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http://dx.doi.org/10.5423/PPJ.OA.08.2013.0084

Development of the Large-Scale Oligonucleotide Chip for the Diagnosis of Plant Viruses and its Practical Use  

Nam, Moon (Institute of Plant Medicine, Kyungpook National University)
Kim, Jeong-Seon (Agricultural Microbiology Division, National Academy of Agricultural Science, RDA)
Lim, Seungmo (Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology)
Park, Chung Youl (School of Applied Biosciences, Kyungpook National University)
Kim, Jeong-Gyu (Department of Applied Biology, Chungnam National University)
Choi, Hong-Soo (Crop Protection Division, National Academy of Agricultural Science, RDA)
Lim, Hyoun-Sub (Department of Applied Biology, Chungnam National University)
Moon, Jae Sun (Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology)
Lee, Su-Heon (Institute of Plant Medicine, Kyungpook National University)
Publication Information
The Plant Pathology Journal / v.30, no.1, 2014 , pp. 51-57 More about this Journal
Abstract
A large-scale oligonucleotide (LSON) chip was developed for the detection of the plant viruses with known genetic information. The LSON chip contains two sets of 3,978 probes for 538 species of targets including plant viruses, satellite RNAs and viroids. A hundred forty thousand probes, consisting of isolate-, species- and genus-specific probes respectively, are designed from 20,000 of independent nucleotide sequence of plant viruses. Based on the economic importance, the amount of genome information, and the number of strains and/or isolates, one to fifty-one probes for each target virus are selected and spotted on the chip. The standard and field samples for the analysis of the LSON chip have been prepared and tested by RT-PCR. The probe's specific and/or nonspecific reaction patterns by LSON chip allow us to diagnose the unidentified viruses. Thus, the LSON chip in this study could be highly useful for the detection of unexpected plant viruses, the monitoring of emerging viruses and the fluctuation of the population of major viruses in each plant.
Keywords
Large-scale oligonucleotide chip; LSON chip; oligo chip; plant virus; virus diagnosis;
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1 Abdullahi, I., Gryshan, Y. and Rott, M. 2011. Amplificationfree detection of grapevine viruses using an oligonucleotide microarray. J. Virol. Methods 178:1-15.   DOI   ScienceOn
2 Boonham, N., Tomlinson, J. and Mumford, R. 2007. Microarrays for rapid identification of plant viruses. Annu. Rev. Phytopathol. 45:307-328.   DOI   ScienceOn
3 Boonham, N., Walsh, K., Smith, P., Madagan, K., Graham, I. and Barker, I. 2003. Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. J. Virol. Methods 108:181-187.   DOI   ScienceOn
4 Everett, K. R., Rees-George, J., Pushparajah, I. P. S., Janssen, B. J. and Luo, Z. 2010. Advantages and disadvantages of microarrays to study microbial population dynamics-a minireview. New Zealand Plant Protect. 63:1-6.
5 Lapa, S., Mikheev, M., Shchelkunov, S., Mikhailovich, V., Sobolev, A., Blinov, V., Babkin, I., Guskov, A., Sokunova, E., Zasedatelev, A., Sandakhchiev, L. and Mirzabekov, A. 2002. Species-level identification of orthopoxviruses with an oligonucleotide microchip. J. Clin. Microbiol. 40:753-757.   DOI
6 Lee, G. P., Min, B. E., Kim, C. S., Choi, S. H., Harn, C. H., Kim, S. U. and Ryu, K. H. 2003. Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit infection Tobamoviruses. J. Virol. Methods 110:19-24.   DOI   ScienceOn
7 Nicolaisen, M. 2011. An oligonucleotide-based microarray for detection of plant RNA viruses. J. Virol. Methods 173:134-143.
8 Lenz, O., Petrzik, K. and Spak, J. 2008. Investigating the sensitivity of a fluorescence- based microarray for the detection of fruittree virus. J. Virol. Methods 148:96-105.   DOI   ScienceOn
9 Nam, M., Park, S. J., Kim, Y. J., Kim, J. S., Park, C. Y., Lee, J. S., Choi, H. S., Kim, J. S., Kim, H. G. and Lee, S. H. 2012a. First report of Peanut stunt virus on Glycine max in Korea. Plant Pathol. J. 28:330.   과학기술학회마을   DOI   ScienceOn
10 Nam, M., Kim, J. S., Park, S. J., Park, D. Y., Lee, J. S., Choi, H. S., Kim, J. S., Kim, H. G., Lim, S. M., Moon, J. S. and Lee, S. H. 2012b. Biological and molecular characterization of soybean yellow common mosaic virus, a new species in the genus Sobemovirus. Virus Res. 163:363-367.   DOI   ScienceOn
11 Tiberini, A., Tomassoli, L., Barba, M. and Hadidi, A. 2010. Oligonucleotide microarray-based and identification of ten major tomato viruses. J. Virol. Methods 168: 133-140.   DOI   ScienceOn
12 Vernet, G. 2002. DNA-chip technology and infectious diseases. Virus Res. 82: 65-71.
13 Wang, D., Coscoy, L., Zylberberg, M., Avila, P. C., Boushey, H. A., Ganem, D. and DeRisi, J. L. 2002. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99:15687-15692.   DOI   ScienceOn
14 Wilson, W. J., Strout, C. L., DeSantis, T. Z., Stilwell, J. L., Carrano, A. V. and Andersen, G. L. 2002. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell Probes 16:119-127.   DOI   ScienceOn
15 Engel, E. A., Escobar, P. F., Rojas, L. A., Rivera, P. A. and Fiore, N. 2010. A diagnostic oligonu-cleotide microarray for simultaneous detection of grapevine viruses. J. Virol. Methods 163:445-451.   DOI   ScienceOn
16 Zhang, Y., Yin, J., Li, G., Li, M., Huang, X., Chen, H., Wenjun Zhao, W. and Zhu, S. F. 2010. Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses. J. Virol. Methods 167:53-60.   DOI   ScienceOn
17 Bystricka, D., Lenz, O., Mraz, I., Piherova, L., Kmoch, S. and Sip, M. 2005. Oligonucleotide-based microarray: a new improvement in microarray detection of plant viruses. J. Virol. Methods 128:176-182.   DOI   ScienceOn
18 Sainsbury, F., Canizares, M. C. and Lomonossoff, G. P. 2010. Cowpea mosaic virus: The plant virus-based biotechnology workhorse. Annu. Rev. Phytophthol. 48:437-455.   DOI   ScienceOn