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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #321613

Research Project: IMPROVED RESISTANCE TO SOYBEAN PATHOGENS AND PESTS

Location: Soybean/maize Germplasm, Pathology, and Genetics Research

Title: Assessment of common soybean-infecting viruses in Ohio, USA, through multisite sampling and high-throughput sequencing

Author
item Han, Junping - The Ohio State University
item Domier, Leslie
item Cassone, Bryan - The Ohio State University
item Qu, Feng - The Ohio State University

Submitted to: Plant Health Progress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2016
Publication Date: 6/10/2016
Citation: Han, J., Domier, L.L., Cassone, B.J., Qu, F. 2016. Assessment of common soybean-infecting viruses in Ohio, USA, through multisite sampling and high-throughput sequencing. Plant Health Progress. 17:133-140.

Interpretive Summary: Soybean provides essential nutrients for both humans and food animals, and is also an important source of bioenergy. Like major crops, soybean is a host of diverse microbial pathogens including many viruses that can significantly reduce yields and seed quality. To identify and quantify the viruses infecting soybean in Ohio, a survey was conducted during the 2011 and 2012 soybean growing seasons. Soybean leaf samples were collected from 80 soybean fields in 42 Ohio counties and analyzed by high-throughput sequencing. The surveys confirmed the widespread distribution of Bean pod mottle virus, Soybean vein necrosis virus, Tobacco ringspot virus and, to a lesser extent, Tobacco streak virus in Ohio soybean fields. It additionally revealed the occasional association of Alfalfa mosaic virus, Bean yellow mosaic virus, Clover yellow vein virus, and Soybean mosaic virus with soybean. Finally, our survey identified soybean Putnam virus, a new soybean-infecting pararetrovirus. This is the first state-wide survey of soybean viruses in Ohio, and the data are expected to offer guidance in the diagnosis and management of soybean virus problems in Ohio and neighboring states.

Technical Abstract: To assess the scope of virus disease problems of soybean in Ohio, USA, a survey was conducted during 2011 and 2012 soybean growing seasons. A total of 259 samples were collected from 80 soybean fields distributed in 42 Ohio counties, accounting for more than 90% of major soybean-growing counties in Ohio. A high throughput RNA-Seq approach was adopted to identify all viruses in the samples. To minimize sequencing costs, total RNA extracted from up to 20 samples were first pooled to make up regional pools, resulting in eight regional pools per year in both 2011 and 2012. These regional pools were further pooled into two master pools of RNA, one for each year, and subsequently processed for sequencing using the Illumina’s HiSeq2000 platform. Bioinformatic analyses of sequence reads led to the identification of signature sequences of nine different viruses. The field locations of these viruses were then mapped with PCR or RT-PCR. This survey confirmed the widespread distribution of Bean pod mottle virus, Soybean vein necrosis virus, Tobacco ringspot virus and, to a somewhat lesser extent, Tobacco streak virus in Ohio soybean fields. It additionally revealed the occasional association of Alfalfa mosaic virus, Bean yellow mosaic virus, Clover yellow vein virus, and Soybean mosaic virus with soybean. Finally, our survey identified soybean Putnam virus, a new soybean-infecting pararetrovirus. This is the first state-wide survey of soybean viruses in Ohio, and provides the much needed baseline information for the control and management of virus diseases of soybean.