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United States Department of Agriculture

Agricultural Research Service

Research Project: INTEGRATED RESEARCH AND EDUCATION RELATED TO DEVELOPMENT OF A UNIVERSAL PLANT VIRUS MICROARRAY
2010 Annual Report


1a.Objectives (from AD-416)
To demonstrate the ability of an oligonucleotide microarray to detect and differentiate plant viruses from random amplification of plant total nucleic acid extracts, and to provide education, through training, of both undergraduate interns and a graduate student, and the incorporation of microarray techniques into curricula.


1b.Approach (from AD-416)
ARS will acquire the lists of viral taxa to be represented on the viral detection microarray, and virus-infected samples from which to amplify nucleic acids to validate the microarray. This information and material will be utilized by both ARS and the Cooperator to jointly develop and validate the microarray for detection of target viruses, and to make validation results available to collaborators via a web server. The COOPERATOR will perform analysis of viral sequences to identify suitable sequences for the development of oligonucleotides, and participate in analysis of microarray hybridization results to determine with a high degree of confidence which viruses were present in validation samples. The COOPERATOR will also integrate microarray techniques into curricula, and educate students on the theory and application of microarrays.


3.Progress Report

This research is part of a larger collaboration including USDA-ARS scientists at Beltsville, MD; the Donald Danforth Plant Science Center, St. Louis, MO; Washington University, St. Louis, MO; the University of Utah, Salt Lake City, UT; Oklahoma State University, Stillwater, OK; and Cornell University, Ithaca, NY. The overall goals are to be able to detect any plant virus in extracts of infected plants, and to identify previously characterized viruses to the species level, or previously uncharacterized viruses to at least the viral family or genus level.

Progress was made towards Utilization of the Universal Plant Virus Microarray oligonucleotide probe set to identify novel viruses in silico. The ability to control plant viral and viroid diseases requires the ability to correctly detect and identify the virus or viroid, and thus obtain knowledge about the likely vectors or other means of transmission. The ability to assign a previously uncharacterized virus to a known taxonomic group allows inference of many important characters, and facilitates the selection of appropriate methods to obtain further specific sequence information to develop specific detection and identification reagents. The first step in developing a Universal Plant Virus Microarray (UPVM) is to design and select oligonucleotide probes that will collectively provide information allowing identification of isolates of a previously characterized virus to the correct species, and of a previously uncharacterized species to the correct genus or family. A collaborating scientist at the University of Utah designed a set of oligonucleotides, each 60 nucleotides in length, and selected a subset of 9,392 oligonucleotides as the initial UPVM core probe set. The sequences of the UPVM core probe set were utilized as an additional bioinformatic screen of sequences derived from deep sequencing of ecological samples from the Plant Virus Biodiversity and Ecology study of tall grass prairie plants. Using the UPVM probe sequences as an in silico screening tool, two additional viral sequences were identified, which had not been identified by previously applied bioinformatic tools; these sequences represent a novel isolate of Cucumber mosaic virus, and a previously uncharacterized representative of the genus Ampelovirus. Additional analyses are being carried out to determine whether all novel viral sequences previously detected in tall grass prairie samples by deep sequencing are recognized by appropriate probes among the UPVM set. This information will be of most immediate application to the UPVM collaborators, but will also be of value to regulatory agencies, plant diagnostic clinics, germplasm repositories, and producers operating plant certification schemes.

Communications to monitor progress were carried out by e-mail and conference calls between the various partners, by a group meeting during the Annual meeting of the American Phytopathological Society, and by written and oral reports to the NRI Plant Biosecurity Program.


Last Modified: 12/22/2014
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