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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #426160
Research Project: Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Genomic and biological characterization of blackberry calico virus

Author
item FAGER, DAN - Oregon State University
item Stockwell, Virginia
item Grinstead, Samuel
item MOLLOV, DIMITRE - Animal And Plant Health Inspection Service (APHIS)

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2025
Publication Date: 10/28/2025
Citation: Fager, D., Stockwell, V.O., Grinstead, S.C., Mollov, D. 2025. Genomic and biological characterization of blackberry calico virus. Plant Disease. https://doi.org/10.1094/PDIS-06-25-1232-RE.
DOI: https://doi.org/10.1094/PDIS-06-25-1232-RE

Interpretive Summary: Surveillance tools are needed to detect viruses that impact blackberry production, an important crop in Oregon. We sequenced a RNA virus from multiple blackberry cultivars with symptoms of blackberry calico disease and demonstrated that the virus and disease symptoms can be transmitted to healthy plants via grafting. We developed two specific detection methods for the virus for use in certification programs and clean plant centers that will help nursery growers produce blackberry plants without blackberry calico disease.

Technical Abstract: Over 40 million lbs. of blackberries are produced in the U.S., predominantly in Oregon. Blackberry calico disease (BCD) is known to occur in many commercial cultivars including Marionberry, which accounts for over half the Oregon blackberry production. BCD has been observed in a wide range of Rubus spp. hosts: in blackberry-raspberry hybrids, California blackberry (Rubus ursinus Cham. & Schltdl.), and in the naturalized variety Himalaya (R. armeniacus Focke) among others. Symptomatic blackberry plants were screened by high throughput sequencing. Nine genomic ssRNA virus sequences, ca. 8 kb, were obtained. BLAST analysis revealed these sequences share 75% identity with 24% query coverage at the nucleotide level with blackberry virus E (BVE), genus Allexivirus, family Alphaflexiviridae. Additionally, phylogenetic analysis grouped the newly sequenced blackberry virus within the allexiviruses. End-point RT-PCR and RT-qPCR based detection methods were developed for routine detection of the virus targeting the replicase and coat protein regions of the genome respectively. Graft bioassay analysis was carried out to observe the symptom development and transmission of the virus in blackberry, black raspberry, and red raspberry confirming the newly characterized virus is most likely the causal agent of blackberry calico disease.