No description available.

No description available.

Net blotch is one of the most devastating diseases of barley (<i>Hordeum vulgare</i> L.) and occurs in two distinct forms, net-type net blotch (NTNB) and spot-type net blotch (STNB), caused by the fungal pathogens <i>Pyrenophora teres</i> f. sp. <i>teres</i> Smedeg. and <i>P</i>. <i>teres</i> f. sp. <i>maculata</i> Smedeg., respectively. Several sources of resistance have been previously reported, however, few barley cultivars with high levels of resistance have been developed from these sources. Efficient utilization of available resistance sources is dependent upon successful characterization of genes governing resistance in each resistant parent. Five net blotch resistant parents and one susceptible parent were crossed to identify novel resistance genes, postulate gene number and mode of inheritance, and conduct linkage mapping of novel genes for net blotch resistance. Results indicate that the highly resistant spring barley lines CIho 2291 and CIho 5098, and the winter barley cultivar Nomini each have single dominant genes for NTNB resistance. Resistance to NTNB in CIho 5098 is controlled by the same dominant gene conferring resistance in Nomini. Resistance to NTNB in CIho 2291 is controlled by one dominant gene which putatively is the same gene conferring resistance in ND B112, but differs from the resistance genes carried by the other parents in this study. An F2 population of 238 individuals derived from a cross between Nomini and the susceptible parent "Hector", and an F2 population of 193 individuals derived from a cross between CIho 2291 and Hector were used to map the genes governing NTNB resistance in Nomini and CIho 2291. The dominant gene governing resistance in Nomini, temporarily designated <i>Rpt-Nomini</i>, was mapped to a 9.2 cM region near the centromere of barley chromosome 6H between the flanking microsatellite markers Bmag0344a (r2=0.70) and Bmag0103a (r2=0.90), which were 6.8 cM and 2.4 cM away from <i>Rpt-Nomini</i>, respectively. The dominant gene governing resistance in CIho 2291, temporarily designated <i>Rpt-CIho2291</i>, was mapped to the distal region of barley chromosome 6H between the flanking microsatellite markers Bmag0173 (r2=0.65) and Bmag0500 (r2=0.26), which were 9.9 cM and 24.4 cM from <i>Rpt-CIho2291</i>, respectively. Previous studies have reported genes governing net blotch resistance in this region; however, allelism tests have not been conducted to determine the relationship between these genes. Identification of the chromosomal location of <i>Rpt-Nomini</i> and <i>Rpt-CIho2291</i> will facilitate future efforts in pyramiding multiple independent genes for net blotch resistance. / Ph. D.

