Thesis (MSc)--Stellenbosch University, 2002. / ENGLISH ABSTRACT: The species Haliotis midae is the only abalone species of commercial importance to the South African fisheries industry. The species is currently under substantial pressure due to commercial harvest and illegal poaching, to the extent that genetic and biodiversity may be under threat. The species is also being cultured in commercial systems for supply to international markets. The South African production for 2002 amounted to 350 tons. The commercial production of abalone may also have implications with regard to genetic diversity of natural and commercial populations. The aim of this project was to assess the genetic diversity of the natural and commercial populations of abalone at the I&J Abalone Farm, Danger Point, Gansbaai, in South Africa, in order to make recommendation with regard to possible impact on natural diversity as well as internal management systems. Distortion of natural genetic diversity or a loss of internal diversity will have detrimental consequences. Representative samples have been obtained from the surrounding natural population, as well as the commercial populations, including the broodstock and various progeny groups. Both mtDNA and AFLP molecular techniques were used to assess genetic diversity. Data analysis showed that the genetic profile of the commercial population display sufficient genetic variation. The genetic structure of the commercial population also displays no significant deviation from that of the surrounding natural population, i.e. the population of origin. The results through give indication of a small, though unsignificant loss of genetic variation from the broodstock to the subsequent progeny groups. The investigation conclude that the commercial populations of abalone at the I&J Abalone Farm, Danger Point, Gansbaai, in its current format holds no threat to the disruption of the genetic diversity of the surrounding natural population. Further, the commercial population possesses sufficient genetic variation in view of future genetic development. There is signs of a slight loss of genetic variation in the change over from the broodstock to the progeny groups. This would necessitate careful and controlled replacement of the original broodstock with new animals from the commercial progeny groups as part of an ongoing process of domestication. / AFRIKAANSE OPSOMMING: Die spesie Haliotis midae is die enigste perlemoen spesie van kommersiële belang vir Suid Afrikaanse visserye. Die spesie verkeer tans onder toenemende druk as gevolg van kommersiële en onwettige vangste, tot so 'n mate dat genetiese en biodiversiteit daardeur geaffekteer kan word. Die spesie word in toenemende mate kunsmatig gekweek vir voorsiening aan internasionale markte. Suid Afrikaanse produksie vir 2002 beloop reeds sowat 350 ton per jaar. Die kunsmatige produksie van perlemoen het ook moontlike implikasies op die genetiese diversiteit van natuurlike en kommersiële populasies van die perlemoen, Haliotis midae. Die doel van die projek was om die aard van genetiese diversiteit van die natuurlike en kommersiële populasies van perlemoen by die I&J Perlemoen Plaas, Danger Point, Gansbaai in Suid Afrika te ondersoek, ten einde aanbevelings te maak ten opsigte van moontlike impak op natuurlike diversiteit asook ten opsigte van interne genetiese bestuurstelsels. Versteuring van natuurlike diversiteit of verlies van interne diversiteit hou nadelige gevolge in. Verteenwoordigende monsters is versamel vanuit die omliggende natuurlike populasies, sowel as van die kommersiële populasie op die plaas, insluitend die teelmateriaal en verskillende nageslaggroepe. Beide mtDNA en AFLP-molekulêre tegnieke is gebruik tydens die ontleding van genetiese diversiteit. Dataontleding het aangetoon dat die genetiese profiel van die kommersiële populasie voldoende genetiese variasie demonstreer. Die genetiese struktuur van die kommersiële populasie toon verder geen betekenisvolle verskil met die omliggende natuurlike populasie nie, dit wil sê met die populasie van oorsprong nie. Die resultate toon verder 'n geringe, dog nie betekenisvolle verlies van genetiese variasie wat waargeneem word met oorgang van die teelmateriaal na die onderskeie nageslaggroepe. Die bevindinge van die ondersoek is dus dat die kommersiële populasie op die I&J Perlemoen Plaas, Danger Point, Gansbaai, in die huidige formaat, geen bedreiging inhou vir die versteuring van die omliggende natuurlike genetiese diversiteit nie. Verdere bevindinge is dat die kommersiële populasie oor voldoende genetiese diversiteit beskik met die oog op toekomstige genetiese ontwikkeling. Daar is tekens van 'n geringe afname in genetiese diversiteit met die oorgang vanaf die teelmateriaal na die nageslaggroepe. Dit beklemtoon die belang van 'n gekontroleerde vervanging van die oorspronklike teelmateriaal met nuwe teeldiere vanuit die kommersiële populasie as deel van die domestikasieproses.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Haliotis midae (locally also known as perlemoen) is the largest of five endemic species found along the coast of South Africa. It is the only species with commercial value contributing to the exploitation of these animals. Due to declines of natural stocks, farming practices were established during the early 1990s in order to supply the international demand. To facilitate efficient breeding methods and ensure the sustainability of these commercial populations, genetic management, which can be accomplished with the use of molecular markers such as single nucleotide polymorphisms (SNPs), is necessary. Single nucleotide polymorphisms have become the markers of choice in various applications in aquaculture genetics due to their abundance in genomes, reduction in developmental costs and increased throughput of genotyping assays. Identification of SNPs in non-model species such as H. midae