In this study, we investigated the occurrence of viral diseases in the early growth stage of soybean to establish management practices. We collected 83 soybean samples showing abnormal symptoms, approximately 3–4 weeks after seeding in the breeding field of the National Institute of Crop Science. Viruses were detected in the collected samples using reverse transcription polymerase chain reaction (RT-PCR) and metatranscriptome analysis of all those samples. The incidence of viral diseases in the field was less than 1% overall and up to 50% in certain cultivars and lines. RT-PCR and metatranscriptome analysis detected Soybean yellow mottle mosaic virus (SYMMV), Soybean mosaic virus (SMV), Soybean yellow common mosaic virus, Peanut stunt virus, and soybean geminivirus A (SGVA). Among these detected viruses, SYMMV and SMV were identified as major viruses causing infection in the early growth stage of soybean, with detection rates of 53.7% and 42.6%, respectively. Soybeans infected with SYMMV showed typical mosaic symptoms, whereas those infected with SMV showed a variety of symptoms such as mosaic, mottle, stunt, and chlorotic spots. Transmission characteristics of these viruses are variable, such that SMV is primarily transmitted by seeds, whereas SYMMV could be transmitted by insects, soil, and seeds. In this study, SGVA was detected in the early growth stage of soybean, and research on the current status and its effects on soybean after the early growth stage should be conducted.
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