Thesis (M.Sc.) - Carleton University, 2006. / Includes bibliographical references (p. 137-151). Also available in electronic format on the Internet.

Thesis (MSc (Genetics))--University of Stellenbosch, 2007. / The aim of this study was to develop a DNA-based diagnostic system that can be used to distinguish between genotypes in the wheat breeding program at the University of Stellenbosch. Known marker systems were investigated and the chosen marker system would then be implemented to determine its utility in the breeding program. Three marker systems were considered, i.e. microsatellites, Amplified Fragment Length Polymorphisms (AFLPs) and various retrotransposon-based markers. Each system is based on polymerase chain reaction (PCR) amplification from specific primer pairs. The multitude of primer options was narrowed down during a review of published literature regarding wheat molecular markers. Thirty nine microsatellite primer pairs and nine AFLP primer combinations were chosen for the initial genotype evaluation. Four different retrotransposonbased techniques were investigated; namely Inter-Retrotransposon Amplified Polymorphism (IRAP), REtrotransposon-Microsatellite Amplified Polymorphism (REMAP), Sequence- Specific Amplified Polymorphism (SSAP) and, a derivative of these developed in this study, Wis-2 Retrotransposon Amplification. The study started with twenty genotypes which included varieties/breeding lines from five breeding programmes. The genotypes were chosen as representative of the respective breeding populations and were used in the initial testing of the marker systems. Eighteen microsatellites were evaluated using the panel of twenty genotypes. From this, six primer pairs (Xgwm190, Xgwm437, Xgwm539, Xwmc11, Xwmc59 and Xwmc177) were chosen to test the semi-automated DNA sequencer detection system. A single band/peak in each microsatellite profile was used for genotyping. Four of the primer pairs were labelled with different fluorochromes which enabled them to be multiplexed. The differences in amplification products of the six microsatellites meant that all six could be detected in one electrophoresis run. The banding pattern produced by microsatellite Xwmc177 was complex and highly polymorphic and was therefore also analysed in the same way as the AFLP patterns. When analyzed in this manner it proved to be more informative than the combination of six microsatellites (with a single prominent band scored in each). Three AFLP primer combinations could also be multiplexed and visualised together. The three EcoRI selective primers were labelled with different dyes and used with one MseI selective primer. The SSAP system also used fluorescently labelled primers and proved to be the most useful of the retrotransposon-based methods. However, this system produced such a large amount of data that it made analysis too time consuming. Therefore the six microsatellites and three AFLP primer combinations (MseI-CTC and EcoRI-ACA, -AAC, - AGG) were selected for routine genotyping. Due to the numerous highly polymorphic bands produced by the SSAP system it could be very useful to differentiate very closely related genotypes that cannot be distinguished with the markers proposed for routine use. A panel of 119 breeding lines were then used to implement the two chosen marker systems. The results obtained for these markers were used to produce a dendrogram of the lines using the SAS cluster analysis function. The clusters showed that most of the lines could be distinguished from each other. The MseI-CTC and EcoRI-AGG primer combination was the most informative. It produced the largest number of clusters (53) and could therefore discriminate between more of the lines than any other method. The dendrograms and clusters allowed sixteen of the breeding lines to be selected to test the optimal number of seeds to represent an entire population (variety/breeding line) as one seed was not sufficient. It was decided that eight seeds could provide a good representation of the intra-line variability.