Au cours des 60 dernières années le développement des infrastructures de transports (Autoroutes, Lignes Grandes Vitesse, Nationales doubles voies) a fragmenté l'habitat des cerfs élaphe (Cervus elaphus). D'après les observations naturalistes, cette anthropisation a causé la fragmentation de deux populations géographiques existantes en sept dans la partie Sud et d'une en trois dans la partie Nord. Afin d'évaluer l'impact de ces infrastructures sur la structuration génétique de ces populations de cerfs, nous avons échantillonné chacune de ces populations grâce à la coopération de trois fédérations de chasse. Le cours laps de temps écoulé depuis la construction de ces infrastructures nous a conduits à choisir comme marqueurs moléculaires les microsatellites, efficaces dans l'inférence d'évènements récents. Les nouvelles techniques de séquençages (NGS) permettent d'obtenir d'importants jeux de données rapidement, nous avons choisi d'utiliser ces méthodes de séquençage pour obtenir nos données. Aucun logiciel ne permettant de traiter les données de séquençage haut débit des microsatellites pour des espèces dont le génome n'est pas complètement séquencé, nous avons alors réalisé un programme, MicNeSs qui permet de génotyper rapidement et objectivement (sans intervention humaine) un grand nombre d'individus et de locus. Nous avons utilisé MicNeSs pour génotyper 345 individus pour 17 locus microsatellites. A partir de ce jeu de données, nous avons montré l'existence d'une structuration génétique des populations de cerfs élaphe en Île-de-France en liaison avec les infrastructures routières et ferroviaires. Nous avons mis en évidence un effet fort des jumelages autoroutes/LGV et une efficacité différentielle des passages grande faune de 2ème et 3ème génération sur les populations de cerfs élaphe en Île-de-France. / During the last 60 years, the development of urban areas, main roads, highways and railways in Île de France, has fragmented the habitat of the red deer (Cervus elaphus). According to naturalistic observations, it caused the fragmentation of the two existing putative populations in the South in to seven putative populations and one in three in the North.In order to estimate the impact of the infrastructure on the genetic structure of these populations we sampled each of the putative population with the help of three hunting societies. Due to the short time passed since the first highway construction we chose microsatellite loci as molecular markers, efficient in the inference of recent events. The next generation sequencing (NGS) enable to have quickly important data set, we chose to use this technic to obtain our data. No software permits to treat microsatellites data from NGS for the species without complete genome, we made one program, MicNeSs which genotypes quickly and objectively a lot of individuals and loci. We used MicNeSs to genotype 345 individuals for 17 microsatellite loci. With this data set we showed the presence of a genetic structure of the red deer populations in association with the road and rail infrastructure. We highlighted a strong impact of the paired of highway/railway and a differential efficiency of the wildlife passages of the second and third generation on the red deer populations in Île-de-France.

Microsatellites are repetitive DNA characterized by tandem repeats of short motifs (2 – 5 bp). High mutation rates make them ideal for population level studies. Microsatellite allele genesis is generally attributed to strand slippage, and it is assumed that alleles are caused only by changes in repeat number. Most analyses are limited to alleles (electromorphs) scored by mobility only, and models of evolution rarely account for homoplasy in allele length. Additionally, insertion/deletion events (indels) in the flanking region or interruptions in the repeat can obfuscate the accuracy of genotyping. Many investigators use microsatellites, designed for a focal species, to screen for genetic variation in non-focal species. Comparative studies have shown different mutation rates of microsatellites in different species, and even individuals. Recent studies have used reciprocal comparisons to assess the level of polymorphism of microsatellites between pairs of taxa. In this study, I investigated the evolution of microsatellites within a phylogenetic context, using comparisons within the rodent family Bathyergidae. Bathyergidae represents a monophyletic group endemic to sub-Saharan Africa and relationships are well supported by morphological and molecular data. Using mitochondrial and nuclear DNA, a robust phylogeny was generated for the Bathyergidae. From my results, I proposed the new genus, Coetomys. I designed species-specific genotyping and microsatellite flanking sequence (MFS) primers for each genus. Sequencing of the MFS provided direct evidence of the evolutionary dynamics of the repeat motifs and their flanking sequence, including rampant electromorphic homoplasy, null alleles, and indels. This adds to the growing body of evidence regarding problems with genotype scores from fragment analysis. A number of the loci isolated were linked with repetitive elements (LTRs and SINEs), characterized as robust phylogenetic characters. Results suggest that cryptic variation in microsatellite loci are not trivial and should be assessed in all studies. The phylogenetic utility of the nucleotide variation of the MFS was compared to the well-resolved relationships of this family based on the 12S/TTR phylogeny. Variation observed in MFS generated robust phylogenies, congruent with results from 12S/TTR. Finally, a number of the indels within the MFS provided a suite of suitable phylogenetic characters.

No description available.

