Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Cultured abalone in South Africa is undomesticated. For the local industry to remain competitive on the international markets it is essential to improve production. This study is part of a selective breeding component of a larger genetic programme that aims to enhance productivity of the local industry by genetic improvement of growth rates. Selective breeding programmes are based on genetic variation and correlations. Molecular studies proved genetic differentiation exist between the broodstock- and offspring populations and among the offspring populations used in this study. Five commercial abalone farms from the Walker bay region each entered 3000 randomly selected animals obtained from synchronised mass spawning of conditioned broodstock into a Performance Recording Scheme (PRS). Microsatellite marker analysis proved these broodstock populations to be representative of the wild populations. The five cohorts were assessed over the five locations represented by three replicates per location with 200 randomly assigned animals per replicate. The average growth rate was used as growth performance parameter by measuring shell length and body weight at three month intervals over a period of 24 months. Interaction was observed between cohort and location effects when analysing the full data set. This was unexpected as the cohorts were constructed from parent stick that was randomly sampled from the same geographical area, the larger Walker bay. The factors suspected of causing this observed interaction were considered in a stepwise analysis. Initial and progressive tag loss, differences in initial size of animals entered into the study and on-farm management errors were considered as possible causes of the observed interaction in a stepwise analysis. Statistically significant differences were observed between the five cohorts and between the five locations in terms of length and weight growth rates. Based on these findings it is advised that a central facility is used to effectively compare the growth rates of different cohorts or populations. Any future research in selective breeding to follow this study should involve the integration of molecular techniques and biotechnologies. / AFRIKAANSE OPSOMMING: In Suid-Afrika is gekweekte perlemoen wild. Vir die plaaslike bedryf om op die internasionale markte kompeterend te bly, is dit noodsaaklik om produksie te verbeter. Hierdie studie vorm deel van ’n selektiewe telingskomponent van ‘n groter genetiese program met die doel om die produktiwiteit van die plaaslike bedryf deur die genetiese verbetering van groeitempo’s te verbeter. Selektiewe teelprogramme word gebaseer op genetiese variasie en korrelasies. Molekulêre studies het bewys dat daar genetiese differensiasie bestaan tussen die teel- en nageslagpopulasies en onder die nageslagpopulasies wat in hierdie studie gebruik is. Vyf kommersiële perlemoenplase in die Walkerbaaistreek het elk 3000 ewekansig geselekteerde diere vanaf gesinkroniseerde massa broei van gekondisioneerde teelpopulasies aan ‘n Performance Recording Scheme (PRS) bygedra. Mikrosatelliet merker-analise het bewys dat hierdie teelpopulasies verteenwoordigend is van die wilde populasies. Die vyf kohorte is oor die vyf liggings geassesseer, elkeen waarvan verteenwoordig is deur drie replikate bestaande uit 200 ewekansig toegedeelde diere per replikaat. Die gemiddelde groeitempo is gebruik as die groeiprestasieparameter deur skulplengte en liggaamsgewig elke drie maande oor ‘n tydperk van 24 maande te meet. Daar is interaksie waargeneem tussen kohort- en liggingseffekte toe die volledige datastel geanaliseer is. Hierdie was onverwags, aangesien die kohorte gekonstrueer is uit teelouers waarvan monsters ewekansig vanuit dieselfde geografiese gebied, naamlik die groter Walkerbaai, geneem is. Die faktore wat vermoedelik hierdie waargenome interaksie veroorsaak het, is in ‘n stapsgewyse analise beskou. Aanvanklike en progressiewe merkerverlies, verskille in die aanvanklike grootte van die diere wat in die studie ingesluit is en bestuursfoute op die plaas is as moontlike oorsake van die waargenome interaksie voorgestel. Statisties betekenisvolle verskille is tussen die vyf genotipes en tussen die vyf liggings in terme van lengte en gewigsgroeitempo’s waargeneem. Op grond van hierdie bevindings word daar voorgestel dat ‘n sentrale fasiliteit gebruik word om die groeitempo’s van die verskillende genotipes of populasies doeltreffend te vergelyk. Enige toekomstige navorsing oor selektiewe teelt wat op hierdie studie sou volg, moet die integrasie van molekulêre tegnieke en biotegnologieë behels.

