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United States Department of Agriculture

Agricultural Research Service

Research Project: MICROARRAY DESIGN AND PREPARATION FOR UNIVERSAL PLANT VIRUS MICROARRAY
2011 Annual Report


1a.Objectives (from AD-416)
To develop and validate a universal plant virus microarray for detection and differentiation of plant viruses. To demonstrate the ability of an oligonucleotide microarray to detect and differentiate plant viruses from random amplification of plant total nucleic acid extracts.


1b.Approach (from AD-416)
ARS and the Cooperator will assemble 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, supervise production of the microarrays based on the selected oligonucleotides, perform assays to validate the array with as many viruses as possible from the collections of all cooperators, and participate in analysis of microarray hybridization results to determine with a high degree of confidence which viruses were present in validation samples.


3.Progress Report

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 the selection of appropriate methods to obtain further specific sequence information to develop specific detection and identification reagents. A total of 9,600 oligonucleotide probes were previously designed and selected to collectively provide information allowing identification of isolates of a previously characterized virus to the correct species, or identification of a previously uncharacterized species to the correct genus or family. To date several hundred UPVM slides have been printed and distributed to the various UPVM collaborating laboratories, where hybridization for validation and other testing of the UPVM is being carried out. UPVM collaborating laboratories include: USDA-ARS in Beltsville, MD; the Donald Danforth Center in St. Louis. MO; Oklahoma State University, Stillwater, OK; and Cornell University, Ithaca, NY. Analysis of the hybridizations performed by the collaborators is occurring through use of software developed by a UPVM collaborator at the University of Utah. 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, and by written and oral reports to the NRI Plant Biosecurity Program.


Last Modified: 10/22/2014
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