Culinary rhubarb (Rheum spp.) comprises herbaceous perennials that are primarily clonally propagated. Like other asexually reproduced crops, rhubarb is vulnerable to virus transmission, but its virome remains poorly characterized. In April 2024, foliar virus-like symptoms including chlorotic and necrotic leaf spots, chlorosis, and stunting were observed on cultivar 'Kerwin' in the rhubarb collection at Cornell AgriTech in Geneva, NY. Symptomatic leaf tissue tested positive for tomato ringspot virus (ToRSV) in double antibody sandwich enzyme-linked immunosorbent assay using specific antibodies. Subsequently, the virome of 40 rhubarb entries was determined using high-throughput sequencing (HTS) and bioinformatic analyses. Sequence information suggested the presence of ToRSV (genus Nepovirus, family Secoviridae), cherry leafroll virus (CLRV, genus Nepovirus, family Secoviridae), Arabis mosaic virus (ArMV, genus Nepovirus, family Secoviridae), broad-leafed dock virus A (BLDVA, genus Macluravirus, family Potyviridae), tobacco streak virus (TSV, genus Ilarvirus, family Bromoviridae), and beet curly top virus (BCTV, genus Curtovirus, family Geminiviridae) in composite leaf samples. The occurrence of these RNA and DNA viruses was confirmed in composite and individual samples after deconvolution by RT-PCR or PCR, respectively, using one or two primer pairs, in combination with bidirectional Sanger sequencing of the amplicons. The symptoms of cultivar 'Kerwin' could not be definitively assigned to ToRSV due to co-infection with BLDVA. This is the first characterization of the rhubarb virome by HTS and the first report of ToRSV, BLDVA, TSV and BCTV in culinary rhubarb. These findings have implications for the propagation of clean material, distribution of germplasm, and future breeding efforts in rhubarb.
Elizabeth J Indermaur, Anna O Wunsch, H. McLane et al.· Phytopathology· 0 citations
To protect global strawberry production, clean plant programs rely on rigorous certification and quarantine testing to prevent the spread of disease. For decades, biological graft indexing has been the "gold standard" for virus detection; however, it often fails to identify viruses that remain latent in single infections or viruses requiring extended periods to induce symptoms. High throughput sequencing (HTS) offers an alternative that identifies all known and emerging viruses independent of the nucleotide sequences of their genomes including those undetected by traditional bioassays. This study compared HTS with graft indexing using 73 virus-infected donor plants, 584 indicator clones, and two replicates to evaluate HTS as a replacement for conventional graft bioassay testing. Donor material was analyzed via HTS and simultaneously grafted onto two replicates of four Fragaria indicator clones (UC-4, UC-5, UC-10, UC-11). Indicator symptoms were monitored weekly over eight weeks and again following natural dormancy. The RT-qPCR/RT-PCR testing for virus transmission was also conducted at eight weeks and after dormancy. HTS identified viral infections in all donor plants, detecting 17 different viruses across eight families, and revealing mixed infections in 75% of plants. In contrast, 83% of indicators developed symptoms within the current standard of eight weeks post graft. Only 61% of the indicator plants displayed symptoms both before and after dormancy, while 7% remained asymptomatic throughout despite receiving grafts from HTS-positive donors. Given the limitations of biological indexing, this research strongly supports the integration of HTS as a frontline detection tool to enhance the reliability and efficiency of certification programs.
Daniel Fager, M. Al Rwahnih, D. Mollov· Plant Disease· 0 citations
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