A gradient of sea temperatures is created along the South African coastline by the confluence of the cold Benguela Current on the West coast with the warm Agulhas Current on the East coast. This temperature gradient allows for an assortment of species to occupy the variety of microenvironments occurring in this area. Amongst these species is commercially important South African abalone, Haliotis midae, which although being capable of existing across this wide range of temperatures grows larger on the cooler West coast. Abalone reared on the warmer East coast however, experience greater mortalities especially during the more thermally variable summer months. The aim of the study was thus to assess the zone of tolerance for H. midae by exposing abalone to fluctuating temperatures in an attempt to model environmental temperature instability, a scenario which may likely be worsened by global climate change. Animals from the West and East coasts were exposed to two thermal treatments of fluctuating temperatures with the first group being kept at 16°C±2 and the second group kept at 16°C±4. The control group was maintained at a constant 16°C indicating that the mean temperature experienced by all three groups was 16°C. Oxygen consumption, nitrogen excretion and O:N ratio were assessed at the organismal level to give an indication of metabolic rate, amount of protein excreted and type of metabolic substrate utilized respectively. At the biochemical level, D-lactate accumulation was quantified to indicate whether metabolism was proceeding aerobically or anaerobically. Heat shock protein 70 (Hsp70) expression and degree of carbonylation were analyzed at the proteomic level with Hsp70 also being assessed at the transcriptomic level. All biological responses were measured at days 1, 3, 7 and 14 of the two week exposure. Oxygen consumption rates were significantly elevated on day 14 when comparing treatment group animals to control group animals of the same biogeographic region. P < 0.05 for both treatment groups from the West coast, while P < 0.001 for the East coast treatment groups. The ammonia excretion rates of the West coast animals were significantly lower than those of the controls at day 14 with P < 0.001 for both treatment groups, while ammonia excretion rates were elevated in East coast animals at day 14, although not significantly. Trends similar to those seen for ammonia excretion rates were exhibited by O:N ratios. West coast animals showed lower than control O:N ratios at day 14 (P < 0.01 for both treatment groups) while East coast animals displayed higher than control values (P < 0.05 only for the 16°C±2 group) at day 14. D-lactate, having been detected only for the West coast animals, showed no significant differences but large degrees of variation were noted on days 1 and 7. Carbonylation was evident for animals from both biogeographic regions with baseline carbonyl accumulation for East coast animals being greater (non-significantly) than that of the West coast animals. The hsp70 gene expression remained low for both biogeographic groups with West coast animals appearing to show slight elevations in expression at days 1 and 7, days which also displayed high degrees of variability. The West coast animals appeared to be better suited to coping with the thermal fluctuations, as they not only transiently reduced oxygen consumption rate to reduce ROS production, but also utilized the assistance of the D-lactate pathway possibly to maintain metabolism, both of which were not observed in the East coast animals. Although West coast abalone seemed to have slightly elevated hsp70 expression (suggestive of a repair response) when compared to their East counterparts, both groups of abalone were shown to have incurred notable amounts of protein damage (i.e. carbonylation). This suggests impairments in both protective and repair responses for animals from both biogeographic regions. The lack or attenuation of physiological responses noted in East coast abalone may be due to limitations in thermal adaptation but subsequent studies are required to confirm this notion. The information obtained from this study may assist in providing an insight into the mechanisms responsible for thermal limitation in H. midae and how this species is likely to respond to future periods of thermal instability which may be worsened by global climate change. An understanding of the processes leading up to limitations may potentially assist the abalone aquaculture industry in altering culturing practices early on to support optimal performance in abalone. / M.Sc. University of KwaZulu-Natal, Durban 2014.