Orientador: Alexandre Magno Sebbenn / Resumo: A presente dissertação de mestrado é composta por uma seção introdutória, seguida de uma revisão da literatura a qual antecede os três capítulos subsequentes. O primeiro capítulo aborda um conjunto de revisões de conhecimentos científicos contemporâneos sobre os efeitos da exploração madeireira em florestas tropicais e as práticas madeireiras utilizadas no Brasil, quais têm se demonstrado insuficientes para garantir a sustentabilidade tanto na produção genética quanto na produção madeireira. O segundo capítulo é um “primer note” descrevendo a identificação de 402 loci putativos (polimorfismos de nucleotídeo único – SNPs, inserções / deleções - INDELs) para Ipe (Handroanthus sp.), destinado à estudos de genética de populações, filogeografia e DNA fingerprinting. O último capítulo discute a viabilidade de DNA fingerprinting para espécies do gênero Handroanthus. Esse traz a análise da diversidade genética, diferenciação genética de populações de Handroanthus sp., bem como entre os países de origem das amostras, análises de auto atribuição de genótipos e testes de atribuição de madeira ao local de origem. / Mestre

Submitted by BÁRBARA ROCHA VENANCIO null (b.rvenancio@outlook.com) on 2017-06-01T12:26:01Z No. of bitstreams: 1 Dissertação_Bárbara Rocha Venancio_2017.pdf: 1455087 bytes, checksum: 52124957d6d5433b1fb34b032cc3d9c5 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-06-02T13:19:34Z (GMT) No. of bitstreams: 1 venancio_br_me_ilha.pdf: 1455087 bytes, checksum: 52124957d6d5433b1fb34b032cc3d9c5 (MD5) / Made available in DSpace on 2017-06-02T13:19:34Z (GMT). No. of bitstreams: 1 venancio_br_me_ilha.pdf: 1455087 bytes, checksum: 52124957d6d5433b1fb34b032cc3d9c5 (MD5) Previous issue date: 2017-04-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A presente dissertação de mestrado é composta por uma seção introdutória, seguida de uma revisão da literatura a qual antecede os três capítulos subsequentes. O primeiro capítulo aborda um conjunto de revisões de conhecimentos científicos contemporâneos sobre os efeitos da exploração madeireira em florestas tropicais e as práticas madeireiras utilizadas no Brasil, quais têm se demonstrado insuficientes para garantir a sustentabilidade tanto na produção genética quanto na produção madeireira. O segundo capítulo é um “primer note” descrevendo a identificação de 402 loci putativos (polimorfismos de nucleotídeo único – SNPs, inserções / deleções - INDELs) para Ipe (Handroanthus sp.), destinado à estudos de genética de populações, filogeografia e DNA fingerprinting. O último capítulo discute a viabilidade de DNA fingerprinting para espécies do gênero Handroanthus. Esse traz a análise da diversidade genética, diferenciação genética de populações de Handroanthus sp., bem como entre os países de origem das amostras, análises de auto atribuição de genótipos e testes de atribuição de madeira ao local de origem. / The present master dissertation is composed by an introductory section, followed by a review of literature, which prefaces the three subsequent chapters. The first chapter of this dissertation is a review assembly contemporary scientific knowledge about the effects of the forest logging in tropical rainforests and the actual logging practices used in Brazil, which seems insufficient to ensure sustainability in both genetic and timber production aspects. The second chapter is a primer note describing the identification of 402 putative loci (single nucleotide polymorphisms –SNPs; and insertion/deletions- INDELs) for Ipe (Handroanthus sp.), intended to help population genetics, phylogeography and DNA fingerprinting studies. The last chapter discuss the feasibility of DNA fingerprinting for Handroanthus species. It brings genetic diversity analysis, genetic differentiation of Handroanthus sp. sample-populations, as well as among countries, self-assignment and timber assignment tests analysis.

