Regulation of transcription is an important molecular mechanism through which organisms can respond to environmental change. Environmentally-related transcriptional variation can play a significant role in evolution, potentially acting as a mechanism for the formation of new adaptive phenotypes. Organisms are most sensitive to the influence of external environmental variation during development, yet very few studies have explored environmentally-related transcriptional variation in early life history stages. Marine invertebrate metamorphosis, where intimate larval-environment interactions trigger settlement onto the benthos and a drastic morphological shift from larval to adult form, exemplifies the influence of environment on development. Variation in both the timing of metamorphosis and the form of specific metamorphic inductive cues, even at an intraspecific level, suggests that larvae have molecular mechanisms for surviving settlement and metamorphosis in a range of environmental conditions. The extent of transcriptional variation at metamorphosis remains largely unknown due to limited information on both the natural inductive cues and the molecular mechanisms directing metamorphosis in marine invertebrates. Contributing to current understanding of the interplay between genes, environment and phenotype during development, I explored molecular and ecological aspects of metamorphosis in a marine invertebrate, the tropical abalone Haliotis asinina. First, I employed cDNA microarray methods to identify candidate genes and document widespread transcriptional changes occurring in Haliotis asinina larvae during larval development and metamorphosis. Microarray results reveal that as the abalone veliger larva matures, it requires coordinated regulation of temporally different gene batteries involved in a wide range of physiological and developmental processes associated with the transition to a new, benthic habitat. All candidate genes showed changes in expression following exposure of larvae to coralline algae, an external inductive cue, demonstrating the remarkable effect of environment on transcription during marine invertebrate metamorphosis. 144 genes, ~40% of which are novel, were identified as candidates for a role in H. asinina metamorphosis. This high proportion of novel genes indicates that the conserved signaling pathways operating in marine invertebrate metamorphosis likely regulate the expression of taxon-specific genes. The relationship between abalone larvae and their natural inductive cue, coralline algae, is species-specific. To characterize the metamorphic cue preferences of Haliotis asinina larvae from Heron Island Reef, Australia, I documented larval induction response to a number of different coralline algae species commonly found in adult H. asinina habitat. H. asinina larvae exhibit highly specific responses to induction of metamorphosis by different coralline algae species, with 0 – 100% metamorphosis by 48 hours post induction depending on algae species. Unlike any other abalone species studied, the most effective inducers of Heron Island Reef H. asinina are articulated corallines of the genus Amphiroa. Comparing the response of different larval families to select species of coralline algae indicated that coralline algae community composition is likely to significantly impact H. asinina population structure. Additionally, I compared larval response to dead and live coralline algae to show that induction specificity is driven by chemical, not physical, properties. Characterization of the surface cell biomarkers of three different coralline algae species indicates that algal biomolecular composition relates to variations in H. asinina induction response. To explore the influence of variation in larval induction environment, I compared transcription patterns of 17 metamorphosis-related genes in Haliotis asinina larvae induced by three different species of coralline algae. H. asinina post-induction gene expression profiles vary according to the species of coralline algae inducer. This transcriptional variation occurs in genes with diverse functions and spatial expression patterns, highlighting the global nature of the impact of benthic microhabitat on gene expression. The environment-specific modulation of gene expression in H. asinina post-induction may be a means for marine invertebrates to cope with changes in their settlement environment at metamorphosis. Genes expressed in the larval sensory structures acting to detect external metamorphic cues may be particularly good candidates for studying environmentally-related transcriptional variation. I identified three novel genes expressed in putative sensory structures of Haliotis asinina larvae just prior to metamorphosis. The spatial and temporal expression patterns of these genes correlate with changes in larval ciliation patterns throughout metamorphosis, strongly suggestive of a role in metamorphic initiation. The three genes exhibit significant overlap in spatial expression profiles, indicative of genetic crosstalk between different sensory systems at metamorphosis. Transcriptional variation in gastropod sensory system genes may have assisted the evolution of different metamorphic inductive cues for different species. The results presented here establish an important role for transcriptional variation during marine invertebrate metamorphosis. Transcriptional variation underlies the morphological change from larval to adult body plan and also appears to assist larval recruitment in variable benthic habitats. Modulation of gene expression at metamorphosis in response to the environment may ultimately influence marine invertebrate species biogeography and evolution.

