Black wildebeest (Connochaetes gnou), a species endemic to South Africa, experienced two bottlenecks in the last century and the number of animals ultimately decreased to approximately 300. These bottlenecks led to a decrease in the genetic diversity of black wildebeest populations across South Africa. An additional threat to the genetic integrity of the black wildebeest was discovered between the 1960s and late 1980s, when researchers noted that hybridization between blue and black wildebeest occurs and that these hybrid animals are fertile. Identification of the hybrid individuals is crucial and various molecular techniques were researched, with microsatellite markers proving to be the most successful. The aim of the current study was to investigate the effectiveness of previously identified cross-species microsatellite markers and statistical approaches for the identification of hybrid herds and individuals on various Nature Reserves in the Free State Province as well as privately owned game farms in and around the Province. Two previously identified diagnostic microsatellite markers (BM1824 and ETH10) were used to screen the populations for putative hybrids. The genetic diversity of the black wildebeest populations studied supported earlier findings showing lower genetic diversity in black wildebeest compared to blue wildebeest. The addition of new reference material in the current study revealed that some of the alleles previously assumed to be unique to a specific species were in fact shared between the two species. This reinforced the need to use more reference populations of adequate size. Nominally blue wildebeest alleles were found in five populations on different game farms and Nature Reserves. The presence of these alleles could be an indication that hybrids are present at these localities or alternatively, support the finding that the number and distribution of reference populations should be increased. Assignment of populations to specific clusters using different software programmes revealed that, due to the large amount of genetic material shared between blue and black wildebeest, no clear assignment of individuals to a specific cluster could be obtained. Molecular analysis of two known hybrid animals did indicate that the two microsatellite markers chosen were able to identify first generation hybrids and possibly even second generation hybrids. The study also investigated the persistence of introgression of blue wildebeest genetic material into black wildebeest populations using simulation software. The simulation tests revealed that introgressed alleles could still be detected after ten generations of backcrossing. This has serious implications for the management of hybrid populations. Various recommendations can be made in terms of the future management and conservation of black wildebeest on Nature Reserves and game farms. The most practical approach for dealing with hybrid animals would first be to develop additional molecular techniques for the accurate identification of populations that contain hybrid animals. Positively identified hybrid populations should be kept separate and no introductions of these animals should be made into pure populations. A more drastic approach would be to cull animals with hybrid ancestry. This would however have serious implications on the already reduced level of genetic diversity in the black wildebeest populations. The most pragmatic approach for dealing with hybrid populations would be to keep pure blue and black wildebeest in protected areas and allow black wildebeest with moderate introgression on game ranches exclusively used for sport hunting.

This study was a first attempt to use microsatellite markers to determine the genetic diversity in an indigenous cattle breed, namely the Afrikaner. It was also the first study to combine genetic markers and pedigree analysis to estimate the genetic variability within an indigenous cattle breed. The objectives of the study were to estimate genetic diversity and inbreeding levels within the breed and to utilize the results to preserve and ultimately improve the genetic resources offered by the breed. A total of 1214 stud animals (representing 28 herds) and 166 commercial animals (nine herds) from different geographical areas within and adjoining South Africa were included in this study. Animals were genotyped at the two major animal molecular laboratories in South Africa, with both using the same standardized 11 marker microsatellite set. Estimates of genetic diversity did not support the hypothesis of significant loss of genetic diversity in the Afrikaner breed. Heterozygosity estimates ranged from 0.737-0.456 within individual populations, with an overall heterozygosity estimate of 0.568 for the Afrikaner breed. Assignment methods (based on STRUCTURE software) revealed a real structure consisting of four genetic populations (K=4). No consistent pattern of significant differentiation between stud- and commercial herds could be identified. Pedigree information, based on a total of 244714 recorded animals from 1940 to 2011, were analysed to determine the mean level of inbreeding (F), effective population size (Ne), generation interval, effective number of founders (fe), effective number of ancestors (fa) and average relatedness (AR). The average inbreeding coefficient calculated was 1.83% and the effective population size computed using the increase in the individual rate of inbreeding was estimated at 167.54. A total of 84138 animals (34.4%) were inbred to some degree. The effective numbers of founders and ancestors were 288 and 226 respectively, with an average relatedness of 0.44% and with results confirming a total of six complete generations. The average generation interval for the whole population was calculated as 6.554 ± 3.883 years. It is concluded that a moderate to high degree of variation is still present within the Afrikaner cattle breed, despite the recent decline in numbers of this indigenous breed. Levels of inbreeding appear to be at acceptable and at manageable levels. The current study provided results than can be utilized by farmers and breedersâ society to conserve the Afrikaner and develop the breed to its full potential.

