Genetic studies for sustainable aquaculture of the sea urchin, Tripneustes gratilla
| dc.contributor.advisor | Roodt-Wilding, Rouvay | en_ZA |
| dc.contributor.advisor | Rhode, Clint | en_ZA |
| dc.contributor.advisor | Macey, Brett Marc | en_ZA |
| dc.contributor.advisor | Cyrus, Mark Digby | en_ZA |
| dc.contributor.author | Brink, Marissa | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of AgriSciences. Department of Genetics. | en_ZA |
| dc.date.accessioned | 2020-11-18T15:45:58Z | |
| dc.date.accessioned | 2021-02-01T07:55:26Z | |
| dc.date.available | 2020-11-18T15:45:58Z | |
| dc.date.available | 2021-02-01T07:55:26Z | |
| dc.date.issued | 2020-12 | |
| dc.description | Thesis (PhDAgric)--Stellenbosch University, 2020. | en_ZA |
| dc.description.abstract | 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. | en_ZA |
| dc.description.abstract | AFRIKAANSE OPSOMMING: Die seepampoentjie, Tripneustes gratilla, is geïdentifiseer as ‘n spesies met die potensiaal vir akwakultuur produksie in Suid-Afrika, aangesien hierdie diere langs die ooskus voorkom, helder oranje gamete produseer met ‘n kenmerkende vinnige groeitempo tot volwassenheid. Die doel van hierdie studie was om verskeie aspekte van T. gratilla, wat kan bydra tot suksesvolle toekomstige akwakultuurprkatyke, te ondersoek. Die navorsing sluit populasiegenetika, heropbou van stambome, kwalitiewe assesserings, kwantitiewe genetika en metagenomiese benaderings in. Hoofstuk 2 evalueer die genetiese diversiteit en genetiese struktuur van T. gratilla populasies langs die Suid Afrikaanse kus met behulp van 22 spesie spesifieke mikrosatelliet merkers. Geografies verteenwoordige steekproefpopulasies het ‘n enkele, telende populasie gevorm, met ‘n matige vlak van genetiese diversiteit. In Hoofstuk 3 is die merkers gebruik in twee T. gratilla nageslagkohorte om die ouerlike bydra te ondersoek, sowel as om die veranderinge in genetiese diversiteit van die akwakultuur populasie te evalueer. In hierdie nageslagkohorte was die skewe verspreiding van ouerlike bydra waargeneem. Dit word dikwels met hierdie diere geassosieer, waar ‘n enkele wyfie en mannetjie die onderskeie broeigeleenthede oorheers. In hierdie studie het dit gelei tot ‘n afname in genetiese diversiteit, wat direkte gevolge kan hê vir die genetiese bestuur van toekomstige kommersiële produksie. Resultate dui daarop dat ander faktore, insluitend dieët, die teelontwerp, gonade- en gameet kwaliteit, die voortplantingsukses verder kan beïnvloed. Gevolglik was die doel van hoofstuk 4 om biologiese en genetiese aspekte in T. gratilla te beoordeel wat betref voorplantingskompetisie, larwegroei en jong seepampoentjie prestasie. Die resultate illustreer dat ‘n faktoriale teelontwerp ‘n effektiewe benadering is om genetiese diversiteit in gekweekte populasies te behou. Teeldiere wat gekondisioneer is met ‘n mengvoedingsregime het beter presteer as diere wat aan die ander diëte blootgestel was (geformuleerde dieet, Ecklonia maxima en Ulva rigida). Hierdie diere, blootgestel aan ‘n wyer verskeidenheid voedingsstowwe, het waarskynlik ‘n hoër voedsel innamedoeltreffenheid en verteerbaarheid gehad en ook waarskynlik verbeterde moedersvoorsiening vertoon as gevolg van bakterieë wat met die natuurlike voere geassosieer word. Die bakteriese gemeenskappe in noue assosiasie met seepampoentjies speel dus ‘n belangrike rol in dieregesondheid. In die bestudeerde akwakultuuromgewing is “bald sea urchin disease” waargeneem. Hoofstuk 5 het hierdie siekte verder ondersoek, deur gebruik te maak van ‘n 16S rDNA metagenomiese benadering waar monsters van gesonde diere in natuurlike populasies langs die ooskus van Suid-Afrika ingesluit is, sowel as verskillende akwakultuur kohorte: gesonde-, siek- en gestresde diere. Resultate wys daarop dat hierdie siekte meer waarskynlik veroorsaak word deur komplekse interaksies tussen opportunistiese bakterieë, eerder as deur ‘n spesifieke patogene agent. Dit is dus noodsaaklik dat ‘n geïntegreerde benadering geïmplementeer word om genetiese diversiteit te handhaaf, reproduksiesukses te bevorder en siekte-uitbrake in die opkomende echinokultuurbedryf te bestuur. | en_ZA |
| dc.description.version | Doctoral | en_ZA |
| dc.format.extent | xviii, 213 pages : illustrations (some color), maps | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/109444 | |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject | Sea urchin aquaculture -- South Africa -- Population | en_ZA |
| dc.subject | Tripneustes gratilla -- South Africa -- Genetic aspects | en_ZA |
| dc.subject | Microsatellites (Genetics) | en_ZA |
| dc.subject | Metagenomics | en_ZA |
| dc.subject | Sea urchins -- Feeding and feeds | en_ZA |
| dc.subject | Echinoculture | en_ZA |
| dc.subject | UCTD | en_ZA |
| dc.title | Genetic studies for sustainable aquaculture of the sea urchin, Tripneustes gratilla | en_ZA |
| dc.type | Thesis | en_ZA |