Student Number : 9704202D - MSc dissertation - School of Clinical Microbiology and Infectious Diseases - Faculty of Science / Meningococcal disease is an important cause of morbidity and mortality worldwide, particularly in children and young adults. Epidemics caused by Neisseria meningitidis continue to plague many countries on a global scale, none more so than countries of the African ‘meningitis belt’, where attack rates can reach up to 1000/100,000 population. It has been well recognized that most epidemic and endemic cases of meningococcal disease are caused by a limited number of genetically defined clonal groups. The objective of this molecular epidemiological study was to genotypically characterize strains of N. meningitidis collected in South Africa from July 1999 to July 2002. Characterization of meningococcal strains belonging to serogroup A, B, C, W135 and Y, by PFGE and MLST allowed us to determine the genetic population structure of N. meningitidis in South Africa, and thus identify the predominant clonal groups responsible for the majority of meningococcal disease in the country over this period. The results from the genotypic characterization revealed that the greatest majority of meningococcal disease in South Africa was caused by a strains belonging to only a few “hyperinvasive lineages”, most notably strains of the ST-44 complex (lineage III), ST-32 complex (ET-5 complex), ST-11 complex (ET-37 complex), and the ST-1 complex (subgroup I/II) which have all been responsible for major epidemics worldwide. These findings have direct implications on public health decision, particularly with regards to the development of effective intervention and control strategies, and emphasize the need for continuous long-term monitoring of the circulation of these strains in the population.

Hierarchical sampling from populations, incipient and recognized varieties within Phacelia dubia and P. maculata has revealed high levels of intraspecific polymorphism in chloroplast DNA. Much of the variation is partitioned between populations as evidenced by population-specific variants at fixation in all three populations of P. dubia var. interior and in both populations of P. maculata. Nine of 16 populations were polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found in a sample of 106 individuals; the most common occurred in eight of the 16 populations and in 31 per cent of the individuals in the entire sample. A phylogenetic analysis revealed four basic plastome types. The two major groups of plastomes were separated by four independent base-pair mutations which suggests an ancient split in the evolution of plastid genomes. Representatives from each major plastome division were found in each of five populations spanning two allopatric varieties of P. dubia. The geographical distribution of haplotypes and lack of evidence for recent admixture argue against migration as a source of the polymorphism. It is more likely that the current taxonomic varieties are descendants of a polymorphic common ancestor.

Quinoa (Chenopodium quinoa Willd.) is a staple grain for the indigenous people of the Andean region of South America with excellent nutritional qualities, including protein content. The objective of this study is to report on the development of fluorescence-tagged simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) to (1) genetically characterize the inherent diversity of 152 accessions of C. quinoa; (2) determine to what degree the CIP-FAO collection represents the range of genetic diversity in quinoa; and (3) test four hypotheses regarding quinoa?s center of diversity, Highland and Lowland clustering patterns, origin of Lowland varieties, and the origin of domestication. Thirty-five SSR loci comprising 432 alleles ranging from 5 (QAAT10) to 28 (QAAT50) alleles per locus (mean=13) were used to survey the 152 accessions of quinoa from the USDA and CIP-FAO collections. Heterozygosity was detected in 14.25% of the accessions for SNP loci and in at least one locus for 51% of the accessions. Both UPGMA and PCA analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina, and extreme northeastern Chile. The other main cluster contained accessions from both the Lowlands of Chile and those collected by Emigdio Ballón The CIP-FAO collection appears to give a good representation of quinoa's genetic diversity within these two main clusters. The significance of patterns of genetic diversity within C. quinoa is discussed.

Cañahua (Chenopodium pallidicaule Aellen) is a poorly studied, annual subsistence crop of the high Andes of South America. Its nutritionally value (high in protein and mineral content) and ability to thrive in harsh climates (drought, extreme elevations, etc.) make it an important regional food crop throughout the Andean region. The objectives of this study were to develop genetic markers and to quantify genetic diversity within cañahua. A set of 43 wild and cultivated cañahua genotypes and two related species (C. quinoa and C. petiolare) were evaluated for polymorphism using 192 microsatellite markers derived from random genomic sequences produced by 454 pyro-sequencing of cañahua genomic DNA. In addition, another and 424 C. quinoa based microsatellite markers were evaluate as potential cross-species marker loci. A total of 48 polymorphic microsatellite marker loci were identified which detected a total of 168 alleles with an average of 3.5 alleles per marker locus and an average heterozygosity value of 0.47. A cluster analysis, based on Nei genetic distance, grouped the cultivated cañahua into a single dominant branch clearly separated from wild cañahua genotypes and the outgroup species. Within the cultivated genotypes, two dominant subclades were present that were further partitioned by AMOVA analysis into five model-based clusters. Significant correlations were found between genetic distance and morphological traits. The isolation by distance test displayed no significant correlation between geographic collection origin and genotypic data, suggesting that cañahua populations have moved extensively, presumably via ancient food exchange strategies among native peoples of the Andean region. The molecular markers reported here are a significant resource for ongoing efforts to characterize the extensive Bolivian and Peruvian cañahua germplasm banks, including the development of core germplasm collections needed to support emerging breeding programs.