Global climate change and habitat fragmentation represent two of the greatest threats to biodiversity and ecological processes worldwide. It is predicted that anthropogenic induced climate change could represent a key factor for extinctions in the near future, considering that the Earth is set to become warmer than at any period in the past 40 million years. Habitat fragmentation and isolation pose a number of challenges for the fauna inhabiting degraded areas, including lack of dispersal opportunities leading to inbreeding resulting in a loss of genetic diversity, reduced reproductive fitness; increases in vulnerability to predation, hunting, and disease, and an inability to deal with or respond to environmental changes and/or disease. Madagascar, the fourth largest island in the world, is home to unprecedented levels of endemism, including over 100 species of lemur. The island has undergone a range of historical and contemporary landscape transformations, both natural and anthropogenic. These landscape transformations combined with additional human-induced disturbances, such as the illegal pet and bushmeat trades, have had devastating effects on the island’s extant primate populations. Thus, Madagascar’s lemurs have been deemed the most endangered group of mammals and now represent the highest primate conservation priority in the world. The ring-tailed lemur (Lemur catta) is endemic to the southern regions of the island and occupies an array of habitats. L. catta is known for its remarkable behavioral and ecological flexibility, which contributes to its ability to exist in a mostly fragmented landscape. While this species represents one of the most well studied Malagasy strepsirhines, there has been a paucity of research regarding the population and conservation genetics of this endangered species. The goal of my dissertation was to examine the influence of habitat fragmentation and isolation on the genetic diversity and population structuring of this flagship species in three populations living in the central highlands of Madagascar: Anja Reserve, Sakaviro, and Tsaranoro Valley. Non-invasive fecal samples from 30 individual lemurs were collected from three fragmented forests and genotyped at six polymorphic microsatellite loci. Population genetic analyses were examined via GenAlEx software and revealed a moderate level genetic diversity. Genetic differentiation (FST) among the three fragmented populations ranged from 0.05-0.11. These data suggest that the L. catta populations within south-central Madagascar have not yet lost significant genetic variation. To examine past and recent demographic declines or genetic bottlenecks, I employed three approaches, including mode-shift and M-Ratio tests, as well as a test to detect heterozygosity excess using three mutation models: the two-phase model (TPM), step-wise mutation model (SMM), and the infinite allele model (IAM). Results were equivocal depending on the test that was applied; however, a mode-shift was detected for Anja, signifying this population underwent a historical bottleneck. M-ratio tests revealed that all three populations suffered historical bottlenecks. A population bottleneck was indicated via heterozygosity excess under the IAM for both the Anja and Sakaviro populations. To understand the impact of natural (e.g., mountains) and anthropogenic disturbances (e.g., roads, habitat fragmentation) on male reproductive strategies (dispersal) and population structuring, I utilized both GenAlEx and STRUCTURE software. Population assignment analyses suffered from a likely ‘lack of signal’. Therefore, individuals were unable to be reliably assigned to their population of origin. Genetic population structure was ambiguous. These data suggest that that these three fragmented populations are not genetically differentiated enough for proper population assignment, or perhaps the sample is not robust enough for population assignment analyses to produce unequivocal results. My research represents the first population genetic data for ring-tailed lemurs within the central highlands, and thus, serves as a baseline for future investigations into the genetic health of these populations. These data support the suggestion that these three fragments represent areas in which concerted conservation efforts are necessary if genetic diversity is to be maintained and future demographic declines are to be prevented. My results are informative for the local community conservation associations working within south-central Madagascar and can now be applied to determine areas of conservation priority and where forest corridors will be the most beneficial for maintaining gene flow. The loss and fragmentation of habitat continues across Madagascar, including the central highlands; thus, all remaining L. catta populations should be considered a high conservation priority. If we are to safeguard the long-term viability of this species, continued conservation and research initiatives will be crucial. / Graduate / 0327 / 0369 / lemurgirl.clarke@gmail.com