Little is known about the molecular genetic variation of Ground Pangolin populations in South Africa. In this study it was attempted to assess the genetic diversity of the populations, but this could not be achieved due to insufficient crossâspecies markers amplification. It should, however, be emphasized that the molecular work done in this study is novel, and that the results found during this research are key foundations for future studies. During sample collection it was found that three main populations of Ground Pangolins exist in South Africa in the Eastern, Western and Central parts of the country. Isolation protocols have been optimized, and it has been shown that noninvasive samples yield good quality and quantity DNA that is usable for downâstream applications and perform as well as invasive samples. The PCR protocol was optimized, and the results from the optimization chapter will be of assistance when speciesâspecific markers are optimized. This study has also shown the need for the development of speciesâspecific markers, and the use of said markers will give a better indication of the genetic diversity of the Ground Pangolin populations in South Africa. From the statistical analysis it would seem that there are some correlations between the three sampling localities which may indicate a population divergence at some point. Based on the genetic diversity results, it appears that the diversity within Ground Pangolin populations is much lower based on the markers tested than in Malayan Pangolin populations. This will however have to be confirmed with speciesâspecific markers.

The floriculture and ornamental industry is constantly looking for new products. South Africa is blessed with an exceptional rich bio-diversity and many South African plants have found their way onto international markets. The local development of products for the international market unfortunately is limited. The genus Lachenalia is one of the exceptions, with local development and production of cultivars for the international pot plant market. This thesis thus aimed to establish the different aspects and requirements needed for the development of new Lachenalia cultivars and to use the basic genetic information generated through research to develop specific breeding strategies for the development of new cultivars. The thesis established the wider requirements of the complete value chain for the development of new floriculture crops and identified the strong need to establish basic research information in order to successfully develop new cultivars in the genus Lachenalia. The diversity amongst the 133 described species of Lachenalia and the breeding and research on production that facilitated the release of cultivars to the international market indicated the suitability of the genus for development. The genetic variation present in the genus includes various different basic chromosome numbers, polyploidy, B-chromosomes, different karyotypes within the same basic chromosome number, different phylogenetic groups and the existence of possible hybrid species. Relationships between specific basic chromosome numbers were shown and possible evolutionary history was proposed, but conclusions in this regard needs further investigation. The development of new cultivars is possible from both conventional and mutation breeding processes, but the availability of basic genetic information is essential for future progress. Inter-specific as well as complex hybrid/hybrid crosses are used for the development of new cultivars. To facilitate future crosses the cross-ability among Lachenalia species was investigated. The cross-ability data supports the phylogenetic relationships identified by various authors and both are strongly linked to basic chromosome numbers. Phenotypic characters cannot be used to predict the success of inter-species crosses, except where clear mechanical isolation (female long style species crossed with male short style species) is present. Clear unilateral cross-ability is present among several species and this is not linked to self-incompatibility. Self-incompatibility seems to be present in specific species, but can be overcome by crossing different accessions of the same species. Clear differences in the level of success of crossing combinations were statistical shown through AHC cluster and principle component analysis. A limited number of crosses showed good cross-ability with the production of many normal seeds. Most of these crosses were between species with the same basic chromosome number with only four exceptions, which were between basic x = 7 and x = 8, confirming the close relationship between these two basic chromosome numbers. Some intermediate success rates between basic x = 11 with both x = 7 and x = 8 was also present possible supporting the basal nature of x = 11. Basic chromosome numbers are currently the best criterion for predicting the success rate of inter-species crossing combinations but it does not guarantee success. The data presented clearly indicated the importance of well characterized (phenotypic and genotypic) germplasm material, including the maintenance of various accessions of a species. Good breeding parents were identified to assist breeders to reach specific goals. The importance of an in-depth investigation on the nature and extent of the crossing barriers and continued research on the genetics and molecular systematic of the genus was determined. This study clearly shows that the availability of basic genetic information and data on the cross-ability among species is essential for the selection of breeding parents to ensure better success rates for inter-species crossing combinations and the future development of new Lachenalia cultivars.

