Doctoral Degrees (Genetics)

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Browsing Doctoral Degrees (Genetics) by Subject "Aquaculture"

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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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    Reproduction of the South African abalone, Haliotis midae
    (Stellenbosch : Stellenbosch University, 2011-12) Visser-Roux, Adelle; Roodt-Wilding, R.; Lambrechts, Helet; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.; Roux, Adelle
    ENGLISH ABSTRACT: Currently, South African aquaculture is dominated by the cultivation of Haliotis midae, which is estimated as the most lucrative sector of the industry, with 934 t being export in 2008, totalling an income of ZAR 268 million (40 million USD) in 2008. This represents 81% of the total rand value of the aquaculture sector. Abalone was the highest aquaculture commodity exported during the last two years from South Africa, representing 24% of the total tonnage exported. Employment in the aquaculture sector increased by approximately 80% between 2005 and 2008, and was highest in the abalone sector where the number of people employed increased by 234%. Despite these high production rates, no hatchery procedures have been developed specifically for H. midae. Most procedures and protocols currently used in South African abalone hatcheries have been adopted from cultivation methods used for foreign species. Although certain aspects of reproduction are universally conserved between abalones, it is important to consider the physiology and the origin of the species studied. To date, no scientific research has been conducted on the reproduction of H. midae, except for a few studies in the early 1990s, which focused on the basic reproduction of this species. No further studies have been done on H. midae reproduction under intensive culture. Currently, hatch-out rates obtained by most abalone farms in South Africa averages 80%, with a 50% settlement rate, and a final hatchery output of only 30%. This study reports on various aspects of H. midae reproduction that can influence its commercial culture. A detailed histological characterisation of gametogenesis was developed. Findings indicated that cultured H. midae reaches 50% sexual maturity at a shell width of between 25 mm and 30 mm. During fertilisation trials, a sperm concentration of 50 000 sperm mL-1 and egg concentrations lower than 50 eggs mL-1 produced the highest hatch-out rates. Whilst fertilisation volume did not influence fertilisation success, fertilisation potential of the eggs did decrease with time. Eggs older than 100 minutes showed a lower fertilisation potential than eggs fertilised earlier. A larval stress test was developed to evaluate larval resistance against chemical stress. It was determined that 50% of resultant larvae would exhibit morphological abnormalities after fertilised eggs were incubated in 0.7% dimethyl sulfoxide (Me2SO) for a 24 hour period. If larvae exhibited fewer abnormalities at this concentration, it could be deduced that the larvae had a high resistance to the negative effect of the toxicant, and could thus be seen as good quality larvae. When evaluating hybridisation potential between H. midae and H. spadicea, it was found that it was possible to fertilise spawned H. midae eggs with biopsied H. spadicea sperm. By incorporating the results obtained from the present study into current hatchery systems on South African abalone farms, higher hatchery yield could be achieved, which in turn would lead to an increase in commercial revenue.