can be achieved by in silico approaches. In silico methods are suitable for de novo SNP identification and are both cost- and time-efficient. It is based on the analysis of multiple alignments where mismatches may be reported as candidate SNPs. Various medium-throughput genotyping methods are available to confirm putative SNPs, but the ideal method depends on factors such as cost, accuracy and multiplexing capacity. Although SNP markers can have various applications within the aquaculture environment the focus for this current study was saturating the linkage map of H. midae with additional markers. This would assist in the identification of quantitative trait loci associated with economically important traits, which in turn could ultimately be employed for marker-assisted selection and improved molecular breeding programs. In order to identify in silico SNPs, sequenced transcriptome data from a previous study was used and subjected to a series of criteria: minor allele frequency 10%, minimum coverage 80, 60 bp flanking regions. Selected loci were genotyped using a 192-plex assay with the Illumina GoldenGate genotyping assay with the VeraCode technology on the BeadXpress platform, in individuals from six mapping families. A conversion rate of 69.35% and global success rate of 76.34% was achieved. Polymorphic loci were subjected to linkage analysis using JoinMap® v.4.1 to create sex-average and sex-specific maps and to saturate the current linkage map for H. midae. Along with previously developed markers, 54% of the newly developed SNPs could be successfully incorporated into the linkage map of H. midae. A total of 18 linkage groups were observed with an average marker spacing of 6.9 cM and genome coverage of 79.1%. Bioinformatic analyses and setting stringent criteria to identify SNPs from sequenced transcriptomic data proved to be an efficient way for SNP discovery in the current study. Genotyping of the identified loci with the GoldenGate genotyping assay demonstrated a high success rate; providing a genotyping assay adequate for species with little genomic information. The linkage map created in this study illustrated the utility of SNP markers in conjunction with microsatellite markers for linkage map construction and the adequate marker spacing obtained provides a step closer to quantitative trait loci mapping in this species. / AFRIKAANSE OPSOMMING: Haliotis midae (plaaslik ook bekend as perlemoen) is die grootste van vyf inheemse spesies wat langs die kus van Suid-Afrika aangetref word. Dit is die enigste spesie van kommersiële waarde wat bydraend is tot die uitbuiting van hierdie diere. As gevolg van die afname in hierdie natuurlike hulpbron het boerdery praktyke gedurende die vroeë 1990's ontstaan om in die internasionale aanvraag te voorsien. Ten einde doeltreffende teelmetodes te beoefen en die volhoubaarheid van hierdie kommersiële populasies te verseker is genetiese bestuur, wat bewerkstellig kan word deur die gebruik van molekulêre merkers soos enkel nukleotied polimorfismes (ENPs), baie belangrik. Enkel nukleotied polimorfismes is gewilde merkers in verskeie toepassings in akwakultuur genetika as gevolg van hul oorvloed in genome, verlaagde ontwikkelingskoste en verhoogde deurset van ENP-genotiperingstoetse. Identifisering van ENPs in nie-model spesies soos H. midae kan uitgevoer word deur in siliko benaderings te gebruik wat geskik is vir de novo ENP identifisering en ook tyd- en koste-effektief is. Dit word gebaseer op die analise van veelvuldige inlynstellings waar nukleotiedes wat nie ooreenstem nie as kandidaat ENPs gerapporteer kan word. Om kandidaat ENPs te bevestig, kan verskeie medium-deurset genotiperingsmetodes uitgevoer word, maar die ideale metode word bepaal deur faktore soos koste, akkuraatheid en multipleks kapasiteit. Alhoewel ENP merkers in verskeie toepassing binne die akwakultuur omgewing gebruik kan word was die fokus van die huidige studie om die koppelingskaart van H. midae te versadig. Dit sal bydrae tot die identifisering van kwantitatiewe eienskap lokusse wat gekoppel kan word aan ekonomies belangrike eienskappe wat dan op die beurt weer vir merkerbemiddelde seleksie gebruik kan word en uiteindelik ten opsigte van die verbetering van molekulêre teelprogramme aangewend kan word. Ten einde in siliko ENPs te identifiseer is transkriptoomdata van 'n vorige studie gebruik en onderwerp aan 'n reeks kriteria: geringste alleelfrekwensie 10%, minimum dekking 80, 60 bp gebiede weerskante van polimorfisme. Geïdentifiseerde lokus-genotipering is met behulp van 'n 192-pleks toets uitgevoer met die Illumina GoldenGate genotiperingstoets met die VeraCode tegnologie op die BeadXpress-platform, in individue afkomsitg vanaf ses karteringsfamilies. 'n Omskakelingskoers van 69.35% en 'n algehele sukseskoers van 76.34% is bereik. Polimorfiese lokusse is onderwerp aan koppelings-analise met behulp van JoinMap® v.4.1 om geslags-gemiddelde en geslags-spesifieke kaarte te skep asook om die kaart wat beskikbaar is vir H. midae te versadig. Saam met voorheen ontwikkelde merkers is 54% van die nuut ontwikkelde ENPs suksesvol opgeneem in die kaart van H. midae. 'n Totaal van 18 koppelingsgroepe is verkry met 'n gemiddelde merker-spasiëring van 6.9 cM en 'n genoomdekking van 79.1%. Die gebruik van bioinformatiese analises en streng kriteria om ENPs vanaf transkriptoomdata te identifiseer blyk doeltreffend te wees in hierdie studie. Genotipering van die geïdentifiseerde lokusse met die GoldenGate genotiperingstoets dui op 'n hoë suksessyfer en verskaf 'n voldoende genotiperingstoets aan spesies met min genomiese inligting. Die koppelingskaart in hierdie studie het geïllustreer dat die ENP merkers suksesvol saam met mikrosatelliet merkers gebruik kan word vir koppelingskaart konstruksie en dat die voldoende merker-spasiëring verkry 'n stap nader aan kwantitatiewe eienskap lokus kartering in hierdie spesie bied.