Thesis (MScAgric)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Abalone production is the largest financial contributor to aquaculture in South Africa and practically all of the abalone produced is exported to Asia. This means that the product must be globally competitive and many technologies have been applied to this cause. One that specifically shows great promise for bivalve mollusc production is triploidy; more precisely, sterility due to the induction of aneuploidy. Under normal maturation, energy is diverted from somatic growth through sexual maturation, therefore inhibiting or retarding gametogenesis through a process such as aneuploidy is expected to increase growth and decrease the time to marketing. Two studies preceding this one investigated the induction of triploidy through hydrostatic shock (De Beer, 2004) and the comparative growth rate of triploid genotypes from 8 to 24 months, prior to the onset of sexual maturation (Schoonbee, 2008). During this comparative growth stage, no convincing statistical evidence of faster growth or of seasonal environmental effects could be obtained. It was recommended that growth between triploid and diploid variants be compared during the age period when sexual maturity becomes a factor to determine whether triploidy in Haliotis midae is a useful biotechnological tool to improve biological productivity and global competiveness of the abalone industry. The growth measured as shell length and wet weight in the period from 29 to 62 months showed a statistically significant difference in mean weight and mean length with diploids showing a superior growth rate compared to their triploid siblings. This difference of 1.99 mm and 5.13 g was however not perceived as being commercially significant. Important production parameters including canning yield percentage and gonadosomatic index were also measured during this trial. For both these parameters, the triploid genotype showed statistically and commercially significant improvement of 10.68% increased canning yield and 28.42% reduction in gonadosomatic index when compared to their diploid counterparts. Triploid abalone was found to be not completely sterile; gametes and even mature gonads were observed in some instances. Even though complete sterility was not achieved there appeared to be a retarded gonadosomatic development in triploid variants. The delay in sexual maturation, together with the improvement in canning yield, may justify triploidy’s commercial application, despite its reduced growth rate. / AFRIKAANSE OPSOMMING: Perlemoen produksie lewer die grootste finansiële bydra tot akwakultuur in Suid Afrika en feitlik al die Perlemoen word uitgevoer na Asië. Dit beteken dat die produk moet kompeteer op die wêreld mark en verskeie tegnologieë word reeds aangewend vir die spesifieke doel. Een so tegnologie wat potensiaal toon ten opsigte van akwakultuur produksie is triploïedie; meer spesifiek, sterieliteit veroorsaak deur aneuploïedie induksie. Onder normale volwassewording, word energie weggeneem van somatiese groei wanneer geslagsrypheid intree en daarom kan groeitempo verhoog word deur gametogenese te inhibeer of te vertraag deur ‘n proses soos aneuploïedie en, word korter tydperk benodig om bemarkingsgrootte te bereik. Twee voorafgaande studies het gehandel oor die induksie van triploïedie deur hidrostatiese druk skok (De Beer, 2004) en die vergelykende groeitempo van triploïede genotipes vanaf ouderdom 8 tot 24 maande (Schoonbee, 2008) alvorens geslagsrypheid intree. Tydens hierdie vergelykende groeifase kon geen statisties betekenisvolle aanduidings van vinniger groei of seisoenale omgewingseffekte aangetoon word nie. Die studie handel vervolgens oor die uitbreiding van die vergelykende groeistudies tussen triploïede en diploïede genotipes tot ouderdom van 62 maande wat die intrede van geslagsrypheid insluit, ten einde te bepaal of die induksie van triploïedie in Haliotis midae voordele inhou ten opsigte van produksiedoeltreffendheid en mededingendheid op wêreldmarkte. Groei gemeet in terme van skulplengte en lewende massa oor die tydperk van 29 tot 62 maande het statisties betekenisvolle verskille getoon in gemiddelde massa en lengte van diploïede genotipes bo die van triploïede verwante individue. Die verskille van 1.99 mm en 5.13 g kan egter nie as kommersieel betekenisvol beskou word nie. Belangrike produksie eienskappe waaronder persentasie opbrengs van eindproduk en die gonadosomatiese indeks is ook bepaal. Vir beide die produksie eienskappe het die triploïede genotipe statisties sowel as kommersieel betekenisvolle verbetering van 10.68% getoon vir opbrengs en 28.42% verlaging in gonadosomatiese indeks in vergelyking met die diploïede genotipe. Triploïede genotipes was nie volledig steriel nie, gegewe die aanwesigheid van gonades en gamete in sommige individue. Selfs al is totale steriliteit nie bereik nie, het dit wel voorgekom asof daar vertraging in gonadosomatiese ontwikkeling plaasgevind het in triploïede genotipes. Die vertraging in geslagsrypheid tesame met die verhoogde persentasie opbrengs van die eindproduk hou voordele in bo die andersins effense stadiger groei van triploïede genotipes.