Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses.
ABSTRACT A major challenge facing agriculture at present is the development of techniques that can screen field samples and other plant materials simultaneously for the presence of many viruses. Microarray techniques show promise in this regard, as their high throughput nature can potentially detect a range of viruses using a single test. In this paper we present an array that can detect a wide spectrum of 169 plant virus species from 13 different genera. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viruses at the genus level. The designed arrays showed a high specificity and sensitivity when tested with a set of standard virus samples. Field samples collected from a severe disease outbreak of Panax notoginseng farms in Yunnan, China, in 2001 were screened, where a potyvirus infection was identified associated with the disease.
- SourceAvailable from: Hong-Soo Choi[Show abstract] [Hide abstract]
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.The plant pathology journal 03/2014; 30(1). · 0.76 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: The ability to correctly identify species in a rapid and reliable manner is critical in many situations. Especially for insects the primary tools for such identifications rely on adult stage morphological characters. For a number of reasons, however, there is a clear need for alternatives. Here we report on the development of a new method employing DNA-biochip technology for the identification of pest species within the family Tephritidae. The DNA-biochip developed and tested here quickly and efficiently identifies and discriminates between several Tephritid species, except for some that are members of a complex of closely related taxa and which may in fact not represent distinct biological species. The use of these chips offers a number of potential advantages over current methods. Results can be obtained in less than 5 hours using material from any stage of the life cycle and with greater sensitivity than other methods currently available. This technology provides a novel tool for the rapid and reliably identification of several major pest species that may be intercepted in imported fruits or other commodities. The existing chips can also easily be expanded to incorporate additional markers and species as needed.Pest Management Science 11/2013; 70(8). · 2.74 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: A disease, supposedly caused by a virus, was observed from Insam (Panax ginseng) fields of Punggi in year 2006. It has long believed to be a physiological disorder. However, the incidence of the disease has increased every year. When several samples were observed under electron microscope, filamentous virus-like particles were observed. The nucleotide sequences of the virus were analyzed by RT-PCR with specific primer sets derived from the results of DNA chip. The results indicated that the disease was caused by Watermelon mosaic virus (WMV). It revealed that the result of the biological assay by the virus was different from that of WMV previously found in other crops. Therefore, this is the first report that WMV causes the disease in P. ginseng and the virus is named to be WMV-Insam.Research in Plant Disease. 12/2013; 19(4).