Haliotis midae is the cornerstone of the South African abalone fishery. For more than a decade, the wild abalone stock of South Africa has suffered decline due to over-exploitation and illegal activities such as poaching. Prior to 1970, no regulations were in place concerning the annual landings. As a result the fishery was exploited as if it were an infinite resource. It is this initial uncontrolled harvesting (regardless of age) and poaching that has driven the abalone resource decline. Due to the slow growth rate exhibited by abalone as a species, natural replenishment of wild stock following exploitation and poaching was far below the rate of exploitation of this resource. Studies on the growth of abalone have mainly been conducted under laboratory conditions. The purpose of this study was to measure the growth of abalone, fed different diets, under commercial culture conditions. Three food types were used namely; commercial pellets, seaweed (Ulva spp.) and dried kelp bars (Ecklonia maxima). Four diets were obtained from the three food types namely; combination of commercial pellets and seaweed (Diet A), commercial pellets only (Diet B), seaweed only (Diet C) and dried kelp bars only (Diet D). The food types used in this study represent both artificial (Commercial pellets) and natural feeds (seaweed and kelp) used in commercial abalone culture. The growth of two cohorts (40-50 mm and 50-60 mm) was followed over a 426 day period, with data for the first 183 days being used for statistical analysis to determine performance of a given diet. The best growth rates were found in abalone fed Diet A (40-50 mm: 2.64 mm.month-1; 50-60 mm 2.78: mm.month-1) and B (40-50 mm: 2.20 mm.month-1; 50-60 mm: 2.35: mm.month-1). These (Diets A and B) gave higher growth rates when compared to Diets C and D (natural diets), whose growth rates ranged between 0.50 mm.month-1 and 1.71 mm.month-1 for both cohorts. Also observed in this study was that, the mixture of formulated diet and seaweed gave better growth than formulated diet given exclusively.

Abalone Haliotis midae farming in South Africa is highly intensive, employing pump-ashore, flow-through systems. Despite the known sensitivity of abalone to water quality, there is only a rudimentary understanding of water quality dynamics on South African abalone farms and its effects on abalone production. Furthermore, the potential for reusing the relatively dilute abalone farm effluent to culture other animal species has not been investigated. This study investigated the dynamics of water quality and growth on a South African abalone farm and assessed the suitability of the effluent for the culture of silver kob Argyrosomus inodorus and bloodworm Arenicola loveni loveni. Monitoring of water quality and abalone growth in abalone tanks revealed that oxygen concentrations decreased, while H⁺ ion and free-ammonia (NH₃) concentration increased in a gradient between the inflow and outflow. Abalone growth was positively correlated with oxygen concentration and negatively correlated with free-ammonia and H⁺ ion concentration. The oxygen (O) concentration of the farm influent was dependent upon the influents’ temperature (T) and was described by the relationship O (mg L⁻¹) = 11.244 – 0.208T (r²=0.74). Linear regression analysis of data collected from abalone farm tanks revealed that the concentration of total ammonia at the outflow of abalone tanks (μg TAN L⁻¹) was dependant upon temperature (°C), flow-rate (L s⁻¹ kg⁻¹ H. midae), abalone size (g) and length of time since the tank was last cleaned (d) (n = 125, r² = 0.80). The production of total ammonia (μg TAN s⁻¹ kg⁻¹) was related to temperature, abalone size and days that the tanks remained un-cleaned (n = 125; r² = 0.81). A diurnal cycle of respiration was evident in abalone tanks with higher oxygen consumption and H+ ion production at night. The oxygen concentration of farm effluent was related to temperature, farm biomass and flow rate by means of a linear regression equation (n = 40; r² = 0.69). The results demonstrated the importance of optimising the flow-rate per unit of biomass for various temperatures and sizes of abalone. As abalone size and temperature cannot be controlled under farm conditions, the flow-rate per unit of biomass which the abalone culture system receives will determine the quality of the culture water. The specific growth rate (0.48 ± 0.01 % BW d⁻¹), mortality (1.8 ± 0.5 %), feed conversion ratio (3.0 ± 0.2) and protein efficiency ratio (1.0 ± 0.1) of silver kob kept in either abalone farm effluent or control seawater for 120 days did not differ significantly (t-test, P>0.05). A 90 day growth trial indicated that abalone farm effluent is a suitable culture medium for bloodworm. Bloodworm supplied with control seawater lost weight at 0.19 ± 0.04 % BW d-1, while those given abalone effluent grew at 0.39 ± 0.07 % BW d⁻¹. Mortality was 6 ± 3 % in effluent and 11 ± 8 % in seawater. The bloodworm were efficient at processing solid waste. Abalone farm effluent initially contained 7.7 ± 13 mg L⁻¹ more suspended solids than control seawater, which contained 3.5 ± 0.5 mg L⁻¹, but after passing through bloodworm systems the concentration in abalone effluent was reduced to only 1.4 ± 3.5 mg L⁻¹ above that in control seawater. Therefore, abalone farm effluent could be reused as a culture medium for both silver kob and bloodworm. Future work is needed to investigate aspects of the feasibility of such systems such as growth rates at different sizes and stocking densities.