Thesis (PhD (Genetics))--Stellenbosch University, 2010. / ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is a commercially valuable mollusc and is mostly exported to the Far East. Genetics research on H. midae has increased substantially since a genetic improvement programme was introduced in 2006 by collaboration between Stellenbosch University, government and industry partners. The development of molecular markers, QTL-mapping, gene-expression and genome manipulations are the main focuses of the research currently being conducted. The end goal is to create high quality and fast growing animals for the industry. The present study focused on the development of microsatellite markers and the detection of quantitative trait loci (QTL) affecting growth traits (shell length, shell width, wet weight) in this species. A combination of three methods, namely selective genotyping and bulked segregant analysis (pooling analysis), single marker regression and interval mapping were used to identify putative QTL in two full-sib families from two different farmed locations. Additional methods and protocols were developed that can assist the industry in other molecular research aspects. A total of 125 microsatellite loci were characterised. A total of 82 of these loci were isolated using second generation sequencing, a first for any abalone species. A preliminary, low-density framework linkage map was constructed containing 50 loci that mapped to 18 linkage groups. The observed genome length was 148.72cm with coverage of ±47%. QTL analyses revealed two putative QTL for shell width and wet weight, with 17% and 15% variance explained, that mapped on one linkage group in the first family and three putative QTL, for shell length, shell width and wet weight, with 33%, 28.5% and 31.5% variance explained, that mapped on one linkage group in the second family. Additional methods and protocols developed include an automated high-throughput DNA isolation protocol, a real-time PCR assay for H. midae x H. spadicea hybrid verification, a triploid verification microsatellite assay and a pre- and post-PCR multiplex setup and optimisation protocol. Future studies focussing on QTL and marker assisted selection (MAS) should verify the QTL found in this study and also utilise additional family structures and determine QTL-marker phase within the commercial populations. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is ’n kommersieel waardevolle weekdier en word hoofsaaklik na die Verre-Ooste uitgevoer. Genetiese navorsing op H. midae het aansienlik toegeneem sedert ’n genetiese verbeteringsprogram in 2006 deur samewerking tussen die Universiteit van Stellenbosch, die regering en industrievennote ingebring is. Die ontwikkeling van molekulêre merkers, KEL-kartering, geen-uitdrukking en genoom manipulasies is die hooffokusse van die navorsing wat tans uitgevoer word. Die einddoel is om hoë kwaliteit en snelgroeiende diere vir die industrie te skep. Die huidige studie het op die ontwikkeling van mikrosatelliet merkers en die opsporing van groeiverwante (skulplengte, -breedte en nat gewig) kwantitatiewe eienskap lokusse (KEL) in hierdie spesie gefokus. ’n Kombinasie van drie metodes, naamlik selektiewe genotipering en versamelde segregaat analise (samevoegingsanalise), enkel merker regressie en intervalkartering is gebruik om waarskynlike KEL in twee vol-sibbe families van twee verskillende produksiegebiede te identifiseer. Aanvullende metodes en protokolle is ontwikkel wat die industrie in ander molekulêre navorsingsaspekte kan ondersteun. ’n Totaal van 125 mikrosatelliet lokusse is beskryf. ’n Totaal van 82 van hierdie lokusse is deur die gebruik van derde generasie volgordebepaling geïsoleer, ’n eerste vir enige perlemoen spesie. ’n Voorlopige, laedigtheid raamwerkkoppelingskaart is saamgestel met 50 lokusse wat op 18 koppelingsgroepe gekarteer is. Die waarneembare genoomlengte was 148.72cm met ’n dekking van ±47%. KEL-analises het twee waarskynlike KEL vir skulpbreedte en nat gewig blootgelê wat 17% en 15% variasie verduidelik en is op een koppelingsgroep in die eerste familie gekarteer asook drie waarskynlike KEL, vir skulplengte, -breedte en nat gewig wat 33%, 28.5% en 31.5% variasie verduidelik en is op een koppelingsgroep in die tweede familie gekarteer. Aanvullende metodes en protokolle wat ontwikkel is, sluit ’n geoutomatiseerde hoë-deurgang DNS-isolasieprotokol, ’n intydse PKR-proef vir H. midae x H. spadicea hibried verifikasie, ’n triploïed verifikasie mikrosatellietproef en veelsoortige pre- en post-PKR opstelling en optimaliseringsprotokol in. Toekomstige studies wat fokus op KEL en merker ondersteunde seleksie (MOS) behoort die KEL wat in hierdie studie gevind is te verifieer en ook bykomende familie strukture te benut om KEL-merker fases binne die kommersiële populasie te bepaal.

