Application of sequence-independent amplification (SIA) for the identification of RNA viruses in bioenergy crops

Bright O. Agindotan, Monday O. Ahonsi, Leslie L. Domier, Michael E. Gray, Carl A. Bradley

Research output: Contribution to journalArticlepeer-review

22 Scopus citations


Miscanthus× giganteus, energycane, and Panicum virgatum (switchgrass) are three potential biomass crops being evaluated for commercial cellulosic ethanol production. Viral diseases are potentially significant threats to these crops. Therefore, identification of viruses infecting these bioenergy crops is important for quarantine purposes, virus resistance breeding, and production of virus-free planting materials. The application is described of sequence-independent amplification, for the identification of RNA viruses in bioenergy crops. The method involves virus partial purification from a small amount of infected leaf tissue (miniprep), extraction of viral RNA, amplification of randomly primed cDNAs, cloning, sequencing, and BLAST searches for sequence homology in the GenBank. This method has distinct advantage over other virus characterization techniques in that it does not require reagent specific to target viruses. Using this method, a possible new species was identified in the genus Marafivirus in switchgrass related to Maize rayado fino virus, its closest relative currently in GenBank. Sugarcane mosaic virus (SCMV), genus Potyvirus, was identified in M× giganteus, energycane, corn (Zea mays), and switchgrass. Other viruses identified were: Maize dwarf mosaic virus (MDMV). , genus Potyvirus, in johnsongrass (Sorghum halepense); Soil borne wheat mosaic virus (SBWMV), genus Furovirus, in wheat (Triticum aestivum); and Bean pod mottle virus (BPMV), genus Comovirus, in soybean (Glycine max). The method was as sensitive as conventional RT-PCR. This is the first report of a Marafivirus infecting switchgrass, and SCMV infecting both energycane and M× giganteus.

Original languageEnglish
Pages (from-to)119-128
Number of pages10
JournalJournal of Virological Methods
Issue number1
StatePublished - Oct 2010

Bibliographical note

Funding Information:
We are grateful to British Petroleum (BP) and the Energy Biosciences Institute (EBI) , University of Illinois, Urbana-Champaign, for their support and funding of this research. We thank also the students and staff that established and maintained the SoyFACE farm at Savoy. We are grateful to Prof. Jerald K. Pataky, Department of Crop Sciences, University of Illinois, for providing us with MDMV-infected johnsongrass and SCMV-infected corn leaf samples. Special thanks to Dr. William Anderson, USDA/ARS Crop Genetics and Breeding Research Unit, Tifton, Georgia, for supplying the energycane stems, and Dr. Michael D. Casler, USDA-ARS, U.S. Dairy Forage Research Center, Madison, WI, for the switchgrass samples from his plot.


  • Energycane
  • Maize rayado fino virus
  • Miscanthus×giganteus
  • Random amplification
  • Sugarcane mosaic virus
  • Switchgrass

ASJC Scopus subject areas

  • Virology


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