The largest abalone in South Africa, the perlemoen, Haliotis midae, occurs along approximately two-thirds of the country's coastline, but has only been the target of an extensive commercial fishery in the south-western part of South Africa. Large-scale illegal fishing has however proliferated throughout its entire range over the last 10–15 years, which has had serious effects on stock abundance and once productive populations are facing economic collapse. Abalone stock enhancement has been put forward as an addition or alternative to traditional fisheries management practices, which can potentially rehabilitate overfished abalone populations and enhance natural production. The aim of this project was to investigate the potential of abalone stock enhancement for managing an area in the Eastern Cape Province, which was being subjected to intense illegal fishing pressure. A research approach was adopted to investigate the scale and effects of this poaching and to investigate the survival of artificially cultured abalone seed in the natural environment. A model of a commercial-scale ranching operation was investigated to assess the economic feasibility of such a scheme. Analysis of poaching cases and research samples from Cape Recife indicated high levels of fishing effort that appeared to be causing the observed declines in emergent abalone abundance and average size. Poaching cases from Cape Recife contributed 32% of the total number of cases of known origin in the Eastern Cape Province from 1998–2002, with the majority of the cases (82%) originating from within the Port Elizabeth metropole. There was an exponential increase in the number of poaching cases in the Eastern Cape Province (r²=0.967) and Port Elizabeth over this period but actual annual total catch stabilized, particularly at Cape Recife, where estimates of CPUE declined significantly from 2000–2002 (p<0.001). The annual proportion of emergent abalone under the MLS from Cape Recife was always >85% in confiscations and research collections, and did not change significantly over the period of examination. Comparison of illegal catches with an adjacent site indicated that the emergent abalone population at Cape Recife had a significantly higher proportion of undersized emergent animals (p<0.001) and they were significantly smaller than the abalone from the closest site, Noordhoek, and other areas in Port Elizabeth from 2000–2002 (p<0.001). The apparent declines in emergent abalone abundance indicated by the poaching data were corroborated by sampling of emergent abalone abundance at Cape Recife. Numbers of abalone declined significantly from 125.6 to 53.8 per 20min count (p<0.001), from April 1998–October 2001 and density declined from 1.3 to 0.8m⁻² over a similar period (p<0.001). Juvenile density did not change over this period, although there were significant differences in density observed between two different habitats (p<0.001). Initial releases of cultured juvenile abalone showed that they could be distinguished from their wild counterparts for at least a year after release, by their different shell colouration. Short-term, small-scale trials (7–10 days) using animals between 17 and 30mm SL had mean survival rates of 64–82% (mean 70.4%) and the effect of size on survival was not significant in most cases, although the power to detect differences was low. Attempts to measure the effect of habitat on survival were not conclusive, although refuges under sea urchins appeared to be favoured by both seed and wild abalone, although urchins were not an absolute requirement for survival. Similar medium-term trials (31–74 days) in sheltered sites yielded mean returns of 53.1% using 25mm SL animals and similar trials in a more exposed area had more variable survival rates of between 18.4 and 73.6%, after 25–27 days. A comparison between careful hand-seeding and surface-scattering seed release methods in the open-ocean habitat showed no significant differences in survival rate after 41 days. Larger seed survived significantly better than the smaller seed when scattered on the surface (p<0.0001) and the smaller seed survived significantly better when seeded carefully by hand onto the substrate (p<0.028). Further medium-term releases of large numbers of seed abalone, released using the surface-scattering method in open-ocean habitat, gave mean survival rates of 32.8% over periods of 83–114 days. Assessment of a seeding trial using release modules to seed juvenile animals in the open-ocean was hampered by poor sea conditions and difficult to search substrates, and a mean recovery rate of 3.1% was obtained for the sites that were sampled. Movement of seed was low in the more sheltered sites, and also appeared to be affected by the amount of available habitat. Growth of seed was measured using changes in shell colouration and there were significant differences between areas. An average growth of 1.6mm.month⁻¹ shell length was calculated for all areas. The potential for commercial scale abalone ranching to be used to enhance a territorial user right fishery was investigated using a model of economic feasibility. Internal rates of return of 30.3 and 36.9% were obtained from two harvest regimes using different harvest