M.Sc. / Invasive species are a considerable threat to ecosystems globally, especially on islands where species diversity can be relatively low. Understanding the drivers of invasion is the first step towards an adequate management plan. Although Darwin’s naturalisation hypothesis has fuelled our understanding in this regard, several studies provided mixed results, suggesting that invasion success might be context-dependent. The main objectives of this study are two-fold: (1) testing Darwin hypothesis on Robben Island, and (2) investigating the relative role of invasive alien plants on phylogenetic diversity (PD) loss in native community. I sampled extensively the flora of the island, and using a Bayesian analysis, I reconstructed its phylogeny based on two plastid DNA loci, rbcLa and matK. I also surveyed a total of 127 plots of 50 x 50 m (i.e. local communities) where species presence/absence was recorded. Analysing phylogenetic patterns of the native and invasive floras at both regional (phylogeny level) and smaller scales (plots level), I found that invasive species are, on average, more distantly related to the native communities, giving strong support to the hypothesis tested. Furthermore I found that native communities have accumulated lower PD than alien communities; and that local communities are more overdispersed than expected. These findings suggest that competitive interactions might be the major ecological forces shaping plant communities, with the possibility of alien being higher competitors than native, and therefore decreasing native plant diversity. The implications of these findings for the recovery of native plants are also discussed. Key words: Invasion biology - Darwin’s naturalisation hypothesis - Phylogenetic diversity - Community structure - Conservation - Robben Island, South Africa.

M.Sc. (Botany) / The market and public demand for medicinal plants over the past few decades has increased dramatically with more than 1 000 plant species actively traded for medicinal purposes throughout South Africa. Intensive harvesting of wild material is now acknowledged as a serious threat to biodiversity in this country. Also the substitution of a valuable commodity (medicinal plant) by a cheaper alternative (other plant species), either inadvertently due to misidentification, or deliberately to cheat consumers, raises some serious concerns as these adulterants may not be as effective or may even be toxic and cause harm to consumers. To add to the problem many species are either traded as dried leaf, root, bark products, or extracts and their identification becomes problematic. Therefore, DNA barcoding can help to provide a rapid and accurate identification tool for medicinal plants. In the current study I targeted the most commonly used medicinal plants in South Africa and produced a set of barcodes for fast and easy DNA-based species identification (rbcLa & matK). I tested the efficiency of core barcodes in the identification of medicinal plants using four main analyses, in the R package Spider 1.1-1. Here the extent of specific genetic divergence, DNA barcoding gap, BLAST test, and the ability to discriminate between species were assessed. Overall, the matK region was found to be a more useful tool for the species identification of medicinal plants in South Africa.

Please read the abstract in the section 00front of this document / Dissertation (MSc (Botany))--University of Pretoria, 2005. / Plant Science / unrestricted

Characterization studies on the genetic diversity among cultivated cowpea (Vigna unguiculata (L.) varieties are valuable tools to optimize the use of available genetic resources by farmers, local communities, researchers and breeders. Eight cowpea (Vigna unguiculata (L.) genotypes ( Vegetable cowpea, Ivory grey, Okhalweni, Fahari, Fahari dark, 97K-1069-8, IT93K-73h, and 129-3) were subjected to molecular, morphological and agronomical characterization. DNA amplification fingerprinting markers were used to evaluate the genetic diversity among the eight genotypes. Nine random arbitrary primers were used to screen the eight genotypes to assess their ability to reveal polymorphisms in cowpea, and seven of them were selected for use in characterizing the total sample. A total of 43 bands were generated which are all polymorphic. On the average, the primers generated a total of 6.1 polymorphic bands. The resulting data-matrix included 43 analysed bands with a total of 344 characters. Neighbour joining analysis was used to generate the dendrogram, clustering the genotypes into two groups at an agglomerate coefficient of 0.30 irrespective of their geographical origins. The results also showed the presence of significant differences in morphological and quality traits among the genotypes. Fahari yielded the highest concentration of crude protein (46.51 mg/mg dry leaf) while Vegetable cowpea yielded the lowest (24.41 mg/mg dry leaf). The influence of manure was also found to be effective by increasing the crude protein content of the genotypes as shown by Fahari dark with an average of 53.53 mg/mg dry leaf as opposed to 39.85 mg/mg dry leaf without manure application. Although some small clusters grouped accessions of the same growth habits, a general lack of agreement between clustering and morphological features was observed. It can therefore be concluded that the significant differences between the molecular genetic analysis using DAF-PCR markers, morphologic characters and yield traits can be important tools to identify and discriminates the different cowpea genotypes.

No description available.

No description available.