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An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa
Thesisi (PhD)--Stellenbosch University, 2018.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2018
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| _version_ | 1867613852863037440 |
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| access_status_str | Open Access |
| author | Roos, Wiets Gideon |
| author2 | Bellstedt, D. U. |
| author_browse | Bellstedt, D. U. Roos, Wiets Gideon |
| author_facet | Bellstedt, D. U. Roos, Wiets Gideon |
| author_sort | Roos, Wiets Gideon |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesisi (PhD)--Stellenbosch University, 2018. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/103933 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:42:44.343Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/103933 An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa Roos, Wiets Gideon Bellstedt, D. U. Stellenbosch University. Faculty of Science. Dept. of Biochemistry. Pathogenic viruses Potato leafroll virus Potato industry Seed potatoes Thesisi (PhD)--Stellenbosch University, 2018. ENGLISH ABSTRACT: Potato production in South Africa has steadily intensified through improved pivot irrigation. Since potatoes are vegetatively propagated the potato industry is continuously threatened by Potato leafroll virus (PLRV) which is responsible for increasing yield losses in South Africa. Effective management of PLRV is dependent on its accurate detection in seed potato stocks. PLRV is a small spherical plant virus consisting of a protein capsid and an RNA genome of approximately 5900 bases. This virus is phloem restricted and is vectored by, most notably, by the green peach aphid. Plant RNA viruses pose a threat due to their high mutation rate and the ability to adapt rapidly to a changing environment. To effectively manage PLRV infection, detection of virus infection in seed potatoes is paramount. In this study, five field trials were carried out in potato production fields, to compare the commonly used DAS-ELISA with RT-PCR for PLRV detection. From the results obtained it was concluded that DAS-ELISA detection greatly underestimates the number of infected samples when compared to RT-PCR. The hotter climate of the Sandveld region appears to inhibit PLRV accumulation in infected plants and these infections then remain undetected by DAS-ELISA. PLRV isolates were sequenced and phylogenetic and bioinformatic analyses were performed to identify and characterise local variants of PLRV. PLRV isolates found in the Sandveld region were closely related to PLRV isolates from Australia. Some of these isolates had recombined with variants commonly found in Europe, Asia and the Americas as well as with those similar to PLRV isolates from Peru and Germany. Three locally produced cultivars were graft-inoculated with two PLRV isolates that represent the two main variant groups found to assess symptom development and yield reduction. Symptom development in locally produced cultivars was typical for PLRV. A yield loss resulted from this infection with no difference between the Australian type and the European/Australian recombinant type. The proteins produced by the newly sequenced isolates were further analysed in comparison to other isolates found worldwide. The variation in the proteins produced by the newly sequenced isolates was mainly due to recombination between distinct groups of PLRV in the 5’ half of the genome and through mutation in the 3’region of the genome. A differential RT-PCR was designed to distinguish, in a single reaction, between the Australian type and the European/Australian recombinant type of PLRV. This revealed that simultaneous infections with both types occurred commonly, and could explain why recombination has occurred. AFRIKAANSE OPSOMMING: Aartappelproduksie in Suid-Afrika het geleidelik teogeneem met behulp van verbeterde spilpuntbesproeiing. Aangesien aartappels vegetatief gepropageer word, word die aartappelbedryf deurlopend bedreig deur Aartappelrolbladvirus (PLRV) wat verantwoordelik is vir ‘n toename in opbrengsverliese in Suid-Afrika. Die effektiewe bestuur van PLRV is afhanklik van die akkurate opsporing van die virus in saad aartappels. PLRV is 'n klein sferiese plantvirus wat bestaan uit 'n proteïenkapsel en 'n RNA-genoom van ongeveer 5900 basisse. Hierdie virus is beperk tot die floëem en die mees effektiewe vektor is die groen perskesluis (M. persicae). Plant RNA-virusse is ook 'n bedreiging as gevolg van hul hoë mutasietempo en die vermoë om vinnig aan te pas by 'n veranderende omgewing. Om effektief PLRV infeksie te bestuur, is die opsporing van virusinfeksies in saadaartappels van die grootste belang. In hierdie studie is vyf veldproewe uitgevoer in aartappelproduksielande om die algemeen gebruikte DAS-ELISA te vergelyk met RT-PCR vir PLRV-opsporing. Uit die resultate wat verkry is, is bevind dat DAS-ELISA-opsporing die aantal besmette monsters aansienlik onderskat in vergelyking met RT-PCR. Die warm klimaat van die Sandveldstreek inhibeer PLRV-akkumulasie in geïnfekteerde plante en hierdie infeksies bly dan ongemerk deur die DAS-ELISA. Die volgordes van PLRV-isolate is bepaal en filogenetiese en bioinformatiese ontledings is uitgevoer om plaaslike variante van PLRV te identifiseer en te karakteriseer. PLRV-isolate wat in die Sandveldstreek gevind is, was nou verwant aan die PLRV-isolaat uit Australië. Sommige van hierdie isolate is gerekombineer met variante wat algemeen in Europa, Asië en die Amerikas voorkom, sowel as dié wat soortgelyk is aan PLRV-isolate uit Peru en Duitsland. Drie plaaslik gebruikte kultivars is ingeënt met twee PLRV-isolate wat die twee hoofvariantgroepe verteenwoordig om simptoomontwikkeling en opbrengsverlaging te bepaal. Simptoomontwikkeling in plaaslik vervaardigde kultivars was tipies vir PLRV. ‘n Opbrengsverlies het as gevolg van hierdie infeksie ontstaan, met geen verskil tussen die Australiese tipe en die Europese/Australiese rekombinante tipe nie. Die proteïene wat deur die nuwe opeenvolgende isolate geproduseer word, is verder ontleed in vergelyking met ander isolate wat wêreldwyd aangetref word. Die variasie in die proteïene wat deur die nuwe isolate geproduseer word, was hoofsaaklik te danke aan rekombinasie tussen afsonderlike groepe PLRV in die 5 'helfte van die genoom en deur mutasie in die 3'-streek van die genoom. ‘n Differensiële RT-PCR is ontwerp om in 'n enkele reaksie tussen die Australiese tipe en die Europese/Australiese rekombinante tipe PLRV te onderskei. Dit het aan die lig gekom dat gelyktydige infeksies met albei tipes algemeen voorkom, en kan verduidelik hoekom rekombinasie plaasgevind het. 2018-02-27T14:03:14Z 2018-04-09T11:48:22Z 2018-08-27T03:00:04Z 2018-03 Thesis http://hdl.handle.net/10019.1/103933 en_ZA Stellenbosch University 203 pages application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Pathogenic viruses Potato leafroll virus Potato industry Seed potatoes Roos, Wiets Gideon An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title | An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title_full | An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title_fullStr | An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title_full_unstemmed | An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title_short | An assessment of the diversity and pathogenicity of Potato leafroll virus in South Africa |
| title_sort | assessment of the diversity and pathogenicity of potato leafroll virus in south africa |
| topic | Pathogenic viruses Potato leafroll virus Potato industry Seed potatoes |
| url | http://hdl.handle.net/10019.1/103933 |
| work_keys_str_mv | AT rooswietsgideon anassessmentofthediversityandpathogenicityofpotatoleafrollvirusinsouthafrica AT rooswietsgideon assessmentofthediversityandpathogenicityofpotatoleafrollvirusinsouthafrica |