sizes. There was a high degree of risk associated with these figures owing to a lack of consistent seed survival rate estimates, and the input parameters, which are subject to variation, showed a significant effect on profitability. The operation of this type of ranching scheme is probably not economically feasible as a stand-alone operation but could probably be operated effectively in conjunction with an existing abalone farm. By adding a small wild catch component the profitability of a ranching scheme could be significantly improved. The results of the present study indicate that high levels of poaching at Cape Recife have led to declines in emergent abalone abundance, which will probably lead to stock collapse in the near future. This implies that fisheries managers have failed to fulfil the provisions of fisheries policy in South Africa. The present results from seeding trials show that cultured juveniles can survive and make a contribution to overall stock abundance. Furthermore, while there are obstacles to economic feasibility, commercial ranching has the potential to be a valuable addition to current abalone management strategy.

Terebrasabella heterouncinata is a small K-selected sabellid polychaete. It is a simultaneous hermaphrodite with a semi-continuous mode of reproduction, producing relatively few large eggs that are brooded within the parental burrow until the larvae emerge, to settle on the growing edge of the abalone shell. Despite its low fecundity, this worm has become problematic on abalone farms in South Africa. The present study was conducted to gain an understanding of the life history patterns of T. helerouncinata to determine how they contributed to the success of these worms under altered conditions. This study demonstrated that conditions prevalent on abalone farms were conducive to enhancing the reproductive success of this worm, and suggests that larger, more fecund worms may have been selected for in the decade that these worms have been present on the farms. Increased nutrient availability, and possibly the increased stability of the farm environment relative to its natural environment, has led to a 1.5-fold increase in the average size of the worms. Body size was found to be positively correlated with brood size, and this resulted in worms on farms brooding 3 to 4.5 times more offspring at a time than worms from wild abalone. The ability to increase the number of eggs produced at a time may have been limited by the fact that these worms have only two ovaries. Thus, the increase in fecundity may have been related primarily to the increase in the rate at which the eggs were laid by the worms on the farms, and the increase in the coelomic space available for the storage of these rapidly developing eggs. The ability to increase the rate at which oocytes develop may be related to the vitellogenic mechanisms employed by these worms. Vitellogenic oocytes are able to incorporate high molecular weight yolk precursors from the surrounding coelomic fluid through endocytotic activity. This may allow the oocytes to increase the rate at which they incorporate yolk material under conditions of nutrient enrichment. The increase in fecundity did not occur at the expense of offspring size and, presumably, quality. The increased reproductive output on the farms was compounded by a proportionate increase in the number of reproducing worms within the population. In addition, these worms are long-lived (worms from farmed abalone reached a maximum age of approximately 40 months) and exhibit negligible senescence. Thus, their reproductive output did not change significantly with an increase in age. Furthermore, the proportion of the reproductive worms did not decrease with an increase in age. Thus, within the age range tested, worms of all ages have the potential to make equal contributions to population growth. While diet and abalone stocking density could not be identified as having a significant effect on reproductive output and infestation rate under intensive culture conditions, it was demonstrated that in a naïve abalone population, the total intensity of infestation increased exponentially with time. This increase may be a consequence of an increase in fertilisation success. These worms continuously produce entaquasperm that are released into the water column. The sperm are collected by other individuals that then store the sperm in a single spermatheca. The ability to store sperm relieves individuals of a dependence on the synchronisation of spawning of eggs and sperm. As the population size and density increases, there could be more individuals releasing sperm into the water column, resulting in a continuous supply of sperm. The increased production of eggs would therefore not be constrained by a lack of sperm. The stored sperm are released into the brood chamber to fertilise eggs as they are laid, and this would probably increase the fertilisation success in the species. This study also provides evidence to suggest that reproduction in this worm has a seasonal component. Future studies should concentrate on measuring fertilisation success in greater detail, measuring the effect of season on reproduction, determining whether there are genetic differences between worms on farmed and wild abalone and determining whether wild worms have similar life-spans and age-related fecundity as worms on farms.