Thesis (MScAgric)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Haliotis midae (HM) is one of five indigenous abalone species occurring along the coast of South Africa, and is the only species commercially cultivated in open flow-through systems. Commercial production of HM contributes the most to income generated from aquaculture species in South Africa. Exports in 2011 totalled 1036 ton, which amounts to an income of ZAR 369 million (40 million USD). Commercial production of HM is characterized by a long interval (i.e. up to five years) to harvest. Genetic modification of HM to improve growth rate in HM can potentially decrease the interval from hatch to harvest, which will contribute to optimising the cost-efficient production of HM. However, a major concern in the production of genetically modified (GM) abalone is their escape from production systems, and the potential impact of the GM animals on the natural stocks in the surrounding environment. The implementation of containment methods to prevent the escape from GM abalone from production systems will assist in the management of the potential ecological risks escaped GM abalone may pose. Currently no containment strategies exist for the South African abalone industry, which limits the use of transgenic biotechnologies to optimise the cost-efficient production of HM. The study therefore investigated the potential of biological methods (triploid induction), mechanical methods (polypropylene filter bags and obstructive materials), and chemical methods (sodium hypochlorite and chlorine dioxide) to contain transgenic HM in open flow-through systems. Histological evaluation of gonad tissue samples of 16 triploid male and 15 triploid female HM indicated that triploid induction was unsuccessful in arresting gonad differentiation, development, and function. A combination of immature and mature gametes was observed on both triploid male and female gonads. The fertilizing potential of biopsied sperm obtained from triploid and induced diploid male HM was assessed in fertilization trials using ova obtained from diploid HM. No larvae were observed from the fertilization treatments of triploid male biopsied sperm, however, abnormal larvae (0.01% fertilization) were observed when induced diploid sperm were used to fertilize diploid ova. Polypropylene filter bags (100 μm) were not effective in containing male and female gametes in the broodstock section of the abalone culture system used in this study, and future studies should address specialized methods of containment of HM gametes. Polypropylene filters (100 μm), resulted in effective containment of larvae and settlement larvae, and in this study was not a more effective method of containment than the current on-farm larvae containment protocol. The three obstructive materials were effective in containing HM spat, and did not differ in their ability as containment methods. Sodium hypochlorite and Biox™, chlorine-based chemicals, were effective in containing the five life stages of HM, i.e. sperm, ova, larvae, settlement larvae and spat. The respective life stages were exposed to varying concentrations of the respective chemicals (i.e. 10 ppm, 50 ppm and 100 ppm) over five exposure times (i.e. 4, 6, 8, 10 and 12 minutes). Sodium hypochlorite and Biox™, at the different concentrations and exposure times, resulted in mortalities in all five HM life stages, with higher incidences recorded at the higher concentrations evaluated. Future research on the effect of triploid induction on the endocrine system, and how effective gonad maturation and function is suppressed, needs to be conducted. The aspects of mosaics occurring in induced diploid animals warrant further investigation with a larger sample size to verify the findings of this study. The production of true sterile individuals would improve the results to use of GM animals as a method of biological containment. Incorporation of mechanical containment methods need to be kept in mind when abalone production systems are designed. The use of chemical containment methods warrants additional studies on the practical administration and the economic feasibility of the chemical into the water supply of open flow-through abalone culture systems. / AFRIKAANSE OPSOMMING: Haliotis midae (HM) is een van vyf inheemse perlemoen spesies wat langs die kus van Suid-Afrika voorkom en is die enigste spesie wat kommersieel in oop deurvloeistelsels geproduseer word. Kommersiële produksie van HM dra die meeste tot kommersiële akwakultuur produksie by, met uitvoere van 1036 ton in 2011, wat gelykstaande aan ‘n inkomste van ZAR 369 miljoen (40 miljoen VSA dollar). Kommersiële produksie van HM word gekenmerk deur 'n lang interval (d.i. tot 5 jaar) vanaf uitbroei tot oes. Genetiese modifisering van HM om die groeitempo te verbeter kan potensieel die interval tot slagmassa verkort, wat potensieel tot die optimalisering van die kostedoeltreffende produksie van HM kan bydra. 