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Haliotis midae (commonly referred to as perlemoen) is the only one of five endemic species in South Africa that is commercially valued both locally and internationally. Unfortunately, natural perlemoen populations have become a dwindling resource due to commercial exploitation, poaching and the influx of natural threats, such as the West Coast rock lobster, Jasus lalandii. To preserve the natural diversity and sustainability of natural populations as well as commercial stocks, genetic management and improvement of perlemoen is critical. Genetic management requires the utilisation of molecular markers, which aid in the construction of linkage maps and the identification of quantitative trait loci (QTL) associated with economically significant traits. This will allow improvement of commercial stock management in terms of broodstock selection as well as provide valuable insight into natural population dynamics. Single Nucleotide Polymorphisms (SNPs) were selected as the marker of choice due to their successful employment as molecular markers and their wide distribution and abundance within the genomes of various marine species. This study focuses on the characterisation of novel SNPs from transcript sequences generated by Next Generation Sequencing technology. Approximately 40% of the transcripts facilitated the isolation of 105 putative markers, indicating a SNP frequency of ~1% within the H. midae genome. A subset of 24 markers, in addition to 24 previously developed markers, was characterised using the Illumina GoldenGate genotyping assay with the VeraCode technology, a medium to high-throughput genotyping technology. This is the first reported medium- to highthroughput characterisation of SNPs in H. midae. The selected markers were used to determine the efficiency and overall success rate of the GoldenGate platform. Marker characterisation was completed in both natural and commercial populations to determine the utility of these markers for genetic diversity and population structure inference. An 85% genotyping success rate was achieved with the platform. Statistical analysis indicated that the markers developed in this study are suitable for applications including population genetic structure inference, genetic diversity estimation and possibly other downstream applications such as linkage mapping. These markers are considered to be invaluable for future work regarding the genetic management and conservation of H. midae. / AFRIKAANSE OPSOMMING: Haliotis midae (ook bekend as perlemoen) is die enigste van vyf inheemse spesies in Suid-Afrika wat noemenswaardige kommersiële waarde toon plaaslik sowel as internasionaal. Ongelukkig het kommersiële uitbuiting, wildstropery en natuurlike bedreiging (bv. die Weskus kreef Jasus lalandii), wilde perlemoen populasies noemenswaardig verminder. Dus, om natuurlike diversiteit en die voortbestaan van beide wilde en kommersiële populasies te beskerm, is genetiese bestuur en verbetering absoluut noodsaaklik. Genetiese bestuur vereis die gebruik van molekulêre merkers as ’n hulpmiddel in die opstellingvan koppelingskaarte, en die identifisering van die relevante kwantitatiewe eienskap loki (QTL) tipies geassosieer met ekonomies belangrike eienskappe. Die laasgenoemde beoog om kommersiële voorraad bestuur te verbeter, kragtens deur broeidier seleksie sowel as om insig te verskaf m.b.t. wilde bevolking dinamika. Enkel Nukleotied Polimorfismes (SNPs) is gekies as die toepaslike merker vanweë die omvattende toepaslikheid van hierdie merkers binne die genome van verskeie mariene spesies. Hierdie studie fokus op die karakterisering van nuwe SNPs vanuit transkript volgordes ontwikkel deur middel van Volgende Generasie Volgordebepaling (“Next Generation Sequencing”). ’n Beraamde 40% van transkripte het gelei tot die ontwikkeling van 105 potensiëlemerkers, aanduidend van ’n SNP frekwensie van ~1% binne die H. midae genoom. ’n Sub-versameling van 24 merkers, tesame met 24 bestaande merkers, is gekarakteriseer deur die Illumina GoldenGate genotiperings toets met die VeraCode tegnologie, ’n medium tot hoë deurvloei genotiperingstegnologie. Hierdie is die eerste berig van medium tot hoë deurvloei karakterisering van SNPs in H. midae. Die geselekteerde merkers is gebruik om die doeltreffendheid van die GoldenGate platform te bepaal. Merker karakterisering is uitgevoer in beide wilde en kommersiële bevolkings om die effektiewe bruikbaarheid van hierdie merkers m.b.t. genetiese diversiteit, en bevolking struktuur bepaling, te ondersoek. Die platform het ’n 85% genotiperingsukses syfer getoon. Statistiese analise dui daarop dat merkers ontwikkel tydens hierdie studie toepaslik is vir bevolking genetiese struktuur bepaling, genetiese diversiteitberaming en moontlik ook genetiese koppelingskartering. Hierdie merkers word bestempel as onmisbaar vir toekomstige navorsing in genetiese bestuur en bewaring van H. midae.