Department of Microbiology

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Browsing Department of Microbiology by browse.metadata.advisor "Brink, Danie"

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    An analysis of population structure using microsatellite DNA in twelve Southern African populations of the Mozambique tilapia, Oreochromis mossambicus (Peters)
    (Stellenbosch : Stellenbosch University, 2001-12) Hall, Edward G.; Lewis, Rupert; Brink, Danie; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: DNA micro satellite loci express extensive allelic variation making them convenient markers for research in many fields employing population genetic tools, including aquaculture and conservation genetics. Twelve Oreochromis mossambicus populations from wild, captive and introduced sources in Southern Africa were screened for genetic variation at ten CA repeat micro satellite loci. Three of the loci - UNHI04, UNHlll, and UNH123 - were sufficiently well resolved to screen extensively and were interpreted according to a model of Mendelian inheritance. Data was analyzed in terms of genetic structure and levels of genetic variation, the effect of management regime in captivity through successive generations on genetic diversity, and the nature of phylogenetic relationships present between populations. Exact tests, carried out using Monte Carlo type multiple resampling techniques, and F-Statistics were used to detect and quantify genetic structure among the twelve populations. The Exact test X2 (P < 0.001), a FST of 0.27 (P < 0.001), eST of 0.26, RsT of 0.28, and a ST of 0.17 all indicated significant structuring among the populations. The evident genetic structuring endorsed the practice of maintaining the populations as separate genetic stocks, in separate tanks, in order to preserve unique genetic material for aquaculture strain development. Populations also exhibited some significant deviations from Hardy Weinberg equilibrium characterised by an overall reduced heterozygosity across the loci. In microsatellite studies, null alleles are often suggested as major contributors to heterozygote deficits. To test for null alleles, two controlled crosses of 0. mossambicus were made. The progeny from each cross were examined for expected parental allelic ratios at the UNHI04, UNHlll and UNH123 loci. All three loci presented evidence of possible null alleles. Accelerated inbreeding and genetic drift through successive generations in captivity can reduce heterozygosity and gene diversity. To investigate loss of diversity a sample taken from the Bushmans population in 1999 (N = 25) was compared with a Bushmans 2000 sample (N = 36). The comparison highlighted altered allele frequencies, a significant increase in average observed heterozygosity and a non-significant change in average expected heterozygosity using the UNHI04 and UNH123 loci. Calculation of genetic distances and phylogenetic comparisons between the populations provided insight into the degree of management required in conserving genetic diversity in natural populations of Mozambique tilapia. UPGMA and Neighbour-Joining techniques were used to construct phylogenetic trees using Dm and ({)~)2 distance matrices. Clustering of populations appeared to reflect geographic locality of the source populations, however certain populations were not congruent with geography. Mantel tests were used to expose a possible association between genetic distance matrices generated from each individual locus. An association would support a geographic background to population genetic structure. The Mantel tests did not provide conclusive evidence. Mantel tests for association between the combined locus Dm and (81l)2 genetic distance matrices and a geographic distance matrix were similarly non-significant. Multi-dimensional scaling (MDS) plots of Euclidean distance values for Dm and (81l)2 matrices presented a two-dimensional view of the genetic distance data. The degree of similarity with the UPGMA and Neighbour-Joining tree-clustering pattern was higher for the (81l)2 than for the Dm MDS plots. Scatter plots indicated a reliable non-linear correlation between Euclidean distance and genetic distance for the two-dimensional MDS. The micro satellite markers employed in this research provided molecular information needed for complimenting a co-study on quantitative genetic evaluation of the twelve populations. The quantitative co-study provided measures of average length and weight gain indices for the populations based on progeny growth trials. No significant correlation of average heterozygosity (gene diversity) with either average weight or length gain was found. The significant genetic diversity and structure present between the twelve populations provided rationale for implementing strategies to conserve natural 0. mossambicus populations as genetic resources, and manage captive populations for long term maintenance of genetic diversity.
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    Molecular analysis of genetic variation and relationships within the population of abalone (Haliotis midae) at the Sea Plant Products abalone hatchery, Hermanus, R.S.A.
    (Stellenbosch : Stellenbosch University, 2004-12) Slabbert, Ruhan; D'Amato, M. E.; Brink, Danie; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: The species Haliotis midae is the only commercially exploitable abalone species of the six found in the South African coastal waters. This species is under substantial pressure from both legal and illegal harvesters, to such an extent that it could be commercially extinct within four years. Efforts to alleviate the pressures on the natural populations of both illegal and legal harvesting are being made. The genetic management systems for abalone farming and ranching activities should be carefully evaluated. The loss of genetic diversity and the risks of contaminating the gene pools of natural populations in the vicinity of a farm should be minimized. Genetic evaluation studies will be at great importance to acquire the necessary data needed for genetic diversity and differentiation analysis. The aim at this study was to develop species-specific microsatellite DNA markers to assess the genetic diversity and differentiation within and between the brood stock and commercial stock of the Sea Plant Products abalone farm (Hermanus, Republic of South Africa) and natural populations related to the brood stock. The species-specific DNA markers were also used for parentage assignments within the tarm population (first for abalone) and preliminary OTL (quantitative trait loci)-discovery analysis studying growth rate segregation. Samples were taken of the farm's brood stock and commercial stock (Rows 2, 3, 4) as well as from two natural populations (Saldanha Bay and Black Rock) related to the brood stock. Various statistical parameters and software packages were used to assess genetic diversity and differentiation, to infer parentage and to look for OTL's. Eight species-specific microsatellite DNA markers were designed and used for data analysis. Data analysis showed a loss at genetic diversity from the brood stock to the commercial stock caused by the subdivision of the original brood stock into rows and the differential contributions of parents to the offspring. No genetic differentiation (Fst) was detected between the farm and natural populations, except for the offspring of Row2. levels of inbreeding (ns) were high for all loci within the populations. Thirty-eight percent of all studied offspring were confidently assigned to a couple. The preliminary QTldiscovery suggested the segregation of a number of alleles and genotypes with growth rate. The study concluded that the commercial abalone population of the Sea Plant Products abalone farm holds no threat to the disruption of the genetic diversity of the natural populations. It is proposed that the farm implement a rotational breeding program to increase the genetic diversity of the commercial population. Any newly acquired brood stock must be profiled before their introduction into the breeding program to assess the influence of the animals on the current levels of genetic diversity within the farm. The accuracy and reliability of parentage assignments and QTl-discovery need to be optimised by adding more loci and sampling more animals or even by trying and developing new methods.