First report of Pepper yellow dwarf strain of Beet curly top virus and spinach curly top Arizona virus in red table beet in Idaho, United States

Authors: Ramachandran, Vanitharani; Wyatt, Nathan; Rivera Santiago, Eric; NEHER, OLIVER - Amalgamated Sugar Company; WEILAND, JOHN - Beet Sugar Development Foundation; Bolton, Melvin

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/24/2023
Publication Date: 7/4/2023
Citation: Ramachandran, V., Wyatt, N.A., Rivera Santiago, E.E., Neher, O.T., Weiland, J.J., Bolton, M.D. 2023. First report of Pepper yellow dwarf virus, Spinach curly top Arizona virus, and Beet necrotic yellow vein virus in red table beet in Idaho, United States. Plant Disease. https://doi.org/10.1094/PDIS-12-22-2855-PDN.
DOI: https://doi.org/10.1094/PDIS-12-22-2855-PDN

Interpretive Summary: Curly top is an important diseases of sugar beet and vegetables that impacts quality and yield. The disease is caused by a group of viruses named curtoviruses. These viruses are transmitted to plants by leafhopper insects. Red table beet is a vegetable crop cultivated for both the leaves and roots that are consumed as vegetables. In the fall 2021, red table beet plants showing foliar symptoms resembling curly top disease and hairy roots, reminiscent of rhizomania, a devastating root disease of sugar beet caused by Beet necrotic yellow vein virus (BNYVV), were observed in a table beet production field in Idaho. Symptomatic leaves and roots were obtained and subjected to molecular methods that can provide the genomic sequence information of the virus. Application of these technologies enabled the identification of Pepper yellow dwarf strain of Beet curly top virus (BCTV-PeYD) and Spinach curly top Arizona virus (SpCTAV) associated with foliar symptoms; both belong to the genus Curtovirus as predicted. Further, analysis of root samples revealed the presence of BNYVV, indicating the occurrence of rhizomania in red table beet. To our knowledge, this is the first report of BCTV-PeYD, SpCTAV, and BNYVV infecting red table beet in Idaho, United States. The presence of multiple viruses in naturally infected red table beet indicates the need for rigorous monitoring of the production fields for pathogen identification and disease management.

Technical Abstract: In fall 2021, red table beet plants (Beta vulgaris L. cv. Eagle) exhibiting stunted growth and shorter petioles were observed at 10 to 15% incidence in a production field in Payette County, Idaho, United States. In addition to stunting, leaves had yellowing and mild curling and crumpling, and roots had hairy root symptoms. To identify potential causal viruses, total RNA was isolated from leaf and root tissue and subjected to high-throughput sequencing (HTS). Following adapter trimming and removal of host transcripts, 5.9 and 16.2 million reads were obtained from the leaf and root samples, respectively. BLAST search analysis of the de novo assembled leaf sample contigs identified a single contig of 2,845 nt (GenBank OP477336) that shared 96% coverage and 95.6% sequence identity to the pepper yellow dwarf strain of beet curly top virus (BCTV-PeYD, EU921828), and 98% coverage and 98.39% identity with an isolate of BCTV-PeYD (KX529650) from Mexico. To validate BCTV-PeYD detection, total DNA was isolated from the leaf sample and a 454-bp fragment of the C1 gene (replication-associate protein) was PCR amplified, and Sanger sequencing of the amplicon revealed 99.7% identity to the HTS assembled BCTV-PeYD sequence. Further, two contigs of 2,201 and 523 nt were assembled, generating a nearly complete genome of spinach curly top Arizona virus (SpCTAV) in the leaf sample with 99% coverage and 99.3% identity (OQ703946) to the reference genome of SpCTAV (HQ443515). To validate the HTS results, total DNA was isolated from the leaf tissue and PCR amplified a 442-bp fragment overlapping the V1, V2, and V3 ORFs, and its sequence had 100% identity with the HTS assembled SpCTAV. The root sample also showed HTS reads corresponding to BCTV-PeYD and SpCTAV. Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, was also detected in the root sample with 30% coverage, but no sequence reads matching BNYVV were detected in the leaf sample. To further confirm the BNYVV HTS results, total RNA was extracted separately from root and leaf tissue, and RT-PCR analysis generated the appropriate amplicons with expected sequences corresponding to the RNA-1, RNA-2, RNA-3, and RNA-4 of BNYVV as determined by Sanger sequencing. Similar to observations of BNYVV infection in conventional sugar beet varieties, no amplification was detected for BNYVV in the RNA from leaf tissue, so the RT-PCR results are consistent with the HTS. This is the first report of BCTV-PeYD and SpCTAV naturally infecting red table beet in Idaho, suggesting the geographical expansion of the viruses. The coexistence of BCTV-PeYD and SpCTAV with limited host range needs to be investigated to determine the actual cause of the observed leaf symptoms. This report provides a basis for research on the pathogenic nature of these viruses and their threat to red table beet and sugar beet production in Idaho.