'n Groot bron van kommer met die produksie van geneties gemodifiseerde (GM) perlemoen is hul ontsnapping uit produksiestelsels en die potensiële impak van die GM diere op die natuurlike perlemoenpopulasies in die omliggende omgewing. Die implementering van beheermetodes om die ontsnapping van GM perlemoen uit produksiestelsels te voorkom sal die bestuur van die potensiële ekologiese risiko's wat GM perlemoen mag inhou, vergemaklik. Tans bestaan daar geen inperking strategieë vir GM diere vir die Suid-Afrikaanse perlemoenbedryf nie, wat die gebruik van transgeniese biotegnologieë vir die kostedoeltreffende produksie van HM beperk. Die studie het dus die potensiaal van biologiese metodes (triploïed induksie), meganiese metodes (polipropileen filters en obstruktiewe materiaal) en chemiese metodes (natriumhipochloriet en Biox™) om as inperk strategieë vir die bestuur van transgeniese HM in oop deurvloei produksiesisteme gebruik te word, ondersoek. Histologiese evaluering van gonadeweefsel monsters van 16 manlike en 15 vroulike triploïed HM het aangedui dat triploïed induksie onsuksesvol was om gonade differensiasie, ontwikkeling, en funksie te onderdruk. 'n Kombinasie van onvolwasse en volwasse gamete is in gonades van beide manlike en vroulike triploïed HM waargeneem. Die bevrugtingsvermoë van sperme wat versamel is met behulp van ʼn biopsie metode van triploïed en geïnduseerde diploïed HM is geëvalueer in bevrugtingsproewe met ova wat van diploïed HM versamel is. Geen larwes is waargeneem met die gebruik van die triploïed sperme nie, maar abnormale larwes (0.01% bevrugting) het wel voorgekom met die evaluering van sperme versamel van geïnduseerde diploïed HM. Die voorkoms van mosaïek diere (d.i. ʼn kombinasie van beide diploïed en triploïed selle in een individu) wat ontstaan a.g.v. onvolledige triploïed induksie noodsaak verdere navorsing met ʼn groter monster diere om die vermoë van triploïed induksie om HM steriel te maak, te verifieer. Polipropileen filters (100 μm) was nie effektief om beide manlike en vroulike gamete wat in die teelafdeling in die perlemoenkultuursisteem in hierdie studie geproduseer is, vas te vang nie. Toekomstige studies moet gespesialiseerde metodes wat insluiting van HM gamete moontlik sal maak, ondersoek. Polipropileenfilters (100 μm) was effektief met die inkamping van larwes en vestigingslarwes, met die filters wat nie meer doeltreffend as die bestaande inkampingsmetodes in die produksiesisteem was nie. Die drie obstruktiewe materiale was doeltreffend ten opsigte van die inkamping van onvolwasse perlemoen individue, met die 3 materiale wat ewe doeltreffend in hulle vermoë was om die onvolwasse HM se ontsnapping uit die sisteem te voorkom. Natriumhipochloriet en Biox™, chloor-gebaseerde chemikalieë, was effektief om die onderskeie 5 lewenstadiums, d.i. HM sperme en ova, larwes, vestigingslarwes en onvolwasse HM se voorkoms tot hulle onderskeie afdelings binne die produksiesisteem te beperk. Die onderskeie lewensstadiums is blootgestel aan verskillende konsentrasies van die onderskeie chemikalieë (d.i. 10 dpm, 50 dpm en 100 dpm) oor vyf tydsintervalle (d.i. 4, 6, 8, 10 en 12 minute). Natriumhipochloriet en Biox™ het ʼn letale effek op al vier lewensstadia gehad, met hoër sterftes wat met hoër konsentrasies aangeteken is. Toekomstige navorsing oor die uitwerking van triploïed induksie op die endokriene stelsel en hoe doeltreffend die rypwording en funksie van die gonades onderdruk word, moet aandag geniet. Die voorkoms van mosaïek diere regverdig ook spesifieke aandag in toekomstige navorsing. Die produksie van ware steriele individue sou die gebruik van GM perlemoen as 'n metode van biologiese inkamping moontlik maak. Inlywing van meganiese inkampingmetodes moet in gedagte gehou word wanneer perlemoen produksiestelsels ontwerp word. Die gebruik van chemiese inkampingmetodes benodig verdere studies om te verseker dat die chemiese middels so bekostigbaar en prakties as moontlik in water van 'n oop deurvloei perlemoen produksiestelsel toegedien kan word.

Abalone (Haliotis spp.) are marine broadcast spawners that inhabit temperate and tropical waters across the globe. Their importance as a fisheries resource has resulted in considerable research into key aspects of their biology, particularly around growth and reproduction. In addition, there has been ongoing interest regarding the genetic variation in both wild and hatchery populations. The majority of abalone dispersal probably occurs during a pelagic lecithotrophic larval stage. In general, oceanographic features, life history characteristics, and larval dispersal ability can manipulate dispersal and gene flow patterns of marine fauna. In the case of abalone, considerable research has examined the population genetic structure of a variety of species, and several papers implicate ocean currents and life history characteristics as important factors that define population genetic structure. In comparison to other abalone species, little information regarding the genetic structure of New Zealand's endemic H. iris exists. The goal of this thesis was to elucidate the genetic structure of H. iris using mitochondrial and nuclear markers in regards to two potential barriers to gene flow, the Cook Strait region and the gamete recognition protein, lysin. The genetic structure of H. iris was first examined in regards to a consistent pattern of genetic structure emerging in recent literature of coastal marine invertebrates around New Zealand: specifically, a north-south genetic split that occurs in the Cook Strait region (Chapter 2). Two regions of the mitochondria (totaling 1055 bp) were amplified across 477 individuals from 25 locations around New Zealand. A north-south split around the Cook Strait region was evident among H. iris samples. Unlike the other studies of New Zealand coastal marine invertebrates, the