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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #242170

Title: Sequence Diversity, Population Genetics and Potential Recombination Events in Rupestris stem pitting-associated virus in Pacific Northwest Vineyards

Author
item ALABI, O - Washington State University
item Martin, Robert
item NAIDU, R - Washington State University

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/11/2009
Publication Date: 1/4/2010
Citation: Alabi, O.J., Martin, R.R., Naidu, R.A. 2010. Sequence diversity, populationgenetics and potential recombination events in Rupestris stem pitting-associated virus in Pacific Northwest vineyards. Journal of General Virology. 91:265-276.

Interpretive Summary: Rupestris stem pitting-associated virus (RSPaV) is a graft-transmissible virus that is widely distributed in most grape growing regions of the world and part of the rugose wood virus complex. Cloning and sequencing of two sections of the genome of 57 isolates showed that this virus is very diverse with as low as 80% nucleic acid sequence identity between strains. This data along with previously published data on this virus suggest there are four major lineages of subspecies of RSPaV. In addition to the diversity within a specific region of the genome of RSPaV, it is clear that recombination has occurred with this virus, since isolates were identified with one part of the genome belonging to subspecies 1, with the second part of the genome clearly belonging to a second subspecies. The biological significance of the different subspecies is unknown at this time. Grafted vines often contained two distinct subspecies suggesting the scion and rootstock may have been infected with different RSPaV subspecies prior to grafting. In several vineyards that have been topworked (regrafted with a new cultivar), three subspecies of the virus were found in individual vines. Ungrafted vines, generally contained a single subspecies of the virus. The diversity of RSPaV in the Pacific Northwest was very high compared to other geographic regions, which may be explained by the diversity of grape cultivars grown in the region. The virus diversity highlights the need for careful selection of primers used for PCR detection.

Technical Abstract: Rupestris stem pitting-associated virus (RSPaV; genus Foveavirus; family Flexiviridae) is present in many grape-growing regions of the world. A total of 84 full-length coat protein (CP) sequences and 57 sequences representing the helicase-encoding region (HR) of the replicase gene were obtained from wine grape cultivars grown in the Pacific Northwest (PNW) region of the United States and their molecular diversity compared with corresponding sequences previously reported from other grape-growing regions. In pairwise comparisons, the CP sequences from PNW showed identities ranging between 80 and 100% at the nucleotide (nt) level and the HR sequences showed identities between 79 and 100%. A global phylogenetic analysis of the CP and HR sequences revealed segregation of RSPaV isolates into four major lineages with RSPaV isolates from PNW distributed in all four lineages, confirming a lack of clustering by geographical origin. Scion cultivars grafted onto rootstock were found to contain mixtures of more genetic variants belonging to different lineages than own-rooted cultivars. An assessment of population genetic parameters suggested that the CP is the most variable among the two coding regions. The discordant gene phylogenies obtained for some CP and HR sequences and the identification of potential intergenic recombination events involving parents from different lineages provided strong evolutionary evidence for genetic diversity among RSPaV isolates. These results underscored the highly variable nature of the virus with implications for grape production and distribution of virus-tested planting materials. This study also contributes to an increased understanding of molecular population genetics of viruses infecting deciduous woody perennials.