Detection and identification of viruses and viroids in nuclear grapevine material in South Africa
Date
2024-12
Authors
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Stellenbosch : Stellenbosch University
Abstract
Grapevine (Vitis spp.) is one of the most widely cultivated crops and one in which several viral
diseases exist, many of which can severely impact crop yield and grapevine health. It is therefore
necessary for the grapevine industry to be supplied with healthy and virus-free plant material. This
generally starts with virus-tested nuclear plants from which the entire industry’s material is
propagated. Over three years, 97 of these nuclear Vitis accessions were subjected to next
generation RNA sequencing for the identification of virus and virus-like agents present in these. Five
viruses were observed in six nuclear accessions and four viroids were identified and found to be
prevalent in the accessions. The viruses found were grapevine Rupestris stem pitting-associated
virus, grapevine fleck virus, grapevine Syrah virus, grapevine leafroll-associated virus 4, grapevine
Rupestris vein feathering virus, while the viroids hop stunt viroid (HSVd), grapevine yellow speckle
viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), and Australian grapevine viroid
(AGVd) were identified. In addition, grapevine hammerhead viroid-like RNA (GHVd) was also
detected, which is currently only considered a putative viroid species. The occurrence of grapevine
fleck virus (GFkV) as a single infection in accession BA8 of the nuclear material provided the
opportunity to obtain more definitive sequence data for this understudied virus. Fortuitously, a
second GFkV positive sample (I4233) was obtained in a parallel study and was therefore also
subjected to NGS analysis along with the isolate BA8. From these two RNA sequence datasets, two
genomes of GFkV were generated. For GFkV BA8, 77% of the putative whole genome was
assembled from NGS data, and PCR amplification, and Sanger sequencing of amplicons obtained
using primers designed to fill the gaps in the genome. A genome of 90% coverage was assembled
for sample I4233. Analysis revealed regions of high variability and high cytosine content. This study
has extended the sequence information available for this poorly characterised virus. Given the
presence of viroids in many of the nuclear accessions, and the availability of NGS datasets from the
South African Vitis germplasm collection, the viroid presence of the collection was assessed. This is
the first study on the diversity of grapevine infecting viroids in South Africa, which apart from
identifying five grapevine infecting viroids also provides only the second report of Japanese
grapevine viroid (JGVd) internationally and the first report of it outside of Japan.
Description
Thesis (PhDAgric)--Stellenbosch University, 2024.