north-south split for H. iris was not located across regions of reported upwelling; instead the split was located across Cook Strait narrows. The north-south split was reflected in increased haplotype diversity for the northern samples. Genetic structure was also examined using microsatellite loci. After unsuccessful attempts at cross-species amplification using 8 loci developed for H. rubra and 11 loci developed for H. midae, 13 polymorphic loci were isolated de novo for H. iris (Chapter 3). Of these, three very polymorphic loci were optimized for population genetic analyses. These three loci were used to genotype 447–459 individuals from the same 25 locations examined with mitochondrial DNA (Chapter 4). Like the mitochondrial DNA, the microsattelites indicated population genetic structure around the Cook Strait region; however the split identified with microsatellites occurred in the greater Cook Strait region with two sample sites from the north of the South Island grouping with the North Island. Extrinsic barriers, like the Cook Strait region, are the primary focus of studies examining differentiation in marine invertebrate fauna. However, dispersal of an individual to a new population does not necessarily mean it can successfully reproduce with individuals of the new population. Potentially, populations may be diverging at genes essential for reproduction, i.e. gamete recognition proteins. The abalone egg recognition protein, lysin, is one of the best characterized gamete recognition proteins in marine broadcast spawners. Despite its well-understood function and structure, studies examining variation in lysin have been limited to small sample sizes (N ≤ 11) and have found very little variation. Here, lysin was screened across 287 individuals from 17 sampling sites around New Zealand to assess intraspecific variation and genetic structure across the Cook Strait region (Chapter 5). The majority of the variation in a 783 bp fragment spanning from exon 4 to 5, was located in the intron. The variability in this fragment detected no genetic structure among samples or across the Cook Strait region. The variation in lysin was considerably lower than the variation in either the mitochondrial DNA or the microsatellite loci. To determine whether this was an artifact of being a nuclear sequence, which, in general, have a lower mutation rates than microsatellite markers and mitochondrial DNA and a larger effective population size then mitochondrial DNA, or was a signature of a recent selective sweep, 857 bp of the Gα1 intron was assessed for genetic variation in 227 H. iris individuals from 14 sampling locations (Chapter 6). The Gα1 intron was considerably more diverse than the lysin fragment examined, suggesting that the relative lack of variation in the lysin fragment has resulted from a recent selective sweep. Additionally, the Gα1 intron was used to examine population genetic structure across the Cook Strait region and detected a weak but significant pattern of structure consistent with that detected using the microsatellite loci. Overall, the a priori tests of genetic structure based on mitochondrial DNA, microsatellite markers, and the across Gα1 intron all identified a north-south genetic split around the Cook Strait region; however, the patterns of this split was slightly inconsistent among molecular markers. When cluster analyses were applied the patterns of genetic structure became more similar: for the mitochondrial, microsatellite, and Gα1 intron data, cluster analyses indicate that only one sample from the north of the South Island groups with the North Island, while a few discrepancies existed in regards the grouping of samples from the east coast of the North Island.

Thesis (MSc)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: The genetic status of H. midae broodstock in the South African aquaculture industry reflects that of random samples originating from undomesticated wild populations. The nature of growth in abalone is very slow, taking between three and four years to reach a marketable size of between 60 to 100 grams. It is therefore of paramount importance to improve this trait in order to ensure global competitiveness and economic viability within the industry. Improving this negative characteristic through conventional selection methods is a long-term venture and alternative means that would yield instantaneous results had to be considered. Crossbreeding was identified as an alternative, short-term strategy to improve growth rate. A crossbreeding experiment was performed between two populations of the abalone, Haliotis midae, from the East (E) and West (W) Coast of South Africa. This was done to investigate the occurrence of heterosis for growth among the crossbred genotypes (East x West, West x East). Fifteen males and females from both the East and the West Coast populations were mated in a complete dialelle crossbreeding experiment to produce four progeny groups (WW, EE, EW and WE). Progeny groups were evaluated for weight (bW) and length gain (bL) over a specific growth period of 9 months. The results provided no evidence of significant differences in weight (P = 0.085) or length gain (P = 0.244) between the four progeny groups, giving no indication of significant heterosis for weight and length gain among the crossbred progenies of these East and West Coast populations. It is recommended that further efforts