Plant Pathol J > Volume 27(2); 2011 > Article
The Plant Pathology Journal 2011;27(2):148-155.
DOI: https://doi.org/10.5423/PPJ.2011.27.2.148    Published online June 30, 2011.
Genetic Reassortment of Rice stripe virus RNA Segments Detected by RT-PCR Restriction Enzyme Analysis-based Method
Miranda Gilda Jonson, Sen Lian, Hong Soo Choi, Gwan Seok Lee, Chang Suk Kim, Kook Hyung Kim
Abstract
Our previous sequence and phylogenetic analyses of the Korean Rice stripe virus (RSV) suggested possible genetic reassortment of RNA segments, but whether this RNA variation contributed to the recent RSV outbreaks in Korea is yet unclear. To further clarify these RSVRNA segment variations, we developed a reverse transcription- polymerase reaction/restriction enzyme (RTPCR/ RE) analysis-based method. We identified five REs, including DraI, EcoR1, NdeI/AseI, and SpeI, that could differentiate RSV RNA 1-4 subtypes, respectively. Our RT-PCR/RE results provided a clear pattern of RNA reassortment, i.e., different groups of isolates having their RNA segments derived from two to three different RSV ancestors, such as from Eastern and Southwestern Chinese or Japanese M and T isolates. We also found that the migratory small brown planthopper from Eastern China caught by aerial net traps that possesses RSVRNA3 genotypes corresponds mainly to Eastern China, with a few for Southwestern China based on RT-PCR/ RE, sequence and phylogenetic analyses, indicating that RSV populations in Eastern China may also have strong RNA variation. The development of an RE analysisbased method proved a useful epidemiological tool for rapid genotyping and identification of mixed infections by RSV strain and by different subtype.
Key Words: genotyping, genetic structure, phylogenetic relationships, restriction enzyme analysis, Rice stripe virus
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