Abstract
Soybean (Glycine max L.) is one of the most important crop plants in the Republic of Korea. Here, we conducted a soybean virome study. We harvested a total of 172 soybean leaf samples showing disease symptoms from major soybean-growing regions in the Republic of Korea. Individual samples were examined for virus infection by RT-PCR. Moreover, we generated eight libraries representing eight provinces by pooling samples and four libraries from single samples. RNA-seq followed by bioinformatics analyses revealed 10 different RNA viruses infecting soybean. The proportion of viral reads in each transcriptome ranged from 0.2 to 31.7%. Coinfection of different viruses in soybean plants was very common. There was a single dominant virus in each province, and this geographical difference might be related to the soybean seeds that transmit viruses. In this study, 32 viral genome sequences were assembled and successfully used to analyze the phylogenetic relationships and quasispecies nature of the identified RNA viruses. Moreover, RT-PCR with newly developed primers confirmed infection of the identified viruses in each library. Taken together, our soybean virome study provides a comprehensive overview of viruses infecting soybean in eight geographical regions in the Republic of Korea and four single soybean plants in detail.
Highlights
Soybean (Glycine max L. (Merrill)), a legume species native to East Asia, is widely cultivated and consumed in many Asian countries
We examined infection of virus in 172 soybean leaf samples by reversetranscription-polymerase chain reaction (RT-PCR) using virus-specific primer pairs for five viruses: Soybean mosaic virus (SMV), Soybean yellow mottle mosaic virus (SYMMV), Soybean yellow common mosaic virus (SYCMV), Peanut mottle virus (PeMoV), and Peanut stunt virus (PSV)
RT-PCR results showed that most soybean samples except three samples were infected by at least a single virus (Table S1)
Summary
Soybean (Glycine max L. (Merrill)), a legume species native to East Asia, is widely cultivated and consumed in many Asian countries. Diverse diseases and insects can seriously affect soybean production [1]. Several viruses infecting soybean are major problems [2]. Soybean mosaic virus (SMV) in the genus Potyvirus (the family Potyviridae) is the most prevalent and destructive soybean virus in the world [2]. In the United States, seven different strains (G1–G7) from various SMV isolates have been classified according to their response to susceptible and resistant soybean cultivars [3], whereas 21 different SMV strains (SC1–SC21) have been identified in China [4]. Bean pod mottle virus (BPMV) in the genus Comovirus (the family Secoviridae) has been widespread in the United States, reducing yield and seed quality [5]
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