Assessment of common soybean-infecting viruses in Ohio, USA, through multi-site sampling and high-throughput sequencing

Junping Han, Leslie L. Domier, Bryan J. Cassone, Anne Dorrance, Feng Qu

Research output: Contribution to journalArticle

Abstract

Multi-site sampling was conducted during 2011 and 2012 to assess the scope of virus disease problems of soybean in Ohio, USA. 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 that share sufficient sequence similarities with known plant viruses. 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 yearly master pools of RNA, and sequenced using the Illumina's HiSeq2000 platform. Bioinformatic analyses of sequence reads led to the identification of signature sequences of nine different viruses. The originating locations of these viruses were then mapped with PCR or RT-PCR. This study confirmed the widespread distribution of Bean pod mottle virus, Soybean vein necrosis virus, Tobacco ringspot virus, and Tobacco streak virus in Ohio. It additionally revealed occasional association of Alfalfa mosaic virus, Bean yellow mosaic virus, Clover yellow vein virus, Soybean mosaic virus, and Soybean Putnam virus with Ohio soybean. This is the first statewide survey of soybean viruses in Ohio, and provides the muchneeded baseline information for management of virus diseases of soybean.

Original languageEnglish (US)
Pages (from-to)133-140
Number of pages8
JournalPlant Health Progress
Volume17
Issue number2
DOIs
StatePublished - Jan 1 2016

Fingerprint

soybeans
viruses
sampling
RNA
Clover yellow vein virus
Bean pod mottle virus
Tobacco streak virus
Tobacco ringspot virus
Bean yellow mosaic virus
Soybean mosaic virus
Alfalfa mosaic virus
information management
plant viruses
bioinformatics
necrosis
reverse transcriptase polymerase chain reaction

ASJC Scopus subject areas

  • Plant Science
  • Horticulture

Cite this

Assessment of common soybean-infecting viruses in Ohio, USA, through multi-site sampling and high-throughput sequencing. / Han, Junping; Domier, Leslie L.; Cassone, Bryan J.; Dorrance, Anne; Qu, Feng.

In: Plant Health Progress, Vol. 17, No. 2, 01.01.2016, p. 133-140.

Research output: Contribution to journalArticle

Han, Junping ; Domier, Leslie L. ; Cassone, Bryan J. ; Dorrance, Anne ; Qu, Feng. / Assessment of common soybean-infecting viruses in Ohio, USA, through multi-site sampling and high-throughput sequencing. In: Plant Health Progress. 2016 ; Vol. 17, No. 2. pp. 133-140.
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