The abalone (Haliotis midae) culture industry in South Africa is becoming increasingly dependent on the use of formulated feeds, due to limitations in the supply of kelp. The bulk of the feeds that are currently available were developed based on the requirements of juvenile abalone cultured within the optimal temperature range for growth (18 - 20 °C). However, most abalone farming facilities are land-based pump ashore operations and are thus mostly exposed to temperatures outside of this range. In addition, these feeds have been found to be unsuitable for abalone cultured at elevated water temperatures (> 20°C). The aim of the study was to develop size and temperature specific diets for H midoe through optimisation of dietary protein, energy and lipid levels. Abalone were cultured under farm-like conditions in three partially recirculating temperature controlled systems at either 18, 22 or 24°C and fed formulated diets containing graded levels of protein (18,22 and 26 %) and energy (11.6, 13.5 and 16.2 MJ.kg·I ). Abalone were stocked into baskets at 5 % of available of surface area (n=36) and each diet (n=9) was fed to four baskets of abalone at each of the three temperature regimes for ten weeks. Abalone growth was temperature dependent, with growth declining from 4.33 g.month-I for abalone cultured at 18°C to 0.77 g.month-I at 24°C. Dietary protein could be reduced from 26 to 18 % provided dietary energy levels were maintained at 13.5 MJ.kg- l • A dietary energy level of 11.6 MJ.kg-1 was insufficient to meet the energetic requirements of H midae regardless of the protein content of the diet. The effects of water temperature and body size on the protein requirements of H midae were investigated by culturing abalone at temperatures within the optimal range for abalone farming (i.e. 14, 16 and 18°C). Three size classes of abalone (15, 50 and 80 mm) were fed formulated feed containing graded levels of dietary protein (20, 26, 32, 38 and 44 %) under controlled laboratory conditions for 12 weeks, and, in a separate experiment, under commercial farm conditions for 24 weeks. It was not possible to convincingly define the optimal protein levels for abalone of different sizes in this experiment because growth rates fell below average commercial growth rates obtained on farms. Growth was temperature dependent in the laboratory trial, with the rate of weight gain of the 15 mm (ANOV A: p=0.002) and 50 mm abalone (ANOV A: p=0.02) increasing significantly with an increase in temperature from 14 to 18°C. In the farm trial, dietary protein content did not affect the growth rate of the 10-15 or 80 mm abalone (ANOVA: p>0.05), however, the 50 mm abalone displayed significantly higher weight gain on the 32 % (4.72±0.20 g.month-I ) and 38 % (5.01±0.34 g.month-I ) protein diets compared to those fed the 20 % protein diet (3.75±0.13 g.month-I ) (ANOVA: p=O.OI). Although definition of optimal dietary protein levels were not possible, the effects of dietary protein content and water temperature on the growth of H midae were independent signifying that the protein requirements of abalone are temperature independent. In addition, there was no evidence to indicate that abalone of the different sizes tested here had different dietary protein requirements. The size specific dietary lipid and protein requirements of H midae were investigated by feeding two size classes of abalone (30 and 60 mm initial shell length) diets containing graded levels of dietary lipid (4, 7, 10, 13 and 16 %) and protein (34 - 39 %) for 12 weeks. The 30 and 60 mm abalone were stocked at 7 (n=200) and 9 % (n=36) of the available basket surface area respectively and each diet was fed to four baskets of abalone of each size class. The protein requirements of H. midae are influenced by the amount of available dietary energy and thus it is possible that the ability of abalone to utilise lipids as a source of energy differs in the presence of varying levels of dietary protein. High levels of dietary lipid negatively affected the growth, condition factor and soft tissue glycogen content of both size classes of abalone. This negative effect was greater in the 30 mm size class compared to the 60 mm abalone. The corresponding increase in feed consumption and feed conversion ratio in response to increasing levels of dietary protein also provides evidence that abalone are unable to utilise dietary lipids as an energy source and high levels of dietary lipid probably inhibit the uptake of carbohydrates and protein. High dietary lipid levels did however appear to promote gonad maturation. It was possible to reduce dietary protein from 34 to 20 % without negatively affecting growth through the maintenance of dietary energy levels and thus it is recommended that future experiments on the energy content of formulated feeds should focus on the improved use of carbohydrates. Reductions in the protein portion of formulated feeds for H. midae are possible provided the diet contains sufficient levels of energy supplied from carbohydrates. As the ability of abalone to utilise dietary lipid is limited, lipids are unlikely to play a significant role as an energy source in abalone feeds. Further investigations should focus on the utilisation of various carbohydrate sources in abalone feeds.

