A new protocol was developed to transmit BNYVV to sugar beet with Polymyxa betae zoospores in a soil-free controlled assay and genetically characterized organisms. A comparative transcriptomic analysis of the tripartite interaction in rhizomania was then applied. With this aim, transcriptomes from sugar beet roots inoculated with P. betae alone (five samples) or with BNYVV (six samples) were compared to the transcriptomes of healthy sugar beet (five samples).