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Occurrence, detection, and variability of two new grapevine viruses in South Africa.
Thesis (MScAgric)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867613942907404288 |
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| access_status_str | Open Access |
| author | Lesailane, Mmapula |
| author2 | Pietersen, Gerhard |
| author_browse | Lesailane, Mmapula Pietersen, Gerhard |
| author_facet | Pietersen, Gerhard Lesailane, Mmapula |
| author_sort | Lesailane, Mmapula |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125915 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:44:09.875Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125915 Occurrence, detection, and variability of two new grapevine viruses in South Africa. Lesailane, Mmapula Pietersen, Gerhard Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Grapevine Pinot gris virus -- Diagnosis Grapevine rupestris vein feathering virus -- Diagnosis Vitis vinifera (grapevine) -- Economic aspects Grapes -- Virus diseases -- South Africa UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Grapevine Pinot gris virus (GPGV) and Grapevine rupestris vein feathering virus (GRVFV) are two apparently widespread, emerging viruses internationally, that have not been reported in South Africa, but have also not been actively tested for locally. To determine the presence of these two viruses in well-established cultivars in South Africa, a total of 229 grapevine samples Illumina data sets from the Vitis Gene bank were analysed for the presence of GPGV and GRVFV using CLC genomics workbench. Reference mapping at determined optimal stringencies and de novo synthesis using bioinformatics tools were used for analysis. The presence or absence of these viruses was confirmed using RT-PCR and ELISA tests. GPGV was not detected in any of the vines from the Vitis spp. Germplasm bank. As GPGV was recently intercepted in imported planting material we also wished to determine whether this virus is present in other relatively recently imported grapevine planting material to South Africa. Field and greenhouse samples were selected after an ELISA survey testing of recently imported plant material from numerous plant improvement organisations. Using a selection of the GPGV infected, recently imported material, we determined several detection parameters for this virus. In summer (2020), 41 of the 150 imported samples yielded absorbances values greater than the threshold. Six samples were selected and tested in all four seasons, they all yield positive results. The optimal detection time for GPGV was determined to be either in spring using fresh young leaves, or in winter using phloem scrapings of matured canes. 28 samples from 2020 were retested in spring (optimal season) and all yielded positive RT-PCR results. Field sample 20-1587, analysed during this study, was found to be GPGV infected even after having undergone meristem-tip excision and thermotherapy treatment. GRVFV was detected in 36 samples (as per reference mapping analysis and de novo assembly) from the Vitis spp. Germplasm bank. Of the 36 pooled samples containing GRVFV, 14 appeared to have a co-infection with grapevine fleck virus (GFkV) a related virus in the Marafivirus genus, among other viruses. A subset of 28 GRVFV positive accessions were selected and confirmed to be positive using RT-PCR and Sanger sequencing. This study was unable to associate any symptom with GRVFV due to the large number of other viruses present. AFRIKAANSE OPSOMMING: Grapevine Pinot gris virus (GPGV) en Grapevine rupestris vein feather virus (GRVFV) is twee skynbaar wydverspreide, opkomende virusse internasionaal, wat nie in Suid- Afrika aangemeld is nie, maar ook nie aktief vir plaaslik getoets is nie. Om die teenwoordigheid van hierdie twee virusse in goed gevestigde kultivars in Suid-Afrika te bepaal, is 'n totaal van 229 wingerdmonsters Illumina datastelle van die Vitis spp. Gene bank ontleed vir die teenwoordigheid van GPGV en GRVFV met behulp van CLC genomics werkbank. Verwysingskartering by bepaalde optimale stringensies en de novo sintese met behulp van bioinformatika-instrumente is vir analise gebruik. Die teenwoordigheid of afwesigheid van hierdie virusse is bevestig met behulp van RT- PCR en ELISA toetse. GPGV is nie in enige van die wingerde van die Vitis Germplasm-bank opgespoor nie. Aangesien GPGV onlangs in ingevoerde plantmateriaal onderskep is, wou ons ook vasstel of hierdie virus teenwoordig is in ander relatief onlangs ingevoerde wingerdplantmateriaal na Suid-Afrika. Veld- en kweekhuismonsters is gekies na 'n ELISA-opnametoetsing van onlangs ingevoerde plantmateriaal van talle plantverbeteringsorganisasies. Deur 'n seleksie van die GPGV-geïnfekteerde, onlangs ingevoerde materiaal te gebruik, het ons verskeie opsporingsparameters vir hierdie virus bepaal. In die somer (2020) het 41 van die 150 ingevoerde monsters absorbansiewaardes groter as die drempel gelewer. Ses monsters is in al vier seisoene geselekteer en getoets, hulle lewer almal positiewe resultate. Die optimale opsporingstyd vir GPGV is bepaal om óf in die lente te wees deur vars jong blare te gebruik, óf in die winter deur gebruik te maak van floëemskraapsels van volwasse riete. 28 monsters van 2020 is in die lente (optimale seisoen) hertoets en almal het positiewe RT-PKR resultate opgelewer. Veldmonster 20-1587, wat tydens hierdie studie ontleed is, is gevind dat dit GPGV-geïnfekteer is selfs nadat dit meristeempunt-uitsnyding en termoterapiebehandeling ondergaan het. GRVFV is opgespoor in 36 monsters (soos per verwysing kartering analise en de novo samestelling) van die Vitis spp. Germplasm bank. Van die 36 saamgevoegde monsters wat GRVFV bevat, het 14 blykbaar 'n mede-infeksie gehad met wingerdvlekvirus (GFkV), 'n verwante virus in die Marafivirus genus, onder andere virusse. 'n Subset van 28 GRVFV positiewe toetredings is geselekteer en bevestig as positief deur gebruik te maak van RT-PCR en Sanger volgordebepaling. Hierdie studie was nie in staat om enige simptoom met GRVFV te assosieer nie as gevolg van die groot aantal ander virusse teenwoordig. Masters 2022-10-25T10:08:36Z 2023-01-16T12:41:07Z 2022-10-25T10:08:36Z 2023-01-16T12:41:07Z 2022-12 Thesis http://hdl.handle.net/10019.1/125915 en_ZA Stellenbosch University xiv, 93 pages : illustrations (some color), maps application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapevine Pinot gris virus -- Diagnosis Grapevine rupestris vein feathering virus -- Diagnosis Vitis vinifera (grapevine) -- Economic aspects Grapes -- Virus diseases -- South Africa UCTD Lesailane, Mmapula Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title | Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title_full | Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title_fullStr | Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title_full_unstemmed | Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title_short | Occurrence, detection, and variability of two new grapevine viruses in South Africa. |
| title_sort | occurrence detection and variability of two new grapevine viruses in south africa |
| topic | Grapevine Pinot gris virus -- Diagnosis Grapevine rupestris vein feathering virus -- Diagnosis Vitis vinifera (grapevine) -- Economic aspects Grapes -- Virus diseases -- South Africa UCTD |
| url | http://hdl.handle.net/10019.1/125915 |
| work_keys_str_mv | AT lesailanemmapula occurrencedetectionandvariabilityoftwonewgrapevinevirusesinsouthafrica |