology 80: 263-268. https://doi.org/10.1094/Phyto-80-263
  3. Hammond, R. W. and Zhang, S. 2016. Development of a rapid diagnostic assay for the detection of tomato chlorotic dwarf viroid based on isothermal reverse-transcription-recombinase polymerase amplification. J. Virol. Methods 236: 62-67. https://doi.org/10.1016/j.jviromet.2016.06.013
  4. Hashimoto, J. and Koganezawa, H. 1987. Nucleotide sequence and secondary structure of apple scar skin viroid. Nucleic Acids Res. 15: 7045-7052. https://doi.org/10.1093/nar/15.17.7045
  5. Henson, J. M. and French, R. 1993. The polymerase chain reaction and plant disease diagnosis. Annu. Rev. Phytopathol. 31: 81-109. https://doi.org/10.1146/annurev.py.31.090193.000501
  6. Heo, S., Kim, H. R. and Lee, H. J. 2019. Development of a quantitative real-time nucleic acid sequence based amplification (NASBA) assay for early detection of apple scar skin viroid. Plant Pathol. J. 35: 164-171. https://doi.org/10.5423/PPJ.OA.10.2018.0206
  7. Higgins, M., Ravenhall, M., Ward, D., Phelan, J., Ibrahim, A., Forrest, M. S. et al. 2019. PrimedRPA: primer design for recombinase polymerase amplification assays. Bioinformatics 35: 682-684. https://doi.org/10.1093/bioinformatics/bty701
  8. Khan, S., Mackay, J., Liefting, L. and Ward, L. 2015. Development of a duplex one-step RT-qPCR assay for the simultaneous detection of apple scar skin viroid and plant rna internal control. J. Virol. Methods 221: 100-105. https://doi.org/10.1016/j.jviromet.2015.04.032
  9. Kim, D.-H., Kim, H.-R., Heo, S., Kim, S.-H., Kim, M.-A., Shin, I.-S. et al. 2010. Occurrence of apple scar skin viroid and relative quantity analysis using real-time RT-PCR. Res. Plant Dis. 16: 247-253. (In Korean) https://doi.org/10.5423/RPD.2010.16.3.247
  10. Kim, H. R., Lee, S. H., Lee, D. H., Kim, J. S. and Park, J. W. 2006. Transmission of apple scar skin viroid by grafting, using contaminated pruning equipment, and planting infected seeds. Plant Pathol. J. 22: 63-67. https://doi.org/10.5423/PPJ.2006.22.1.063
  11. Kim, N.-Y., Lee, H.-J., Kim, N.-K., Oh, J., Lee, S.-H., Kim, H. et al. 2019. Occurrence pattern of viral infection on pear in korea and genetic characterization of apple scar skin viroid isolates. Hortic. Sci. Technol. 37: 767-778.
  12. Kumar, S., Singh, L., Ram, R., Zaidi, A. A. and Hallan, V. 2014. Simultaneous detection of major pome fruit viruses and a viroid. Indian J. Microbiol. 54: 203-210. https://doi.org/10.1007/s12088-013-0431-y
  13. Lee, H.-J., Kim, H.-J., Lee, K. and Jeong, R.-D. 2020. Rapid detection of peach latent mosaic viroid by reverse transcription recombinase polymerase amplification. Mol. Cell Probes 53: 101627. https://doi.org/10.1016/j.mcp.2020.101627
  14. Lee, S. H., Ahn, G., Kim, M.-S., Jeong, O. C., Lee, J. H., Kwon, H. G. et al. 2018. Poly-adenine-coupled LAMP barcoding to detect apple scar skin viroid. ACS Comb. Sci. 20: 472-481. https://doi.org/10.1021/acscombsci.8b00022
  15. Osaki, H., Kudo, A. and Ohtsu, Y. 1996. Japanese pear fruit dimple disease caused by apple scar skin viroid (ASSVd). Jpn. J. Phytopathol. 62: 379-385. https://doi.org/10.3186/jjphytopath.62.379
  16. Panno, S., Matic, S., Tiberini, A., Caruso, A. G., Bella, P., Torta, L. et al. 2020. Loop mediated isothermal amplification: principles and applications in plant virology. Plants 9: 461. https://doi.org/10.3390/plants9040461
  17. Piepenburg, O., Williams, C. H., Stemple, D. L. and Armes, N. A. 2006. DNA detection using recombination proteins. PLoS Biol. 4: e204. https://doi.org/10.1371/journal.pbio.0040204
  18. Walia, Y., Kumar, Y., Rana, T., Bhardwaj, P., Ram, R., Thakur, P. D. et al. 2009. Molecular characterization and variability analysis of apple scar skin viroid in india. J. Gen. Plant Pathol. 75: 307-311. https://doi.org/10.1007/s10327-009-0168-y