Thesis (MEng (Electrical and Electronic Engineering))--University of Stellenbosch, 1995. / 189 leaves single sided printed, preliminary pages and numbered pages 1-126. Includes bibliography, list of appendixes, figures, notation and symbols. Digitized at 300 dpi (OCR), using a Bizhub 250 Scanner. / ENGLISH ABSTRACT: The Sunsat microsatellite is being developed at the University of Stellenbosch. It is equipped with a high resolution earth imager which requires a sophisticated attitude determination and control system. Precise control of the satellite is impossible without high precision attitude sensors. The most accurate attitude sensor presently used by satellites is the star sensor. The aim 'of this thesis is to develop a low cost, high precision star sensor for the Sunsat microsatellite. The development included the selection of electronic and optical hardware followed by the design, construction and testing of the sensor. Software algorithms were developed and programmed to control the imager, extract stars from images and match the observed constellations to a star catalogue. A set of matching observed and reference vectors are passed to the attitude determination and control system which calculates the three axis orientation of the satellite. / AFRIKAANSE OPSOMMING: Die Sunsat mikrosatelliet word tans by die Universiteit van Stellenbosch ontwikkel. Dit is toegerus met 'n hoeresolusie aardwaarnemingskamera en vereis 'n gevorderde orientasiebepaling-en beheerstelsel. Presiese beheer is onmoontlik sonder akkurate sensore. 'n Stersensor is die mees akkurate tipe sensor waarmee satelliete tans toegerus word. Die doelwit van hierdie tesis is die ontwikkeling van 'n hoe resolusie, laekoste stersensor vir die Sunsat mikrosatelliet. Die ontwikkeling behels die seleksie van elektroniese en optiese apparatuur wat gevolg is deur die ontwerp, opbou en toets van die sensor. Programmatuur algoritrnes is ontwerp om die kamera te beheer, sterre in fotos te herken en waargenome konstellasies in die sterkatalogus te vind. 'n Stel waargenome en verwysingsvektore stel die orientasiebepaling-en beheerstelsel in staat om die orientasie van die satelliet te bereken.

The biology of South African Bryde’s whales (Balaenoptera brydei/edeni), with a focus on the inshore form, was investigated through estimates of abundance and survival rate, seasonality of occurrence and variation in mitochondrial and nuclear DNA. Photographs, sightings data and biopsy samples were collected in Plettenberg Bay, on the south-east coast of South Africa. Additional genetic material was obtained from the Iziko South African Museum, Marine and Coastal Management, and the Port Elizabeth Museum. Mark-recapture methods applied to photo-identification data were used to estimate abundance and survival rate. Estimates of abundance ranged from 130 to 250 (CV = 0.07 - 0.38) and the estimated annual survival rate was 0.93 (CV = 0.047, 95% CI = 0.852 - 1.0). Seasonal increases in the encounter rate and number of individual whales were observed during summer and autumn, with a peak in April, which corresponded to increased feeding activity and larger average aggregation sizes. Chlorophyll-a, sea surface temperature and wind speed were all significant factors in explaining the variability in the occurrence of whales. No seasonality in the occurrence of calves was detected. Mitochondrial DNA control region sequences (685bp) were compared to published sequences. This confirmed the offshore form as Balaenoptera brydei and the inshore form as closely related to B.brydei, possibly at the sub-specific level, but excluded it as B.edeni. Phylogenetic analyses support complete separation between the two forms. The use of 10 polymorphic microsatellite loci revealed no population structure among the inshore samples (FST = 0.006). Pairwise estimates of relatedness found most individuals to be unrelated, with only a few distant relatives detected.