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United States Department of Agriculture

Agricultural Research Service

Research Project: Physiology and Genetic Improvement of Small Fruit Crops Title: First report of Raspberry bushy dwarf virus in blackberry in Ecuador

Authors
item Quito-Avila, D -
item Peralata, E -
item Ibarra, M -
item Alvarez, R -
item Ratti, M -
item Espinoza, L -
item Martin, Robert

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 8, 2013
Publication Date: July 3, 2013
Citation: Quito-Avila, D.F., Peralata, E.L., Ibarra, M.A., Alvarez, R.A., Ratti, M.F., Espinoza, L., Martin, R.R. 2013. First report of Raspberry bushy dwarf virus in blackberry in Ecuador. Plant Disease. 97:1003.

Interpretive Summary: Through a cooperative project to determine virus risks for blackberry production in Ecuador and movement of plant material between the United States and Central America, a virus survey was carried out in blackberry in Ecuador. Raspberry bushy dwarf virus (RBDV) was found to be widespread in commercial blackberries in Ecuador. In addition, RBDV was found in symptomatic as well as in asymptomatic plants. This suggests that symptomatic plants are likely infected with multiple viruses, but at this time additional viruses have not been detected using dsRNA analysis or a range of primers specific for many different viruses known to occur in blackberry and raspberry in other parts of the world. Further work will focus on identifying additional viruses in the symptomatic plants and evaluating the potential risks these viruses pose to raspberry and blackberry production in other parts of the world.

Technical Abstract: During the past two decades, several viruses have been identified from Rubus (blackberry and raspberry) in wild and commercial plantings around the world (1) In Ecuador; approximately 14 tons of blackberries (Rubus glaucus) are produced each year in an estimated area of 5,500 hectares. This crop provides subsistence for hundreds of Ecuadorean families who produce and harvest the berry. Little has been done to identify viruses that could compromise the profitability of this crop. In 2012, a preliminary survey was conducted to determine the presence of viruses in ‘Castilla’ blackberry, the most common cultivar in Ecuador. Leaf samples were collected from symptomatic plants in several fields in the province of Azuay. Samples of 20g were used for double-stranded RNA (dsRNA) extraction. Three dsRNA segments of approximately 5 kbp, 2 kbp, and 900 bp were observed from all 12 dsRNA preparations. DsRNA was used as template for reverse transcription-polymerase chain reaction (RT-PCR) (2). PCR products were cloned using a StrataClone Kit (Agilent, USA) and sequenced. Sequence analysis revealed the presence of Raspberry bushy dwarf virus (RBDV), a pollen-borne idaeovirus naturally found in several Rubus species worldwide. Approximately 120 RBDV sequences obtained from the Ecuadorean isolate were assembled into two contigs belonging to RNA1 and RNA2. Both sequences were re-confirmed by RT-PCR using the original dsRNA as template and specific primers. Partial sequences were deposited in the NCBI GenBank and assigned the accession numbers KC315894, KC315893, and KC315892 for the replicase, MP and CP, respectively. Furthermore, blast searches showed that the nucleotide sequence corresponding to the replicase shared 95% identity with its closest relative—an isolate from the resistance breaking R15 strain (NCBI acc. numb. S51557.1)—(3). Whereas the MP and CP nucleotide sequences shared up to 98% identity with a Slovenian isolate (NCBI acc. numb. EU796088.1). Specific primers designed to amplify a 427 base fragment of the CP were used to detect the virus from several blackberry plantings in two distantly located production areas: Ambato in the province of Tungurahua, and Paute in the province of Azuay.A total of 90 leaf samples were randomly collected from both symptomatic and asymptomatic plants in each location. In Ambato, RBDV was detected in 50% and 40% of symptomatic and asymptomatic plants, respectively. In Paute, RBDV was present in 70% of symptomatic plants and 29% of asymptomatic plants. It is not known whether RBDV is the causal agent of the observed virus-like symptoms in plants sampled for this survey. However, the presence of RBDV in asymptomatic plants suggests otherwise, but RBDV may be part of virus complex that results in symptoms, which has been observed in other Rubus spp (4). Nevertheless, this is the first time that RBDV is reported form blackberry (R. glaucus) in Ecuador.

Last Modified: 10/22/2014
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