Soybean mosaic virus (SMV) is a prevalent pathogen that causes significant yield reduction in soybean production worldwide. SMV belongs to potyvirus and causes typical symptoms such as mild mosaic, mosaic and lethal necrosis. SMV is seed-borne and also transmitted by aphid. Eleven SMV strains, G1 to G7, G5H, G6H, G7H, and G7a were reported in soybean varieties in Korea. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) method allowed one-step detection of gene amplification by simple procedure and needed only a simple incubator for isothermal template. This RT-LAMP method allowed direct detection of RNA from virus-infected plants without thermal cycling and gel electrophoresis. In this study, we designed RT-LAMP primers named SML-F3/B3/FIP/BIP from coat protein gene sequence of SMV. After the reaction of RT-LAMP, products were identified by electrophoresis and with the detective fluorescent dye, SYBR Green I. under daylight and UV light. Opmtimal reaction condition was at 58℃ for 60min and the primers of RT-LAMP showed the specificity for nine SMV strains tested in this study.

Generally, the virus was detected by the ELISA using the serological method and RT-PCR based on the genetic information. Recently, NGS (next-generation nucleotide sequencing) has been used in genome analysis and diseases diagnostics. To identify distribution aspects of viruses, we collected diseased samples twice in soybean breeding field. After extraction of total RNA from the collected bulk samples, RNA was sequenced by the NGS method. The NGS data were analyzed using the bioinformatics software. With newly produced NGS data, the identification of distribution aspects of organisms in field was estimated in this study. Sequence based identification method should be more accurate diagnostic tools of the target diseases and be able to predict occurrence of potential and new pathogens. NGS method will also provide the basic data by identifying the distribution of using bacteria. In this study, we analyzed the extracted RNA from the collection of approximately 3000 samples. Consequently, we confirmed the following types: the 7,089 kinds of bacteria including Burkholderiaceae, the 13,397 kinds of Eukaryota, the 952 kinds of viruses from the first bulk samples, the 4,160 kinds of bacteria including Burkholderiaceae, the 10,475 kinds of Eukaryota, and the 576 kinds of viruses from the second bulk samples