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The decline of Haliotis midae (perlemoen) populations together with the ensuing collapse of commercial abalone fisheries in South Africa have shifted the responsibility to abalone farms to meet the demand for perlemoen. Attention has recently turned to the genetic enhancement of cultured abalone in order for the farms to remain competitive in the international aquaculture market. To develop a successful breeding programme it is imperative to draw on a good foundation of high levels of genetic diversity and to successfully maintain these levels in order to create an enhanced strain of cultured abalone. A Performance Recording Scheme (PRS) was established as the first breeding programme for Haliotis midae to utilise molecular tools. This programme was aimed at enhancing the growth rate of abalone in order to shorten the production times on farms. The current study made use of 12 species-specific microsatellite markers to assign parentage to a group of faster-growing PRS animals, as selected by the abalone farms, in order to select a diverse on-farm generation of broodstock. Additionally, the influence of standard selection practises on the genetic diversity of a population compared to genotypic selection was investigated. This data was also used to study the differentiation and levels of genetic diversities within and between cultured and wild populations. Selection based on genotypic traits successfully retained genetic diversity while some diversity was lost in phenotypically selected populations. These phenotypic populations differed significantly from each other and wild populations, while the genotypic populations were similar in genetic composition to each other and wild populations of the West coast. The broodstock populations used in the PRS spawning event were representative of the wild populations from where they were sourced, with no significant differentiation between the broodstock and West coast population. When these broodstock populations were compared to their corresponding offspring populations, only two populations displayed a significant loss in diversity; although all of the offspring populations showed significant differentiation with their corresponding broodstock populations. This was attributed to the differential contribution of broodstock and the effect of artificial selection. It was established that the cultured populations of the participating abalone farms should be used with caution in ranching and reseeding programmes. These populations differed significantly from both the East and West coast wild populations. This study concluded that it is possible to retain genetic diversity by selecting breeding animals based on genotypic traits. The loss of diversity in some cultured populations and significant differentiation from the wild populations indicate that animals are exposed to different selection pressures in the cultured environment. The results found in this study highlight the need for the effective management of hatchery practices and the genetic monitoring of the breeding animals. / AFRIKAANSE OPSOMMING: Die afname in Haliotis midae (perlemoen) populasies en die daaropvolgende ineenstorting van die kommersiële perlemoen bedryf in Suid-Afrika het die verantwoordelikheid om in die aanvraag na perlemoen te voorsien, na perlemoen plase verskuif. Die genetiese verbetering van verboude perlemoen geniet tans aandag in ‘n poging om kompeterend te bly in die internasionale mark. Dit is noodsaaklik vir die sukses van ‘n broeiprogram om gebruik te maak van ‘n goeie genetiese basis met hoë vlakke van genetiese diversiteit en die suksesvolle behoud van die vlakke om so ‘n verbeterde lyn te skep. ‘n Groeiprestasie aanteken stelsel [Performance Recording Scheme (PRS)] is gestig as die eerste broeiprogram vir Haliotis midae wat gebruik maak van molekulêre tegnieke. Die doel van hierdie program was om die groeitempo van verboude perlemoen te verbeter om produksie tye te verkort. Die huidige studie het gebruik gemaak van 12 spesie-spesifieke mikrosatelliet merkers om ouerskap toe te ken aan ‘n groep vinnig-groeiende PRS-diere, soos geselekteer deur die perlemoen plase, om ‘n diverse generasie gekultiveerde diere te selekteer wat as broeidiere kan dien. Die invloed van standaard seleksie metodes op die genetiese diversitiet van ‘n populasie in vergelyking met genotipiese seleksie is ook ondersoek. Die ouerskap data is ook gebruik om differensiasie en vlakke van genetiese diversiteit tussen verboude perlemoene en wilde populasies vas te stel. Seleksie gebasseer op genetiese eienskappe het daarin geslaag om genetiese diversiteit te behou, terwyl diversiteit verlore gegaan het in die fenotipies geselekteerde populasies. Hierdie fenotipiese populasies het ook beduidend met mekaar sowel as met die wilde populasies verskil, terwyl genotipiese populasies soortgelyk was in hul genetiese samestelling en nie van die wilde populasies van die