to obtain improved growth rate in the abalone, Haliotis midae, through crossbreeding only be considered in light of clear evidence of substantial genetic differentiation between such populations. / AFRIKAANSE OPSOMMING: Die huidige status van perlemoen, soos dit voorkom in akwakultuur bedrywighede in Suid Afrika, weerspieël dié van ‘n ewekansige monster vanuit wilde, natuurlike populasies. Perlemoen is inherent ‘n stadig groeiende organisme wat tussen drie en vier jaar neem om tot ‘n bemarkbare grote van 60 tot 100 gram te groei. Dit is dus uiters noodsaaklik om hierdie eienskap te verbeter ten einde die bedryf ekonomies lewensvatbaar en mededingend op wêreld markte te maak. Konvensionele seleksie as ‘n metode om hierdie negatiewe eienskap te verbeter is ‘n langtermyn onderneming wat die identifisering van ‘n korttermyn metode, wat ondmiddellike resultate lewer, noodsaak. Kruisteelt is geïdentifiseer as geskikte korttermyn oplossing aangesien dit onmiddellike resultate lewer. ‘n Kruisteel eksperiment is uitgevoer tussen twee populasies van die perlemoen, Haliotis midae, van die Ooskus (E = East) en die Weskus (W = West) van Suid Afrika. Dit is gedoen om die omvang van heterose vir groeitempo in die gekruisde nageslag (East x West, West x East) te bepaal. Fyftien mannetjies en wyfies van beide die Oos- en Weskus populasies is met mekaar gepaar in ‘n volledige dialleel kruising om vier nageslag groepe (WW, EE, EW en WE) te vorm. Die nageslag is geëvalueer ten opsigte van massa (bW) en lengte (bL) toename oor ‘n spesifieke groei tydperk van 9 maande. Die eksperimentele resultate dui daarop dat die vier nageslag groepe nie betekenisvol van mekaar verskil het ten opsigte van massa (P = 0.085) en lengte (P = 0.244) toename nie en dat daar dus geen aanduiding van heterose vir massa en lengte toename in die nageslag van kruisings tussen die Ooskus en Weskus populasies bestaan nie. Daar word aanbeveel dat kruisteling as ‘n metode van genetiese verbetering van groeitempo in Haliotis midae slegs oorweeg word in die lig van nuwe molekulêre bewyse van genoegsame genetiese differensiasie tussen sulke populasies.

M.Sc. / Abalone are among the world’s leading shellfish consumed by human populations. Harvesting in California began in the late 1800s from intertidal zones and in the early 1900s wild abalone were collected by diving. Popular demand for abalone products in the Far East then led to extensive harvesting of wild abalone and a drastic decline in population numbers. This problem was overcome to a degree by the development of land-based abalone farms. At these farms it was possible to breed abalone on a large scale. Currently twelve abalone farms operate in South Africa and the estimated production for 2006 was 537 tons of meat, worth R 80 mil. Parasites and diseases pose threats to the production of abalone, especially under farmed conditions, and can cause considerable financial loss. Labyrinthuloides haliotidis, Haplosporidium nelsoni and Terebrasabelle heterouncinata are a few parasites that contribute to the above mentioned problems. Lately, a new protozoan parasite was discovered in the digestive glands of Haliotis midae farmed in the Western Cape Province, during routine health assessments. For the purposes of this dissertation it is designated an unidentified digestive gland parasite (UDP). The aims of this study are thus to undertake a comprehensive literature review of parasites infecting wild and farmed abalone, as well other shellfish species, describe and characterise the UDP infecting the digestive gland of Haliotis midae based on its structure and ultrastructure, evaluate the role of this parasite in disease by analysing data from histological studies, provide a preliminary indication of the life cycle of this parasite, attempt analysis of DNA from the UDP, and identify potential areas for further research into control of the parasite. A total of 180 abalone, (Haliotis midae) were collected from three abalone farms in the Western Cape during May 2005, October 2005, January 2006 and January 2007. To establish whether this parasite also occurs in wild abalone, a single sampling (six H. midae and 28 H. spadicea) took place during 2006 in Tsitsikamma National Park. Collected farmed and wild abalone were weighed and measured, removed from their shells and then killed according to accepted methods before their digestive glands were removed.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / Abalone are among the most expensive and sought-after seafood subjects. In South Africa, Haliotis midae is the only commercially significant abalone species and it has become increasingly sold on the global market. The importance of abalone as a mariculture subject has triggered extensive research into maximizing production, with particular emphasis on optimizing growth rates. This study aimed to assess the growth performance of Haliotis midae relative to 1) standard pelleted feed, and 2) kelp-inclusive pelleted feed. I assessed feed stability of the dietary treatments and growth parameters associated with abalone weight gain. Temperature and time of feed submersion were found to significantly affect feed stability. Although there were no significant differences in water stability between feeds, the kelp-inclusive feed produced significantly lower total suspended solids (TSS) than the standard pelleted feed at upper time-temperature combinations.