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This study examined population genetics of greater sage-grouse (Centrocercus urophasianus) in Strawberry Valley, Utah located in the north-central part of the state. The Strawberry Valley population of sage-grouse experienced a severe population decline with estimates of abundance in 1998 less than 5% (~150 individuals) of similar estimates from the 1930s (>3,000 individuals). Given the population decline and reduced genetic diversity, recovery team partners translocated sage-grouse from four different populations into Strawberry Valley over 6 years (2003-2008). Translocations have been used as a strategy to increase both population size and genetic diversity in wildlife populations. We assessed whether genetic diversity increased following the translocation of sage-grouse into Strawberry Valley by looking at both nuclear and mitochondrial DNA indices. We observed an overall increase of 16 microsatellite alleles across the 15 loci studied (x̅ =1.04 alleles per locus increase, SE ± 0.25). Haplotype diversity increased from 4 to 5. Levels of genetic diversity increased for both nuclear and mitochondrial DNA (16% and 25% increases for allelic richness and haplotype diversity, respectively). These results show that translocations of greater sage grouse into a wild population can be an effective tool to increase not only population size but also genetic diversity.Second, we studied fitness-related traits and related them to genetic diversity indices in a population of greater sage-grouse in Strawberry Valley, Utah from 2005 to 2013. We captured 93 sage-grouse in Strawberry Valley and fitted them with a radio collar and drew and preserved blood. We monitored sage-grouse weekly, throughout each year. From blood, we extracted and amplified DNA with 15 microsatellite loci. We determined genetic diversity as multilocus heterozygosity and mean d2. To determine if there was a relationship between genetic diversity and survival, we used known-fate models in Program MARK. We also determined if there was a relationship between genetic diversity measures and nest initiation, nest success, clutch size, and number of eggs hatched using generalized linear models where reproductive measures were modeled as a function of genetic diversity. We found no significant relationship between mean d2 and microsatellite heterozygosity with measures of survival or reproductive fitness. Overall, these results suggest that the often-reported strong heterozygosity-fitness correlations detected in small, inbred populations do not reflect a general phenomenon of increasing individual survival and reproductive fitness with increasing heterozygosity.

Vetiver grass or Chrysopogon zizanioides (L.) Roberty (1960) is a sterile grass which can regenerate vegetatively from clumps of the rootstock. This, as well as its vigorous and deep root system and flood tolerance makes it an ideal candidate for the use in soil remediation and erosion control. In South Africa, Hydromulch (Pty) Ltd. is part of the landscape, soil reclamation and erosion control industry. The company uses vetiver grass on a wide scale and has accumulated a collection of isolates to serve as possible germ lines for industrial use. Due to the different approaches in environmental management as well as environmental factors, a variety of ecotypes form during the planting and acclimatisation of this genus. Chrysopogon nigritanus (Benth.) Veldkamp (1999), which is a native species to Africa, is closely related to C. zizanioides and differs only slightly from C. zizanioides on a morphological level. The major difference between the two species is that C. nigritanus is able to seed freely and thus the use of this species should be avoided. The need arose to screen other non-fertile plants to uncover additional genotypic variety to enable diversification of vetiver plantings. The aim of this study was to characterise the genotype of 19 isolates of vetiver obtained from Hydromulch (Pty) Ltd. via sequencing analyses of three DNA fragments, ITS, ndhF and rbcL. In addition, the radial root anatomy was also investigated and compared with the genetic analyses. According to the results generated during this study, very little or no genotypical differences exist amongst the different isolates available from the Hydromulch (Pty) Ltd. plant collection. Only in the case of the ITS inference were differences observed between three of the studied isolates. There was no significant difference between the different isolates based on the root anatomy, with the exception of two of the studied isolates which formed starch granules. / MSc (Botany), North-West University, Potchefstroom Campus, 2014

Vetiver grass or Chrysopogon zizanioides (L.) Roberty (1960) is a sterile grass which can regenerate vegetatively from clumps of the rootstock. This, as well as its vigorous and deep root system and flood tolerance makes it an ideal candidate for the use in soil remediation and erosion control. In South Africa, Hydromulch (Pty) Ltd. is part of the landscape, soil reclamation and erosion control industry. The company uses vetiver grass on a wide scale and has accumulated a collection of isolates to serve as possible germ lines for industrial use. Due to the different approaches in environmental management as well as environmental factors, a variety of ecotypes form during the planting and acclimatisation of this genus. Chrysopogon nigritanus (Benth.) Veldkamp (1999), which is a native species to Africa, is closely related to C. zizanioides and differs only slightly from C. zizanioides on a morphological level. The major difference between the two species is that C. nigritanus is able to seed freely and thus the use of this species should be avoided. The need arose to screen other non-fertile plants to uncover additional genotypic variety to enable diversification of vetiver plantings. The aim of this study was to characterise the genotype of 19 isolates of vetiver obtained from Hydromulch (Pty) Ltd. via sequencing analyses of three DNA fragments, ITS, ndhF and rbcL. In addition, the radial root anatomy was also investigated and compared with the genetic analyses. According to the results generated during this study, very little or no genotypical differences exist amongst the different isolates available from the Hydromulch (Pty) Ltd. plant collection. Only in the case of the ITS inference were differences observed between three of the studied isolates. There was no significant difference between the different isolates based on the root anatomy, with the exception of two of the studied isolates which formed starch granules. / MSc (Botany), North-West University, Potchefstroom Campus, 2014