Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Infection of potatoes by viral pathogens causes reduced crop yield and subsequent economic loss. In
South Africa Potato virus Y (PVY) and Potato leafroll virus (PLRV) are the two most destructive viruses
infecting potatoes. Several other viral pathogens exist, including Potato virus X (PVX), Potato virus M
(PVM), Potato virus A (PVA), Potato virus S (PVS), Potato mop-top virus (PMTV), Tomato spotted wilt
virus (TSWV) and Potato spindle tuber viroid (PSTVd). Although the aforementioned pathogens are
found infecting potatoes around the world, there are no published information pertaining to the prevalence
of these viral agents in South Africa. Currently, the occurrence of PLRV infection in potatoes of South
Africa has reached epidemic proportions. A previous phylogenetic investigation undertaken in our
laboratory of South African PLRV isolates, using coat protein (CP) gene sequences, found large variation
between native South African PLRV isolates and most other isolates from elsewhere in the world; with
their nearest relatives being single isolates from Australia and North America.
In this study the incidence of PVX, PVM, PVA, PVS, PMTV, TSWV and PSTVd was investigated. A
large number of potato plant and tuber samples was collected and infected samples were identified with
reverse transcriptase polymerase chain reaction (RT-PCR) amplification of the CP gene or the whole
genome in the case of PSTVd. The amplified nucleic acid segments were sequenced, aligned with
international reference sequences and analysed phylogenetically to determine their relative relationships
with these reference sequences. The CP genes of PLRV isolates were sequenced and phylogenetically
investigated to determine how these new isolates compared relative to the previous findings from our
laboratory. In addition, the complete genomes of two PLRV isolates were sequenced and phylogenetically
investigated as a preliminary study to investigate the apparent increase of pathogenicity of certain variants
of South African PLRV.
Results obtained showed that only PVX and PVS were present in the samples collected and the
incidences of these viruses were very low (2.0 and 1.1% respectively). The phylogenetic analyses of the
CP genes, indicated that the PVX and PVS variants isolated in this study, were part of the dominant types
of variants found worldwide. From the analyses of the PLRV CP and whole genome sequences, it was
determined that many of the PLRV variants found in South Africa, are genetically distinctly different
from those around the world. This warrants further investigation into the increased pathogenicity
experienced with South African PLRV. / AFRIKAANSE OPSOMMING: Infeksie van aartappels deur virale patogene veroorsaak verlaagde opbrengs en gevolglike ekonomiese
verlies. In Suid-Afrika is Aartappelvirus Y (PVY) en Aartappelrolblad virus (PLRV) die twee mees
vernietigende virusse wat aartappels infekteer. Verskeie ander virale patogene, insluitend Aartappelvirus
X (PVX), Aartappelvirus M (PVM), Aartappelvirus A (PVA), Aartappelvirus S (PVS), Aartappel "moptop"
virus (PMTV), Kromnekvirus (TSWV) en Aartappel "spindle tuber" viroïed (PSTVd) kom ook
wêreldwyd in aartappels voor. Alhoewel hierdie virusse aartappels wêreldwyd besmet, is daar geen
gepubliseerde inligting met betrekking tot die voorkoms van hierdie virusse of die viroïed in Suid-Afrika
nie. Tans het die voorkoms van PLRV infeksie in aartappels in Suid-Afrika epidemiese proporsies bereik.
In 'n vorige filogenetiese ondersoek van die mantelproteïen (MP) nukleotiedvolgordes van Suid
Afrikaanse PLRV isolate in ons laboratorium, is groot variasie tussen hierdie inheemse isolate en die
meeste ander isolate van elders in die wêreld bevind. Die Suid Afrikaanse PLRV variante betree 'n unieke
intermediêre posisie tussen die internasionale isolate en enkele isolate van Australië en Amerika.
In hierdie studie is die voorkoms van PVX, PVM, PVA, PVS, PMTV, TSWV en PSTVd ondersoek.
Groot aantal aartappelplant en -knol monsters is versamel en infeksie is getoets met tru-transkripsie
polimerase kettingreaksie (RT-PCR) amplifisering van die MP geen, of die hele genoom in die geval van
PSTVd. Die nukleïensuurvolgordes is bepaal en vergelyk met internasionale verwysingsvolgordes. Die
relatiewe verhoudings tussen die bepaalde volgordes en die verwysingsvolgordes is geanaliseer met
filogeneties ontledings. Die MP gene van PLRV isolate se volgordes is bepaal en filogeneties ontleed om
hierdie nuwe isolate te vergelyk relatief tot vorige bevindinge in ons laboratorium. Die volledige genome
van twee PLRV isolate se volgordes is bepaal en filogeneties ontleed as 'n voorlopige studie om die
oënskynlike toename in patogenisiteit van Suid-Afrikaanse PLRV te ondersoek.
Resultate het getoon dat slegs PVX en PVS teenwoordig was in die monsters wat versamel is en dat die
voorkoms van hierdie virusse baie laag was (2.0% en 1.1% onderskeidelik). Die filogenetiese ontleding
van die MP gene het aangedui dat die Suid Afrikaanse variante van PVX en PVS, geisoleer in hierdie
studie, van die dominante tipes is wat mees gereeld internationaal voorkom. Uit die ontleding van die
PLRV MP en heelgenoom volgordes, is vasgestel dat baie van die PLRV variante wat in Suid-Afrika
aangetref word, geneties meer verskillend is as die van regoor die wêreld. Dus, regverdig dit, verdere
ondersoek van die verhoogde patogenisiteit van Suid Afrikaanse PLRV variante.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/80313 |
| Date | 03 1900 |
| Creators | Roos, Wiets Gideon |
| Contributors | Bellstedt, D. U., Stellenbosch University. Faculty of Science. Dept. of Biochemistry. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Detected Language | Unknown |
| Type | Thesis |
| Format | ix, 146 p. : col. ill. |
| Rights | Stellenbosch University |
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