Global growth in aquaculture, referred to as the blue revolution, is seen by many to be the solution to future food scarcity. However, this growth has been accompanied by disease emergence. Disease emergence is inevitable when host populations are concentrated and densities exceed the threshold value for occurrence of outbreaks. Abalone farming is a relatively recent development and diseases of abalone are not well characterised. There have been relatively few systematic surveys of abalone diseases in the world. Much of the available information resulted from investigations of specific disease outbreaks, such as withering syndrome in California. The outstanding example of a formal survey of abalone health was conducted in Australia. A methodical survey of abalone health, encompassing all farms and including wild abalone, has never been done in South Africa. However, South Africa has for many years had a herd health program for abalone producers and this has generated the largest body of data on abalone disease occurrence in the world. Although these data have some shortcomings, it was felt that analysis could provide insights into the epidemiology of parasites in farmed Haliotis midae, as well as informing better surveillance techniques for the future. Data for abalone submitted from nine farms as part of the herd health management program during the period 1 January 2000 to 31 December 2004 were analysed. No wild abalone were included in these data and the only abalone species considered was the South African abalone or perlemoen, Haliotis midae. Data on the age of the abalone and their diet were obtained from the farms. The abalone originated from either flow through or recirculation systems. Each animal was weighed and measured at the laboratory. A standard set of tissue sections was fixed and processed for histology. Presence of parasites was recorded, as well as the sex and degree of gonad development. Once data had been captured in Excel, a series of tables was constructed from counts of infected and non infected abalone for all host and environmental factors contained in the data set. Charts of the tables were drawn. Where host and environmental factors appeared to interact, these data were also tabulated and charted. Statistical analyses of the data in Excel followed. All analyses were performed for sessile ciliates, renal coccidia, gut protozoa, digestive gland PAGE 2 OF 137 protozoa and rickettsia like prokaryotes. The rarity of trematode infections made meaningful analyses difficult. The chi square test, effect sizes and odds ratios were used to seek significant associations. When confounding and interaction were suspected, stratum specific odds ratios were calculated. The summary odds ratio used in this study was the Mantel Haenszel summary odds ratio. The Breslow Day test for interaction was performed when necessary. Confidence intervals were determined using the method of Woolf. The overall prevalence of the various parasites was very variable. Sessile ciliates were the most common, with a prevalence of 68.3%. Rickettsia like prokaryotes were found in 13.1% of animals. The other gut associated parasites were more scarce, with prevalences under five percent. Renal coccidia affected less than two percent of animals. Trematode infections were extremely rare, at a prevalence of 0.05%. The results of the chi square test showed a significant association between age and parasite prevalence for all parasites tested. Odds ratios were calculated comparing animals of 24 months and younger to those older than 24 months. In all cases, except trematode and left kidney coccidian infections, risk of parasite infection tended to increase with increasing age. For left kidney coccidian infections, risk of infection decreased with increasing age. Trends for body mass were similar to those for age, which is expected, as animals generally become larger with increasing age. A significant association between growth rate and parasite prevalence existed for some parasites. The chi square test showed a significant association between condition index and parasite prevalence for all parasites tested. A significant association between sex and parasite prevalence was found for all parasites tested. A significant association also existed between parasite prevalence and gonad development for sessile ciliates, renal coccidia and gut protozoa. There were significant differences in parasite prevalences between farms for all parasites tested. The South and West coasts were next compared using the chi square test. There were significant differences in parasite prevalences between coasts for only three of the parasites tested, namely renal coccidia, gut protozoa and rickettsia. Crude odds ratios showed that, with the exception of left kidney coccidia and trematodes, there was a greater risk of parasite infection on the West than the South coast. For left kidney coccidia, the risk was greater on the PAGE 3 OF 137 South coast. A chi square test was performed to examine the relationship between parasite prevalence in Hermanus and other areas. A significant difference was found for renal coccidia and gut associated parasites. The crude odds ratios for parasite prevalence in other areas compared to Hermanus were calculated. With the exception of sessile ciliates and trematodes, there was a greater risk of parasite infection in areas other than Hermanus. In the case of sessile ciliates, there was a greater risk within Hermanus than in other areas. Unfortunately, it was almost