Thesis (MPhil (Animal Sciences. Aquaculture))--University of Stellenbosch, 2006. / T. heterouncinata is a sabellid polychaete endemic to South Africa and found primarily in the shells of the abalone Haliotis midae. With the intensification of abalone aquaculture around the world, T. heterouncinata has become a problematic pest by causing shell deformities, reducing abalone growth rates and, in some instances, high abalone mortalities. The problem of this sabellid was first noticed in Californian in the early 1980’s in Red abalone (Haliotis rufescens) production facilities. Many mitigation methods have been tested over the years and this paper investigates another two methods; a reduction in particulate load in the tank to reduce the food source of the sabellid which perhaps will reduce fecundity, and to use ultrasound as a possible mitigation method. This study found that filtration and reduction in suspended particles did not have a significant effect, but that ultrasound did have a significant effect in reducing T. heterouncinata populations.

Thesis (MSc)--University of Stellenbosch, 2004. / ENGLISH ABSTRACT: The indigenous abalone, Haliotis midae has been a successfully cultured aquaculture species in South Africa since 1990. It has a slow growth rate and takes from two to five years to reach market size. Like for most other commercially important abalone species, the slow growth rate of H. midae is a cause of concern with regard to the profitability of farming and global competitiveness of the species. Ploidy manipulation of the maternal genome, a universally growing practice in shellfish culture, is considered a promising method to improve the growth rate of abalone - a desirable trait in aquaculture organisms from a commercial perspective. This manipulation technique is employed to achieve sterility, which results in limited gonad development. The consequent re-allocation of resources to somatic growth results in improved growth. The purpose of this study was to establish a viable method for the induction and validation of triploidy, on a commercial scale, in the South African abalone, H. midae. The focus was on hydrostatic pressure as a method of induction and flow cytometry as the method of validation. The results obtained confirm hydrostatic pressure as an effective method for the induction of triploidy in H. midae, delivering high percentages of triploidy (>80%) over a wide range of pressures and times, in 48 hour-old larvae. Hydrostatic pressure had a negative effect on survival in 20 hour-old larvae. Flow cytometry was validated as a reliable, fast and accurate, though expensive, method for identification of triploidy in H. midae. As an outcome of this study a manual of “Procedures for the Induction and Validation of Triploidy in the abalone” is presented (Appendix 1) together with recommendations for further studies on triploidy in the South African abalone, H. midae. / AFRIKAANSE OPSOMMING: Die inheemse perlemoen, Haliotis midae, is sedert 1990 ‘n suksesvol gekweekte akwakultuur spesie in Suid-Afrika. ‘n Kenmerk van die spesie is die stadige groeitempo van tussen twee en vyf jaar ten einde bemarkbare grootte te bereik. Soos vir die meerderheid perlemoen van kommersiële belang, is hierdie stadige groeitempo rede tot kommer met betrekking tot die winsgewende kweek en wêreldwye mededingendheid van die spesie. Die manipulasie van ploïdie van die moederlike genoom is ‘n toenemende praktyk in skulpvisboerdery en word gereken as ‘n belowende metode om die groeitempo van perlemoen te verbeter. Hierdie manipulasietegniek word gebruik om steriliteit te verkry wat manifesteer as onderdrukte ontwikkeling van die geslagsklier. Die gevolg is die herkanalisering van bronne na somatiese groei. Die doel van hierdie studie was om ‘n lewensvatbare metode vir die induksie van triploïdie op ‘n kommersiële skaal in die Suid-Afrikaanse perlemoen, H. midae, te vestig. Daar is op hidrostatiese druk as metode vir die induksie en vloei-sitometrie as metode vir die geldigverklaring van triploïdie gefokus. Die resultate van hierdie studie bevestig dat hidrostatiese druk ‘n effektiewe metode vir die induksie van triploïdie in H. midae is. Hoë persentasies van triploïdie (>80%) is oor ‘n wye reeks van drukke en tye in 48 uur oue larwes verkry. Daar is gevind dat hidrostatiese drukbehandeling ‘n negatiewe effek op die oorlewing van 20 uur oue larwes het. Vloei-sitometrie is bevestig as ‘n betroubare, vinnig en akkurate, maar duur metode vir die identifikasie van triploïdie in H. midae. As ‘n uitvloeisel van die studie word ‘n handleiding “Procedures for the Induction and Validation of Triploidy in the abalone” (Appendix 1) aangebied tesame met aanbevelings vir verdere studies rakende triploïdie in die Suid-Afrikaanse perlemoen, H. midae.

