The objective of this study was to characterize an unknown agent associated with
decline in black raspberry (Rubus occidentalis) in Oregon. A virus was found
consistently associated with decline symptoms of black raspberries and was named Black
raspberry decline associated virus (BRDaV). Double stranded RNA extraction from
BRDaV-infected black raspberry revealed the presence of two bands of approximately
8.5 and 7 kilobase pairs, which were cloned and sequenced. The complete nucleotide
sequences of RNA 1 and RNA 2 are 7581 nt and 6364 nt, respectively, excluding the 3'
poly(A) tails. The genome structure was identical to that of Strawberry mottle virus
(SMoV), with the putative polyproteins being less than 50% identical to that of SMoV
and other related sequenced viruses. The final 189 amino acids of the RNA-dependent-
RNA-polymerase (RdRp) reveal an unusual indel with homology to AlkB-like protein
domains, suggesting a role in repair of alkylation damage. This is the first report of a
virus outside the Flexiviridae and ampeloviruses of the Closteroviridae to contain these
domains. An RT-PCR test was designed for the detection of BRDaV from Rubus tissue.
BRDaV is vectored non-persistently by the large raspberry aphid Amphorophora
agathonica, the green peach aphid Myzus persicae, and likely nonspecifically by other
aphid species. Phylogenetic analysis of conserved motifs of the RdRp, helicase, and
protease regions indicate that BRDaV belongs to the Sadwavirus genus.
To assess the rate of spread BRDaV, four newly planted fields of black
raspberries (Rubus occidentalis) in Oregon were studied for three years. In an effort to
characterize the suspected complexity of synergistic interactions between BRDaV and
other Rubus-infecting viruses, the prevalence of ten additional Rubus viruses was also
monitored in the study fields. The timing of BRDaV infection as it relates to aphid
populations and flights was also determined. Testing of nearby vegetation identified
several symptomless Rubus hosts of BRDaV, as well as detection in multiple cultivars of
black raspberry and several non-Rubus weeds. It was determined that BRDaV spreads
rapidly with a low aphid threshold and consistently is associated with decline of black
raspberries in Oregon. / Graduation date: 2006
| Identifer | oai:union.ndltd.org:ORGSU/oai:ir.library.oregonstate.edu:1957/29931 |
| Date | 24 January 2006 |
| Creators | Halgren, Anne B. |
| Contributors | Martin, Robert R. |
| Source Sets | Oregon State University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
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