Browsing by Author "Slabbert, Ruhan"

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    Identification of growth related quantitative Trait Loci within the abalone using comparative microsatellite bulked segregant analysis
    (Stellenbosch : Stellenbosch University, 2010-12) Slabbert, Ruhan; Roodt-Wilding, R.; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics
    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.
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    Looking inside votive creatures : computed tomography (CT) scanning of ancient Egyptian mummified animals in Iziko Museums of South Africa : a preliminary report
    (Stellenbosch University, Department of Ancient Studies, 2012) Cornelius, I.; Swanepoel, L. C.; Du Plessis, A.; Slabbert, Ruhan
    The ancient Egyptians mummified many more animals than humans. The study of ancient Egyptian animal mummies is varied and extensive. Currently new methodologies and modern technology are being used to unlock the secrets of animal mummies. Recently five animal mummies housed in the Egyptian collection of Iziko Museums of South Africa in Cape Town were scanned using a state of the art computed tomography (CT) scanner at Stellenbosch University. Preliminary results revealed two complete bird skeletons, a claw, a fake and the partial skeleton of what appears to be a cat.
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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.
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    Molecular markers to assist the South African abalone industry
    (Academy of Science for South Africa, 2006) Roodt-Wilding, R.; Slabbert, Ruhan
    HALIOTIS MIDAE (PERLEMOEN) IS THE ONLY southern African species of abalone to be commercially exploited. Commercial farms are currently producing 750 tons per annum, making this an economically viable enterprise. Increasing world demand and dwindling natural populations have, however, necessitated the adoption of genetic management practices on South African abalone farms to remain sustainable. This can be done by means of DNA markers, which are employed to investigate various phenomena from genetic diversity, parentage and broodstock contributions to linkage mapping and marker-assisted selection for genetic enhancement of the commercial species. The use of microsatellite markers for various abalone aquaculture applications is highlighted in this review.
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    Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution
    (Public Library of Science, 2018) Van Asch, Barbara; Versfeld, William F.; Hull, Kelvin L.; Leslie, Alison J.; Matheus, Timoteus I.; Beytell, Petrus C.; Du Preez, Pierre; Slabbert, Ruhan; Rhode, Clint
    Nile crocodiles are apex predators widely distributed in sub-Saharan Africa that have been viewed and managed as a single species. A complex picture of broad and fine-scale phylogeographic patterns that includes the recognition of two species (Crocodylus niloticus and Crocodylus suchus), and the structuring of populations according to river basins has started to emerge. However, previous studies surveyed a limited number of samples and geographical regions, and large areas of the continent remained unstudied. This work aimed at a fine scale portrait of Nile crocodile populations at the fringes of their geographic distribution in southern Africa. Wild and captive individuals were sampled across four major river systems (Okavango, Lower Kunene, Lower Shire and Limpopo) and the KwaZulu-Natal region. A multi-marker approach was used to infer phylogeographic and genetic diversity patterns, including new and public mitochondrial data, and a panel of 11 nuclear microsatellites. All individuals belonged to a phylogenetic clade previously associated with the C. niloticus species, thus suggesting the absence of C. suchus in southern Africa. The distribution of mitochondrial haplotypes indicated ancestral genetic connectivity across large areas, with loss of diversity along the north-south axis. Genetic variation partitioned the populations primarily into western and eastern regions of southern Africa, and secondarily into the major river systems. Populations were partitioned into five main groups corresponding to the Lower Kunene, the Okavango, the Lower Shire, and the Limpopo rivers, and the KwaZulu-Natal coastal region. All groups show evidence of recent bottlenecks and small effective population sizes. Long-term genetic diversity is likely to be compromised, raising conservation concern. These results emphasize the need for local genetic assessment of wild populations of Nile crocodiles to inform strategies for management of the species in southern Africa.
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    Wat maak jou mummie? ’n Oorsig van die stand van mummienavorsing aan die hand van die 8ste wêreldkongres
    (Suid-Afrikaanse Akademie vir Wetenskap en Kuns, 2015-01) Slabbert, Ruhan; Swanepoel, Liani; Cornelius, I.
    Die doel van hierdie artikel is om opsommend al die temas en studierigtings te beskryf wat by die 8ste Wêreldkongres oor Mummienavorsing aangebied is om die huidige stand van die bestudering van mummies aan te dui. Mummies is unieke bronne van inligting oor die verlede en die studie van mummies gee ons insig in die lewens van mense uit vervloë dae en van vele kulture. Mummies het nog altyd bekoor, selfs vandag nog. Die 8ste Wêreldkongres oor Mummienavorsing is vanaf 6 tot 9 Augustus 2013 in Rio de Janeiro, Brasilië, gehou. Hierdie kongres bring wetenskaplikes bymekaar wat mummies en hul toebehore bestudeer. Die 8ste kongres het verskeie internasionaal erkende navorsers se werk deur middel van 99 referate en 45 plakkaataanbiedings ten toon gestel. Twee plakkate het selfs oor werk gehandel wat in Suider-Afrika gedoen word, naamlik die studie van antieke Egiptiese dieremummies in Iziko Museums van Suid-Afrika (Kaapstad) en die studie van die Tuli-mummie wat in Botswana gevind is. Die wetenskaplike studie van mummies is goed gevestig en toon merkwaardige groei. Die enigste kritiek teen die kongres is egter die oordrewe klem op suiwer wetenskaplike studie en dat die kulturele en sosiale interpretasie van die mummies grootliks agterweë gelaat is. Die natuur-, mediese en chemiese wetenskappe is goed verteenwoordig en die data is waardevol, maar die ware integrasie van hierdie en die sosiale wetenskappe is nog onvoldoende. ’n Meer gebalanseerde kombinasie van die verskillende dissiplines sal die waarde van so ’n kongres aansienlik verhoog.