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, 30 (1), 51-7

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


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

Moon Nam et al. Plant Pathol J.


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: LSON chip; Large-scale oligonucleotide chip; oligo chip; plant virus; virus diagnosis.


Fig. 1.
Fig. 1.
Hybridization patterns of the LSON chip analysis for detection. For each array, plant samples infected with 11 viruses from different genus were used. (A) Kyuri green mottle mosaic virus (KGMMV) in the genus Tobamovirus, (B) Tobacco rattle virus (TRV) in the genus Tobravirus, (C) Cowpea mild mottle virus (CPMMV) in the genus Carlavirus, (D) Zucchini yellow mosaic virus (ZYMV) in the genus Potyvirus, (E) Melon necrotic spot virus (MNSV) in the genus Carmovirus, (F) Tomato bushy stunt virus (TBSV) in the genus Tombusvirus, (G) Potato leafroll virus (PLRV) in the genus Luteovirus, (H) Tobacco ringspot virus (TRSV) in the genus Nepovirus, (I) Alfalfa mosaic virus (AMV) in the genus Alfamovirus, (J) Cucumber mosaic virus (CMV) in the genus Cucumovirus, (K) Tomato spotted wilt virus (TSWV) in the genus Tospovirus (L).
Fig. 2.
Fig. 2.
Detection of a new virus strain of Peanut stunt virus (PSV) in the soybean using the LSON chip. Specific probes of Peanut stunt virus (PSV) are indicated with red rectangles in block 5. Using a LSON chip would enable the detection of unexpected interactions such as infection of a new strain of PSV in the soybean, which has not been reported in Korea yet.
Fig. 3.
Fig. 3.
Sensitivity comparison using plant dilution sap extracted from both Pepper mild mottle virus (PMMoV)-infected and health plants between the LSON chip and PCR methods. Specific probes of PMMoV are indicated with red rectangles in block 14. PMMoV sample for sensitivity test was diluted with (A) undiluted sample, (B) 1:10, (C) 1:100, (D) 1:1000, (E) Sensitivity of RT-PCR with PMMoV specific primers.

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