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
Raspberry bushy dwarf virus (RBDV) is the sole member of the idaeovirus genus
of plant viruses. It is a pollen-borne virus that economically impacts both red and black
raspberries worldwide. Three ...strains of the bipartite RBDV have been reported. The
common strain found in North America, South America, Australia, New Zealand and
Europe and the resistance breaking strain found only in Europe are serologically
indistinguishable while the black raspberry strain from North America is distinct.
Resistance to RBDV is conferred by a single dominant gene, Bu. The resistance
breaking strain is able to infect all raspberry cultivars containing the Bu loci. The
sequence of a full-length clone of the common strain was determined and compared to
the previously published sequence of the resistance breaking strain. Nucleotide
homology between the two isolates was 97.6% for RNA 1 and 97.6% for RNA 2.
Comparison of the predicted RNA 1 protein product of the two strains showed 97.9%
homology. The predicted amino acid sequence of the movement protein and the coat
protein from RNA 2 demonstrated 98.6% and 98.5% identity respectively.
The differential rate of virus spread under field conditions in the Pacific
Northwest was also investigated. The possibility of higher temperatures inhibiting virus infected
pollen was explored by using in vitro germination and enzymatic staining
procedures. Results from a two year study of virus-infected and virus-free raspberry
pollen viability from both the Oregon and southern Washington region and the northern
Washington and southern British Columbia region suggest temperature does not affect
pollen germination or viability.
Further studies were conducted to determine if a virus-degrading agent could be
present on bee-stored raspberry pollen that becomes active only at higher temperatures.
RBDV infected pollen from hives in northern Washington was collected and tested by
ELISA after receiving either no heating or 32 hours of heating at 20, 30 or 40 C.
Preliminary results indicate no such agent exists in red raspberry pollen from hives in the
Pacific Northwest.
Graduation date: 2000
The effects of fenamiphos on soil and root populations of Pratylenchus
penetrans were evaluated in four red raspberry cv. Willamette fields in Northwestern
Oregon. Field 1 was a silty clay loam with ...53% organic matter (OM). Field 2 and
3 were silty loam soils with 3.25 and 2.55% OM, respectively and field 4 was a silty
clay with 7.1% OM. The nematicide, fenamiphos (10 kg a.i./ha) was applied in
broadcast or band treatments on November 15, 1989. Additional plots in field 3,
received a band-nematicide treatment on December 28, 1989 to evaluate the effect
of application date on the control of P. penetrans in red raspberry. Field 4 had plots
in sites with and without grass and weed ground cover in the aisles between raspberry
rows to examine effects of ground cover on nematicide efficacy. Nematodes from
soil and roots were sampled monthly from all plots in each field from October 1989
to October 1990.
Soil populations of P. penetrans sampled within rows decreased between the
October and December sampling dates in all four fields. Soil populations in 3 fields
increased in density during mid-summer and reached their highest peak in the middle
of September. A similar pattern occurred in P. penetrans soil populations from plots
with or without ground cover in aisles between rows of raspberry in field 4.
However, in this field, numbers increased in July and reached their peak density in
August. Root populations of P. penetrans from red raspberry reached their highest
number during spring and summer at all fields.
No significant (P>0.05) differences in effectiveness of fenamiphos were
detected between band and broadcast method of application and, also between the
2 application dates. Seasonal mean densities of soil populations from band
application was only significantly lower than in nontreated controls in areas with
ground cover in field 4, respectively. High variability in the numbers of P. penetrans
in soil and roots of raspberry was observed throughout the year. Therefore,
conclusions about the effectiveness of fenamiphos were difficult to assess.
The efficiency of Baermann funnels was 43.9%, when a known number of P.
penetrans was added to soil. Total yields of P. penetrans extracted from raspberry
roots by mist chamber root extraction (MCRE) were higher (P = 0.05) than yields
extracted by polyethylene plastic bag root incubation (PBRI). Approximately 90% of
the total P. penetrans recovered was achieved after three and seven days of
extraction for PBRI and MCRE, respectively. However, the extraction efficiency of
MCRE was 30% higher than PBRI and the daily recovery lasted 28 and 18 days,
respectively.
Graduation date: 1992
