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Profiling Viral Infections in Grapevine Using a Randomly Primed Reverse Transcription-Polymerase Chain Reaction/Macroarray Multiplex Platform

First, third, and seventh authors: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca, NY 14850; second author: Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; fourth author: Department of Biology, Pamukkale University, Denizli 20070, Turkey; fifth author: Department of Pathology, University of Utah, 15 North Medical Drive East, Salt Lake City 84112; and sixth author: Houghton College, One Willard Avenue, Houghton, NY 14744.

Crop-specific diagnostics to simultaneously detect a large number of pathogens provides an invaluable platform for the screening of vegetative material prior to its propagation. Here we report the use of what is to-date the largest published example of a crop-specific macroarray for the detection of 38 of the most prevalent or emergent viruses to infect grapevine. The reusable array consists of 1,578 virus-specific 60 to 70mer oligonucleotide probes and 19 plant and internal control probes spotted onto an 18 × 7 cm nylon membrane. In a survey of 99 grapevines from the United States and Europe, virus infections were detected in 46 selections of Vitis vinifera, V. labrusca, and interspecific hybrids. The majority of infected vines (30) was singly infected, while 16 were mixed-infected with viruses from two or more families. Representatives of the four main virus families Betaflexiviridae, Closteroviridae, Secoviridae, and Tymoviridae present in grapevines were found alone and in combination, with a notable bias in representation by members of the family Tymoviridae. This work demonstrates the utility of the macroarray platform for the multiplex detection of viruses in a single crop, its potential for characterizing grapevine virus associations, and usefulness for rapid diagnostics of introduced material in quarantine centers or in certification programs.