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Poster: Diseases of Plants: Disease Detection & Diagnosis


Rubus yellow net virus: an integrated element in the raspberry genome
A. Diaz-Lara (1), N. Mosier (2), K. Keller (2), R. Martin (2) (1) Oregon State University, U.S.A.; (2) USDA-ARS Horticultural Crops Research Unit, U.S.A.

Rubus yellow net virus (RYNV) infects Rubus spp. causing a serious decline when present in mixed infections and a vein chlorosis in indicator plants. RYNV belongs to the family Caulimoviridae, which can exist as infectious particles (exogenous) or integrated elements (endogenous). It was observed that RYNV PCR-positive plants often did not induce symptoms in bioassays, suggesting an integrated element. Molecular techniques were used to discriminate between exogenous and endogenous RYNV sequences. Reverse transcription-PCR using RYNV specific primers after DNase treatment produced positive results for the virus in graft transmissible isolates only. To confirm these results, rolling circle amplification on DNA preparations from these plants resulted in amplicons whose sequence belonged to RYNV. This suggested that graft-transmissible isolates contained an exogenous version of the virus. In Southern blot analysis using Rubus genomic DNA digested with BamHI (one recognition site in the RYNV genome), samples that were positive in bioassays for RYNV gave a single band the size of the RYNV genome, while plants with non-transmissible isolates produced three extra bands. Next generation sequencing and appropriate bioinformatics programs are being used to identify the specific integration sites. These results show that RYNV can be integrated into the raspberry genome and highlight the need to consider this phenomenon in future Rubus quarantine and certification programs.