impossible to determine whether a seasonal effect exists for parasite prevalence from the available data. This was shown to be partly due to the effect of prevalence on individual farms. Significant differences in parasite prevalences between diets for all parasites tested were shown using the chi square test. To further test the strength of the association, odds ratios were calculated comparing only kelp and artificial feed. For right kidney coccidia and gut associated parasites, the odds ratios indicated a significantly increased risk of infection in animals receiving kelp compared to those on artificial feed. There was no difference in risk for sessile ciliates and left kidney coccidia. The majority of animals originated in flow through systems. The chi square test showed significant differences in parasite prevalences between systems for sessile ciliates, renal coccidia and rickettsia like prokaryotes. Odds ratios showed a significantly greater risk of sessile ciliate infections, but a smaller risk of left kidney coccidia, in animals in flow through systems when comparing only kelp fed animals. Age is likely to lead to increased prevalences if the risk of infection is constant over time and also if infections are retained. Physiological changes in the animals may also affect their risk of infection. A further important aspect of age in abalone relates to changes in husbandry. Increasing age may be the underlying reason for some of the prevalence patterns seen with mass and sex. The origin of the sample population was considered in terms of farm of origin as well as geographic area. Abalone production in the study area was highly concentrated, with approximately two thirds coming from six farms situated within ten kilometres of each another on the South coast and almost forty percent from Hermanus alone. The present study found no PAGE 4 OF 137 evidence of increased parasite prevalence in areas where abalone farming is concentrated. It was felt that this study could not generate much insight into seasonal occurrence, due to uneven distribution of variables between months. The relationship between diet and parasite prevalence was perhaps the most interesting aspect of this study and possible reasons for the association are explored. Lastly, the results indicated that parasite buildup in recirculation systems was not as problematical as may be expected. It is possible that the increased prevalence of left kidney coccidia in recirculation systems is linked to the resistance of the host population rather than to the dynamics of the actual system. The very low prevalence of sessile ciliates in recirculation systems could not be explained by examination of any other variable considered in this study. Overall, the prevalences of soft tissue parasites in Haliotis midae compared favourably with those found for parasites of other abalone species abroad. Measures which would tend to reduce parasite prevalence include separation of age groups and maintaining a relatively young population on the farm. Culling of underperforming animals is recommended. Kelp should not be used in animals of two years or younger. In older animals, there was still a greater risk associated with kelp than with artificial feed, but it was not as marked. Recirculation systems proved to be less associated with increased parasite prevalence than one may expect. The other major findings of this study did not lend themselves to practical application. / Dissertation (MSc)--University of Pretoria, 2010. / Production Animal Studies / unrestricted

L’aquaculture des ormeaux (Haliotis spp.) fournit un bon cas étude des défis techniques, sociaux et environnementaux concernant l'introduction d’organismes marins nouvellement domestiqués sur le marché. En effet, l'élevage de l'ormeau a débuté au Japon au cours des années 1960 et, d'après la FAO (2012), est aujourd'hui l'une des industries aquacoles les plus dynamiques dans le monde. Pourtant, toutes les tentatives n'ont pas connues le même succès. Cette dissertation vise à comprendre les facteurs qui ont permis ou entravé le succès environnemental, social et technique de l’halioticulture, en mettant l'accent sur la France. Plus précisément, nous examinons trois grandes catégories de facteurs qui peuvent expliquer son évolution: - L'importance des facteurs socio-écologiques dans la gestion de la ressource en ormeaux - Les facteurs socioculturels qui étayent le statut de l'ormeau en tant que ressource éligible pour l'aquaculture. - Le rôle de la science dans l'industrialisation de l'élevage d'ormeaux. / Abalone aquaculture (Haliotis spp.) or halioticulture provides a good case study of the technical, social and environmental challenges of introducing newly domesticated marine organisms into the market. Abalone farming began in Japan in the 1960s and, according to FAO (2012), is now one of the most dynamic aquaculture industries in the world. Yet all attempts have not met with the same success. This essay aims to understand the factors that have allowed or hindered the environmental, social and technical success of halioticulture, with an emphasis on France.More specifically, we examine three main categories of factors that may explain its evolution:- The importance of socio-ecological factors in the management of abalone resource.- Socio-cultural factors that support the status of the abalone as an eligible resource for aquaculture.- The role of science in the industrialization of abalone farming.

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.