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dc.contributor.advisorVisser, B.
dc.contributor.advisorPretorius, Z. A.
dc.contributor.authorSelinga, Tonny Ion
dc.date.accessioned2016-02-09T12:10:58Z
dc.date.available2016-02-09T12:10:58Z
dc.date.copyright2015
dc.date.issued2015
dc.date.submitted2016-02-08
dc.identifier.urihttp://hdl.handle.net/11660/2276
dc.description.abstractEnglish: The hypothesis of whether genotyping complements phenotyping of Puccinia graminis f. sp. tritici (Pgt) and P. triticina (Pt) was tested. Phenotyping (infection type analysis) has been the method of choice for the identification of races, determination of single-step mutations which amount to asexual reproduction and evaluation of inoculum exchange. However, phenotyping can be labour intensive while the non-viability of spores makes it impossible to identify isolates. Genotyping has been used to confirm the identity of specific races but it has never been used to identify isolates on a large scale. Movement of inoculum has been shown by phenotyping to occur in southern Africa, but not by genotyping. A two stage protocol was used to identify stem rust Ug99 and non-Ug99 isolates collected during the 2010 - 2012 surveys. Generally there was a large agreement between genotypes and phenotypes. The SNP genotypes had high sensitivity for identification of 2SA88 phenotypes [73.3% (95% CI = 63.8% to 81.5%)]. There was a poor correlation (r=0.14) between the SSR genotypes and 26 Pgt resistance genes of the non-Ug99 races. The SSR genotypes had a high sensitivity for identification of 2SA105 [95.5% (95% CI = 77.2% to 99.9%)]. However there was strong correlation (r=0.71) between genotypes and 17 Pt resistance genes for Pt isolates. There was a high sensitivity for genotypes to identify 3SA145 [100% (95% CI = 89.72 to 100%)]. It is still not clear whether genotyping is specific in the identification of Pgt and Pt races. Although there was good sensitivity detected, it was difficult to confidently indicate the proportion of isolates with genotypes that could be exclusively found in a single race. Three highly differentiated (FST=0.75) non-Ug99 Pgt and a single Ug99 population were identified in South Africa. Two highly differentiated (FST=0.543; P<0.0001) Pt populations were identified in South Africa. Both the Pgt and Pt populations in South Africa were asexually reproducing. Three Pt populations were detected in southern Africa The fixation index (FST=0.67; P˂0.0001) for the southern African populations was high which suggests that there was significant differentiation between the three southern African populations. The Bayesian model cluster analysis results suggested that there was inoculum exchange between South Africa, Malawi, Zambia and Zimbabwe.en_ZA
dc.description.abstractAfrikaans: Tydens die studie is die volgende hipotese getoets: die fenotipering van Puccinia graminis f. sp. tritici (Pgt) en P. triticina (Pt) word deur genotipering gekomplimenteer. Fenotipering (infeksie tipe analise) was voorheen die mees algemene metode om rasse te identifiseer, enkelstap mutasies weens ongeslagtelike voortplanting te bevestig en inokulum uitruiling te evalueer. Fenotipering is egter arbeidsintensief. Nie-lewensvatbare spore kan verder die identifikasie van isolate verhoed. Hoewel genotipering gereeld gebruik word om rasse te identifiseer, was dit nog nooit voorheen op groot skaal gebruik nie. Hoewel fenotipering vroeër die beweging van inokulum in suider-Afrika bevestig het, is genotipering nog nie gebruik nie. Stamroes isolate wat tydens die 2010 - 2012 opnames versamel is, is met ‘n twee-ledige protokol geïdentifiseer. Oor die algemeen het die genotipes en fenotipes van isolate ooreengestem. Die SNP genotipes het ‘n hoë sensitiwiteit gehad om 2SA88 fenotipes te identifiseer [73.3% (95% CI = 63.8% tot 81.5%)]. Hoewel die nie-Ug99 rasse ‘n swak korrelasie (r=0.14) tussen SSR genotipes en die fenotipes van 26 Pgt gene getoon het, het die SSR genotipes met hoë sensitiwiteit 2SA105 geïdentifiseer [95.5% (95% CI = 77.2% tot 99.9%)]. Daar was ‘n sterk korrelasie (r=0.71) tussen die genotipes en fenotipes van 17 Pt weerstandsgene vir Pt isolate, asook ‘n hoë sensitiwiteit van genotipering om 3SA145 te identifiseer [100% (95% CI = 89.72 tot 100%)]. Dit is egter nog nie duidelik of genotipering spesifiek vir die identifikasie van Pgt en Pt rasse is nie. Hoewel hoë sensitiwiteit gevind is, was dit moeilik om met sekerheid die gedeelte van die isolate met genotipes wat eksklusief in binne ‘n bepaalde ras voorkom, aan te dui. Drie hoogs gedifferensieerde (FST=0.75) nie-Ug99 en ‘n enkele Ug99 Pgt populasie is in Suid-Afrika gevind. Verder is daar ook twee hoogs gedifferensieerde (FST=0.75; P<0.0001) Pt populasies gevind. Beide die Pgt en Pt populasies plant aseksueel voort. In suider-Afrika is drie Pt populasies gevind met ‘n fiksasie indeks van 0.67 (P˂0.0001). Dit was ‘n aanduiding dat die drie populasies betekenisvol van mekaar verskil. Die Bayesian model groeperings analise het aangedui dat inokulum tussen Suid-Afrika, Malawi, Zambië en Zimbabwe uitgeruil word.af
dc.description.sponsorshipNRFen_ZA
dc.language.isoenen_ZA
dc.publisherUniversity of the Free Stateen_ZA
dc.subjectStem rusten_ZA
dc.subjectLeaf rusten_ZA
dc.subjectGenotypesen_ZA
dc.subjectPhenotypesen_ZA
dc.subjectPopulation geneticsen_ZA
dc.subjectDissertation (M.Sc. (Plant Sciences))--University of the Free State, 2015en_ZA
dc.titleGenetic analysis of the Puccinia graminis f. sp. tritici and Puccinia triticina populations in southern Africaen_ZA
dc.typeDissertationen_ZA
dc.rights.holderUniversity of the Free Stateen_ZA


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