Clivia (family Amaryllidaceae; tribe Haemantheae) with its six species is closest related to the genus Cryptostephanus. These genera share the highest chromosome numbers (2n = 22 & 24 respectively) in the tribe and has similar 2C values. Evolution in Clivia correlates with geographical distribution from west to east and genome size from small to large. The tree, character and distance-based analyses are effective in the identification process of three Clivia species. Clivia mirabilis, C. nobilis, C. miniata and C. caulescens / C. Ã nimbicola can be identified with DNA-barcoding. The best barcoding regions regarding discriminatory power are the trnL-F chloroplast region, the matK chloroplast gene and the ITS2 nuclear spacer region. A single DNA-barcoding locus is insufficient to be used in Clivia barcoding. Hybridization events in Clivia may lead to false positive or false negative identifications. Analysis of an unknown sample resulting in a C. miniata, C. gardenii or C. robusta identification should need further analysis on additional data (e.g. morphology, distribution) to confirm the results. All the C. Ã nimbicola natural hybrids included in this study shared the chloroplast DNA of C. caulescens. Alternative methods should be developed to effectively distinguish and identify hybrid species. The genus Lachenalia has 133 species and shows extensive morphological variation and exceptional diverse chromosome numbers (x = 5, 6, 7, 8, 9, 10, 11, 12, 13 and 15). Lachenalia might have evolved from a common ancestor and the two largest basic chromosome number groups, x = 7 and 8 have evolved from a common predecessor. It seems as if the higher basic numbers (x = 9, 10, 11 and 13) evolved independently from the lower numbers. Several speciation events were involved in the evolution of Lachenalia, resulting in the morphological and chromosomal diversity. Many of the species with the same basic chromosome numbers share a common ancestor, and it is expected that there may be incomplete lineage sorting in some species resulting in non-specific DNA-barcodes. The tree-based and character-based analyses are effective methods to identify all the focus species (L. unifolia, L. bifolia, L. punctata and L. mediana) in this study. The matK, trnL-F and ITS2 regions results in the positive identification of an unknown specimen (tree-based analyses). SNP analyses can be used in the analyses of matK and atpH-I. The combination of atpH-I + trnL-F and trnL-F + ITS2 will effectively distinguish an unknown sample of the focus species. Due to the large size of the genus, a two to three DNA-barcode locus is preferred over a single DNA-barcoding locus. The nuclear ITS2 gene region has to be included as a DNA-barcode to detect hybrid species and plastid capture. The chloroplast trnL-F region together with the nuclear ITS2 region can be universally used for barcoding the small genus Clivia and the large genus Lachenalia. Both these regions require an third region (or more in the case of Lachenalia) to be effective for identification of species. Ancient hybridization, introgression and incomplete lineage sorting occurs in both genera. Therefore, certain species will not be effectively identified based on barcodes alone. There are some small differences between the DNA-barcoding of the small (Clivia) and the large genus (Lachenalia). However, the similarities between the genera are that identifications in both genera are influenced by the degree of hybridization (ancient or recent) and the time of divergence (thus incomplete lineage sorting). The classification of Clivia and Lachenalia must be properly resolved before barcodes can be implemented for the species-level identification of these genera.

Genetic information gained through the study of the inheritance of growth pattern and their certain body characteristics in reciprocal crosses of Broad Breasted Bronze - Charlevoix turkeys should provide a basis for the development and improvement of a small type of turkey such as the Charlevoix. Any inherent study of this kind must be carried through at least a three year period, to allow for the necessary reciprocal crosses within the progeny of the initial mating to bring forth Inherent differences existent within the parental types. The results which are presented in this thesis are therefore representative of the FI generation, but cannot be considered definite until future generations are studied.

Those specific autocatalytic enzyme-like entities which we call genes are responsible for the ultimate structure and organization of the developed organism. The mode of action of the genes in producing the phonotype is no doubt intricate, and the action of each gene involves a continued sequence of individual reactions, each new step based on the preceding one. To learn how organisms attain their final structure, we must investigate the nature of these chains of reactions, and this is one of the concerns of Physiological Genetics.

Drosophila females remate generating an opportunity for sperm competition. Normally the second male to mate sires the majority of progeny; however, conspecific sperm precedence is the phenomena whereby the male of the same species as the female fathers the majority of the progeny regardless of mating order. I surveyed D. simulans laboratory strains carrying D. mauritiana P-element insertions (IG lines) for their ability to sire progeny when second to mate. I found significant variation in the proportion of progeny sired by IG lines, with lines showing sperm competitive breakdown (P2< 0.5). I identified two loci that account for conspecific sperm precedence between D. simulans and D. mauritiana. 81 candidate genes were identified and narrowed down the list on the basis of differences in male reproductive tract gene expression to five (P< 0.05) or eight (P<0.1) genes. A larger concentration of differentially regulated genes within the 89B position was found. Using coding sequence data I identified 10 genes as candidate conspecific male precedence genes. Genes in the 89B region come to light as candidates for future functional studies of conspecific male precedence.

Mucopolysaccharidosis (MPS) IX is a lysosomal storage disorder caused by a deficiency of hyaluronidase 1 (HYAL1). With few patients described, to extend our understanding of the skeletal phenotype in MPS IX, we performed micro-computed tomography on HYAL1 knockout (Hyal1-/-) and control mice at 6 months and 1 year of age. Images were examined for changes in the bone shape, microarchitecture, and density. No abnormalities in the shape of the bones of Hyal1-/- mice were detected. However, images of the distal femur of the knee joint showed abnormal periosteal bone in male Hyal1-/- mice. This was also complemented by a significant increase in the periosteal perimeter and periosteal volume. The density of the trabecular and cortical bone did not differ significantly between the two groups. Periosteal bone formation is a pathology shared with other MPSs and indicates that this model may be valuable in understanding the skeletal manifestations of all MPSs.

Developmental genetics of mammals is of necessity largely concerned with embryogenesis. Its task is to delineate the processes by which the genotype is ultimately resolved into the phenotype. In order to describe and explain the normal processes whereby this is accomplished, it has been necessary for the scientist in this field to investigate the abnormal. For this purpose, spontaneous deviations, mutants, have been the main objects of study. Recently, induced abnormalities have been added, to widen and stimulate investigation.