Browsing by Author "Cornelissen, Stephanie"

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    Defining the QTL for chill requirement during dormancy and dormancy release in apple (Malus x domestica Borkh.).
    (Stellenbosch : Stellenbosch University, 2021-12) Cornelissen, Stephanie; Burger, Johan T.; Rees, Jasper; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    ENGLISH ABSTRACT: Dormancy is a physiological stage that all deciduous fruit trees experience during winter. It consists of three sub stages, para-, endo- and ecodormancy. During the endodormic stage, apple trees need to be exposed to cold temperatures for their chill requirement to be fulfilled. Most apple varieties have a unique chill requirement, for instance ‘Anna’ requires less than 300 hours. After this requirement is fulfilled, the plant will break dormancy if the environmental conditions are optimal, i.e. the less the chill requirement the earlier the plant will bud. This study looks at the genetic component of chill requirement by firstly determining the region of the apple genome that is primarily associated with budbreak and thereafter the genes within this region and their expression patterns. A mapping population was created by crossing ‘Lady Williams’ with ‘Anna’. ‘Lady Williams’ is a medium to high chill variety and ‘Anna’ is a low chill variety that requires less than 300 chill units. This population was used to generate a genetic map and subsequent QTL analysis, as well as association mapping, were used to determine the region of the apple genome that is associated with budbreak. A major QTL in the first 10Mb distal region of Linkage Group/chromosome 9 was discovered. This region consists of 741 genes, of which 27 were differentially expressed over time when exposed to cold. An RNA time series analysis was performed by periodically extracting RNA from the meristems of cuttings from ‘Anna’, incubated at 4°C for up to 800 hours. The expression patterns of the 27 genes grouped into seven distinct clusters. The major observation that could be made is that there is a difference between the expression patterns before and after the theoretical time of budbreak (300 hours) in ‘Anna’. The 27 genes were differentially expressed before budbreak but there was little to no differential expression after budbreak. Another observation that was made, is that the biggest differences in gene expression were between 0-hours and a 100-hours. This indicated that the plant could have experienced cold shock by transferring it to low temperature incubation and subsequently the onset of endodormancy. Known dormancy-associated DAM genes, were not differentially expressed over time. However, an ortholog of the predicted transcription factor ICE1-like, bHLH, and the gene RING domain ligase 2, that have been shown to be associated with the regulation of ICE1-like, was differentially expressed over time when first introduced to cold. Furthermore, genes regulating the expression of the plant hormones ethylene and auxin were differentially expressed. Other notable genes include ones that encode Tubulin alpha-2 chain and xyloglucan endotransglucosylase/hydrolase 9 proteins, both known to regulate transport through cell wall/membrane, and 5'-adenylyl phosphosulfate reductase 2 that is associated with oxidation-reduction homeostasis. This study serves as a starting point for further investigations of the complex nature of the onset of dormancy, chill accumulation during dormancy and the eventual budbreak, by identifying genes that are associated with dormancy.
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    The impact of copper on filamentous fungi and yeasts present in soil
    (Stellenbosch : University of Stellenbosch, 2004-04) Cornelissen, Stephanie; Botha, Alfred; Wolfaardt, Gideon M.; University of Stellenbosch. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: Numerous workers studied the impact of pollutants and agricultural chemicals, containing heavy metals such as copper (Cu), on soil microbes. It was found that elevated soil Cu levels do have a detrimental effect on soil bacterial populations however the filamentous fungi seemed to be less affected. Most of these studies were conducted in soils containing already relatively high Cu levels and the effect of this heavy metal on the nonfilamentous fungi (i.e. yeasts) was never investigated. The aim of this study was therefore to determine the impact of elevated Cu levels on filamentous fungi and yeasts occurring in soils containing relatively low natural Cu levels. A synthetic selective medium containing glucose as carbon source, thymine as nitrogen source, vitamins, minerals and chloramphenicol as anti-bacterial agent (TMV-agar), was used to enumerate ascomycetous and basidiomycetous Cu resistant yeasts in a sample of virgin soil containing ~ 2ppm Cu. Media that were used to enumerate Cu resistant filamentous fungi were malt extract agar, malt extract agar with streptomycin sulfate, maltyeast- extract-peptone agar with chloramphenicol and streptomycin sulfate, benomyl–dichloran-streptomycin medium for the enumeration of hymenomycetous fungi and two selective media for the isolation of mucoralean fungi. Cu resistant fungi able to grow on all of the above mentioned solid media supplemented with 32 ppm Cu occurred in the soil sample. To obtain an indication of the level of Cu tolerance of fungi present in this soil sample, a number of fungal isolates were screened for the ability to grow on a series of agar plates, prepared from glucose-glutamate-yeast extract agar, containing increasing concentrations of Cu. It was found that filamentous fungi and yeasts that were able to grow on this agar medium containing up to 100 ppm Cu were present in the soil. A series of soil microcosms was subsequently prepared from the soil sample by experimentally contaminating the soil with increasing amounts of copper oxychloride, were after fungal populations in the microcosms, including Cu resistant fungi, were monitored using plate counts. At the end of the incubation period, after 245 days, fungal biomass in the microcosms was compared by determining the concentrations of the fungal sterol, ergosterol, inthe soil. Generally, Cu had little impact on the numbers of filamentous fungal colony forming units on the plates, as well as on the ergosterol content of the soil. The numbers of filamentous fungi in the soil, including the Mucorales and hymenomycetes, seemed to be less affected by the addition of copper oxychloride than the numbers of soil yeasts able to grow on TMV-agar. The focus of the next chapter was on the response of yeasts in different soils to elevated levels of Cu in the soil. TMV-agar was used to enumerate yeasts in soil microcosms prepared from four different soil samples, which were experimentally treated with copper oxychloride resulting in Cu concentrations of up to 1000 ppm. The selective medium supplemented with 32 ppm Cu was used to enumerate Cu resistant yeasts in the microcosms. The results showed that the addition of Cu at concentrations ≥ ~1000 ppm did not have a significant effect on total yeast numbers in the soil. Furthermore, it was found that Cu resistant yeasts were present in all the soil samples regardless of the amount of Cu that the soil was challenged with. At the end of the incubation period, yeasts in the microcosms with zero and ~1000 ppm additional Cu were enumerated, isolated and identified using sequence analyses of the D1/D2 600-650bp region of the large subunit of ribosomal DNA. Hymenomycetous species dominated in the control soil, while higher numbers of the urediniomycetous species were found in the soil that received Cu. These observations suggest that urediniomycetous yeasts may play an important role in re-establishing overall microbial activity in soils following perturbations such as the addition of Cu-based fungicides.