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: The indigenous abalone Haliotis midae is one of the most remarkable and highly exploited species of marine molluscs in South Africa. It is the only species of southern African Haliotidae to be commercially reared and has been successfully cultured for almost two decades. Its short history of domestication along with market demands and the need to develop efficiency in the production process has resulted in an increased interest in the possible genetic improvement of this species. The unhurried growth rate associated with H. midae is a cause of particular concern to the industry, predominantly with regards to profitability and competitiveness in the market place. A modest amount of work has so far been directed at establishing a means of enhancement for selective breeding on the commercial level. Genetics plays a key role in the establishment of successful improvement programmes in various aquaculture species. The aim of this study was to develop species-specific microsatellite markers for the abalone and subsequently perform parentage assignment on farm produced animals entered into a growth performance recording scheme. Animals were obtained from the hatcheries of three commercial abalone farms situated in the Walker Bay region in the Western Cape. Microsatellites were isolated using the enrichment-based FIASCO method, and characterised into perfect, imperfect and compound repeats according to the structural nature of their repetitive units. From the partial gDNA libraries obtained and 365 screened colonies, a total of 54 loci were located. PCR primers were designed for 36 markers and the 15 primer pairs that displayed loci with the highest level of polymorphism were subsequently chosen for fluorescent labelling. The markers were tested on a subset of 32 wild H. midae individuals to determine their usefulness and efficiency in genotyping. Five markers, along with five others that were previously designed, were chosen for assigning parentage to the animals submitted to the performance recording scheme. Three thousand offspring from each of the three participating farms were equally divided and reared at five different locations. From each location 20 fast growing and 20 slow growing juveniles, as well as the broodstocks, were sampled and genotyped using the ten chosen microsatellite loci. Two farms had 60% of offspring unambiguously assigned to a single parental couple. Assignments showed patterns of dominant male and female brooders, but no trend in brooders specifically contributing to fast or slow growing offspring. Parentage assignment for the third farm was, however, unsuccessful due to lack of broodstock data. In future, screening of all available broodstock will ensure acquisition of relevant pedigree information. The results obtained in this study are an initial step in the development of a genetic improvement programme for commercial Haliotis midae. / AFRIKAANSE OPSOMMING: Die inheemse skulpvis Haliotis midae is een van die mees merkwaardige en hoogs oorbenutte mariene slakspesies in Suid-Afrika. Dit is die enigste suidelike Afrika Haliotidae spesie wat kommersieel benut word en dit word al meer as twee dekades suksesvol geteel. Die spesie se kort domestiseringsgeskiedenis, toenemende mark aanvraag en die behoefte om meer effektiewe produksie daar te stel, het gelei tot toenemende belangstelling in die moontlike genetiese verbetering van die spesie. Die stadige groeitempo geassosieer met H. midae is veral ‘n punt van kommer vir die industrie, veral in terme van winsgewendheid en kompetering in die markplek. Minimale werk is sover gedoen in die daarstelling van verbetering deur selektiewe teling op ‘n kommersiële skaal. Genetika speel ’n sleutelrol in die daarstelling van suksesvolle verbeteringsprogramme van verskeie akwakultuur spesies. Die doel van hierdie studie was om spesie-spesifieke mikrosatelliet merkers vir perlemoen te ontwikkel en vervolgens ouerskapsbepaling van kommersiële diere, wat deelneem aan ‘n groeiprestasie aantekenstelsel, uit te voer. Diere is voorsien deur die teelstasies van drie kommersiële perlemoenplase geleë in die Walker Bay omgewing in die Wes-Kaap. Mikrosatelliete is geïsoleer deur die verrykings-gebaseerde FIASCO metode, en gekarakteriseer as perfekte, onderbroke of saamgestelde herhalings gebaseer op die strukturele aard van die herhalings eenhede. Vanaf die gedeeltelik gDNA biblioteke wat bekom is en 365 gesifte kolonies, is ‘n totaal van 54 loki opgespoor. PKR inleiers is ontwerp vir 36 merkers en die 15 inleierpare, wat loki met die hoogste polimorfisme geamplifiseer het, is vervolgens geselekteer vir fluoreserende merking. Die merkers is getoets op ’n kleiner groep van 32 natuurlike H. midae individue om hulle bruikbaarheid en genotiperingseffektiwiteit te bepaal. Vyf merkers is saam met vyf reeds ontwikkelde merkers gekies vir ouerskapsbepaling van die diere in die prestasie aantekenstelsel. Drieduisend nageslag diere vanaf elkeen van die drie deelnemde plase is gelykop verdeel en grootgemaak op die vyf verskillende lokaliteite. ‘n Monster van 20 vinnig groeiende en 20 stadig groeiende jong perlemoen, sowel as broeidiere, is vanaf elke lokaliteit geneem en gegenotipeer deur middel van die 10 geselekteerde mikrosatelliet loki. Sestig persent van twee van die plase se nageslag is onteenseglik toegesê aan ‘n enkele ouerpaar. Ouerskapstoekenning het patrone van dominante vroulike en manlike broeidiere getoon, maar geen tendens in terme van bydrae tot vinnig en stadig groeiende nageslag kon gevind word nie. Ouerskapstoekenning vir die derde plaas was onsuksesvol as gevolg van ’n gebrek aan data vir die broeidiere. In die toekoms sal genotipering van alle beskikbare broeidiere die daarstelling van relevante stamboominligting verseker. Die resultate verkry in hierdie studie verteenwoordig ‘n eerste stap in die ontwikkeling van ’n genetiese verbeteringsprogram vir kommersiële Haliotis midae.