Identification of early indicators of CTV induced stem pitting to aid the selection of CTV cross protection sources.

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dc.contributor.advisorMaree, H. J. en_ZA
dc.contributor.advisorBester, Rachelleen_ZA
dc.contributor.authorVan Wyk, Lukaen_ZA
dc.contributor.otherStellenbosch University. Faculty of Agrisciences. Dept. of Genetics.en_ZA
dc.date.accessioned2024-02-23T08:54:23Z
dc.date.accessioned2024-04-26T10:52:49Z
dc.date.available2024-02-23T08:54:23Z
dc.date.available2024-04-26T10:52:49Z
dc.date.issued2024-03
dc.descriptionThesis (MScAgric)--Stellenbosch University, 2024. en_ZA
dc.description.abstractENGLISH ABSTRACT: Citrus tristeza virus (CTV) is the most impactful viral pathogen of citrus, having caused the death of more than 100 million citrus trees. CTV elicits several disease syndromes, but continues to affect citrus production through stem pitting disease phenotypes of varying severity. These phenotypes reduce citrus tree productivity and result in smaller, unmarketable fruit. Stem pitting is incompletely characterised, and the mechanisms underlying its induction remain elusive. This poses limitations regarding our understanding of CTV-induced stem pitting and the management thereof. This study aimed to better understand the plant-pathogen interactions underlying stem pitting in CTV-infected citrus over the course of disease onset from an untargeted perspective. To this end, high-throughput sequencing and ultra-performance liquid chromatography-mass spectrometry were used to profile the transcriptome and metabolome of ‘Mexican’ lime and ‘Duncan’ grapefruit plants infected with T3-KB, T68, and RB isolates of CTV. This profiling was carried out prior to infection, early post-infection, and after symptom development, with the goal of identifying determinants of severe CTV-induced stem pitting. It was shown that secondary metabolite profiles of ‘Mexican’ lime plants were able to clearly discern between CTV infections at ten months post-infection. These profiles indicated a common dysregulation of carbohydrate metabolism over disease onset and provided a putative identification of the furcatin molecule as a major driver of differentiation. Similarly, differential gene expression analysis implicated a carbohydrate metabolism gene, along with seven others, as significantly different in severely pitted, T3-KB infected ‘Mexican’ lime plants. These genes were consistently upregulated over the course of disease onset. This provided a candidate metabolic pathway for further study and eight candidate genes to be validated as determinants of CTV-induced stem pitting severity. The characterization of hypersensitive response and systemic acquired resistance in citrus due to CTV infection was also discussed. It was speculated that determinants of stem pitting severity may lie earlier in the infection progression of CTV within the hypersensitive response of citrus. Carbohydrate metabolism was also putatively associated as a factor of systemic acquired resistance in response to CTV infection. This emphasized the importance of the temporal component of citrus’ response to CTV infection that has only been studied in a limited capacity thus far. The utility of complementary transcriptomic and metabolomic analyses was also demonstrated, and the findings therefrom contribute to the understanding of plant responses to CTV over time.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Citrus tristeza virus (CTV) word geag as een van die mees impakvolle virale patogene van sitrus, wat direk tot die dood van meer as 100 miljoen sitrusbome lei. CTV lok verskeie siektesindrome uit, maar bly sitrusproduksie beïnvloed deur verskillende grade van stamputting siektefenotipes. Hierdie fenotipes verminder sitrusboomproduktiwiteit en lei tot kleiner, onverkoopbare vrugte. Stamputting bly onvolledig gekarakteriseer, en die onderliggende meganismes wat dit inlei, bly onduidelik. Daarvolgens, bly ons begrip van CTV-geïnduseerde stamputting en gevolglik, effektiewe bestuur daarvan, beperk. Gegewe die, het die studie daarop gemik om die plant-patogeeninteraksies wat onderliggend is aan stamputting in CTV-besmette sitrus beter te verstaan oor die verloop van siekteontwikkeling deur ‘n ongerigte benadering te implementeer. Deur gebruik te maak van hoëdeurset-opeenvolging en ultraprestasie-vloeistofchromatografie-massaspektrometrie, is die transkriptoom en metaboloom van ‘Mexican’ lemoen en ‘Duncan’ pompelmoes plante wat met T3-KB, T68, en RB isolate van CTV besmet is, verder geprofileer. Hierdie profilering is uitgevoer voor infeksie, vroeg na infeksie, en na simptoomontwikkeling, met die doel om bepalers van ernstige CTV- geïnduseerde stamputting te identifiseer. Sekondêre metabolietprofiele van ‘Mexican’ lemoen plante kon duidelik onderskei tussen CTV-infeksies tien maande na infeksie. Hierdie profiele het 'n algemene ontwrigting van koolhidraatmetabolisme oor siekteontwikkeling aangedui en 'n vermoedelike bevinding van die Furcatin-molekuul as 'n hoofdrywer van differensiasie verskaf. Soortgelyk het differensiële geen-uitdrukkinganalise 'n koolhidraatmetabolismegeen, tesame sewe ander, as beduidend verskillend in ernstig gepitte, T3-KB besmette ‘Mexican’ lemoen plante identifiseer. Hierdie gene is gevolglik opgereguleer oor die verloop van siekteontwikkeling. Dit het 'n kandidaatmetaboliese pad vir toekomstige studies asook agt kandidaatgene verskaf om as bepalers van CTV-geïnduseerde stamputtingsiektestoestande te dien. Die karakterisering van die hipersensitiewe reaksie en sistemiese verwerfde weerstand in sitrus as gevolg van CTV-infeksie is bespreek. Verder, is daar bespiegel dat bepalers van stamputtingsiektestoestande vroeër in die infeksieverloop van CTV tydens die hipersensitiewe reaksie van sitrus mag lê. Koolhidraatmetabolisme is ook vermoedelik geïdentifiseer as 'n faktor van sistemiese verwerfde weerstand in reaksie op CTV-infeksie. Dit het die belangrikheid van die tydsverloop van sitrus se reaksie op CTV-infeksie beklemtoon wat tot dusver slegs in 'n beperkte kapasiteit bestudeer is. Die nut van komplementêre transkriptomiese en metabolomiese ontledings is ook bespreek, en die bevindinge daaruit dra by tot die begrip van plantreaksies op CTV oor die verloop van tyd.af_ZA
dc.description.versionMastersen_ZA
dc.format.extentxii, 88 pages : illustrations (some color)en_ZA
dc.identifier.urihttps://scholar.sun.ac.za/handle/10019.1/130253
dc.language.isoen_ZAen_ZA
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshCitrus tristeza diseaseen_ZA
dc.subject.lcshCitrus fruits -- Diseases and pestsen_ZA
dc.subject.lcshPlant-pathogen relationships -- Genetic aspectsen_ZA
dc.subject.lcshPhenotype -- Molecular aspectsen_ZA
dc.subject.lcshHigh-throughput sequencingen_ZA
dc.subject.lcshGenetics -- Techniqueen_ZA
dc.subject.lcshCitrus -- Effect of pesticides onen_ZA
dc.subject.lcshCitrus tristeza virus -- Identificationen_ZA
dc.subject.nameUCTDen_ZA
dc.titleIdentification of early indicators of CTV induced stem pitting to aid the selection of CTV cross protection sources.en_ZA
dc.typeThesisen_ZA
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