Doctoral Degrees (Genetics)

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Browsing Doctoral Degrees (Genetics) by Author "Brink, Marissa"

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    Genetic studies for sustainable aquaculture of the sea urchin, Tripneustes gratilla
    (Stellenbosch University, 2020-12) Brink, Marissa; Roodt-Wilding, Rouvay; Rhode, Clint; Macey, Brett Marc; Cyrus, Mark Digby; Stellenbosch University. Faculty of AgriSciences. Department of Genetics.
    ENGLISH ABSTRACT: The sea urchin, Tripneustes gratilla, has been identified as a species with potential for aquaculture production in South Africa, as these animals are distributed along the eastern coast, produce bright orange roe and have a fast growth rate. This study aimed to assess various aspects of T. gratilla that could contribute to successful future aquaculture practices, through population genetics, pedigree reconstruction, qualitative assessments, quantitative genetics and metagenomic approaches. Chapter 2 evaluated the genetic diversity and population structure of T. gratilla populations along the South African coast, through the application of 22 species-specific microsatellite markers. Geographically representative sampled populations formed a single, interbreeding population, with a moderate degree of genetic diversity. In chapter 3, the markers were applied in two T. gratilla cultured cohorts to assess parental contributions, as well as changes in genetic diversity from the progenitor natural population. In these cohorts, the parental skew often associated with broadcast spawning animals was observed, where a single female and male dominated the respective spawning events. This resulted in a decline in genetic diversity, which could have implications for the genetic management of future commercial production. These results suggested that other factors, such as diet, breeding design, gonad and gamete quality could affect reproductive success. Consequently, chapter 4 aimed to assess biological and genetic aspects in T. gratilla that could influence reproductive competition, larval growth and juvenile performance. Results illustrated that a factorial breeding design is an effective approach for retaining genetic diversity in cultured populations. Broodstock conditioned on a mixed feeding regime outperformed animals fed the other diets included in this study (formulated feed, Ecklonia maxima and Ulva rigida). These animals could have had a higher ingestion efficiency, may have been exposed to a broader array of nutrients, displayed improved maternal provisioning or had an improved digestibility promoted by the bacteria introduced through natural feeds. The bacterial communities associated with sea urchin systems play an important role in animal health. In the studied aquaculture environment, bald sea urchin disease has been observed. Chapter 5 explored this disease using a 16S rDNA metagenomics approach, where samples included healthy animals from natural locations along the eastern coast of South Africa, as well as different cultured cohorts: healthy-, diseased- and stressed animals. Results showed that this disease is more likely caused by complex interactions between opportunistic bacteria, rather than by a specific pathogenic agent. Overall, this study showed that the preservation of genetic diversity in cultured T. gratilla populations is possible through factorial breeding designs and broodstock conditioning, where precautionary measures and effective animal husbandry practices can contribute to the prevention of diseases associated with opportunistic bacteria. Therefore, an integrated approach should be implemented to maintain genetic diversity, promote reproductive success and manage disease outbreaks in this emerging echinoculture industry.