Weskus verskil het nie. Die broeidiere wat in die PRS broeiprogram gebruik is, was verteenwoordigend van die wilde populasies vanwaar hulle oorspronlik gekom het, met geen beduidende differensiasie tussen die broeidiere en die Wes kus populasies nie. Met die vergelyking van die broeidiere en hul ooreenstemmende nageslag, het dit geblyk dat slegs twee populasies ‘n beduidende verlies aan genetiese diversiteit getoon het, alhoewel al die nageslag beduidende populasie differensiasie met hul ouers getoon het. Hierdie bevindinge is toegeskryf aan oneweredige bydraes van die broeidiere tydens gameetvrystelling en die invloed van kunsmatige seleksie. Hierdie studie het ook vasgestel dat die verboude perlemoen populasies met sorg gebruik moet word om wilde populasies te herstel, aangesien hierdie populasies beduidend verskil het van wilde populasies van beide die Oos en Wes-kus. Hierdie studie het gevind dat dit moontlik is om genetiese diversiteit te behou deur diere te selekteer op grond van genotipiese eienskappe. Die verlies van diversiteit in sommige van die verboude perlemoen populasies en die beduidende verskil met die wilde populasies dui daarop dat diere in die gekultiveerde omgewing blootgestel word aan verskillende tipes seleksiedruk. Hierdie bevindinge beklemtoon die belang vir effektiewe bestuur van broeiery praktyke en genetiese monitering van broeidiere.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Haliotis midae, or more commonly known as Perlemoen, is an abalone species found along the coast of South Africa. It is the only cultured abalone species in South Africa and has a high demand abroad. Due to its popularity as a seafood delicacy, illegal harvesting has taken its toll on Perlemoen numbers. This increases the need for sustainable farming efforts and efficient implementation of law enforcement practices against poachers. Abalone farms make use of a limited number of broodstock for breeding, so it is necessary to ensure that genetic effects such as inbreeding and bottlenecks do not interfere with the viability of the offspring. Research that focuses on the genetics of Perlemoen will greatly aid the farms to continue sustainable production of this species as well as enhance their breeding efficiency. This study focuses on the construction of a linkage map for H. midae that will allow the future identification of markers associated with genes important to production, such as growth and disease resistance. Identification of these genes will allow breeders to select genetically superior abalone that will be used for breeding programmes in which the phenotype of the offspring will be enhanced. For the construction of a linkage map it is necessary to have enough informative markers for mapping. In this study, gene-linked microsatellite markers were developed by screening a contig assembly of H. midae’s transcriptome. Ninety-eight primer pairs could be developed from the contigs and 60 loci produced amplification products. Twenty-six microsatellites were found to be polymorphic (27% success rate). In addition to these markers, 239 previously developed microsatellites and 48 gene-linked SNPs were used to develop sex-average and sex-specific linkage maps in four full-sib families consisting of approximately 100 offspring each. Of these markers 99 were informative in family DS1 (31% success rate), 81 in family DS2 (26%), 77 in family DS5 (24%) and 71 in family DS6 (23%). These markers were used for linkage analysis (LOD>3). The average number of linkage groups for the sex-average maps ranged from 17-19. The average genome length for these maps ranged from 700cM to 1100cM with an average marker spacing of 8cM. The sex-specific maps’ linkage groups ranged from 13-17 with an average genome length of 600cM to 1500cM. The average marker spacing was approximately 16cM. The integrated map was constructed by merging the sex-average maps. This map contained 25 linkage groups with an average genome length calculation of 1700cM and an average marker spacing of 9.3cM. The linkage maps created in this study are the first to utilize SNPs in H. midae. Further incorporation of SNPs into linkage maps will enhance the density. The maps created in this study are of medium-density (65%) and provide a link to the development of high-density linkage maps to facilitate associations of phenotypic traits to certain markers, to so that QTL mapping can be performed. This information can be used for marker-assisted selection to produce genetically superior abalone. / AFRIKAANSE OPSOMMING: Haliotis midae, of meer algemeen bekend as Perlemoen, is 'n klipkous spesie wat langs die kus van Suid-Afrika voorkom. Dit is die enigste gekweekte klipkous spesie in Suid-Afrika en het 'n hoë aanvraag in die buiteland. As gevolg van sy gewildheid as 'n seekos lekkerny, het onwettige stropery sy tol geneem op Perlemoen getalle. Hierdie verhoog die behoefte vir volhoubare boerdery pogings en doeltreffende implementering van wetstoepassing teen stropers. Perlemoenplase maak gebruik van 'n beperkte aantal broeidiere vir teling, dus is dit nodig om te verseker dat genetiese effekte soos inteling en genetiese bottelnekke nie inmeng met die lewensvatbaarheid van die nageslag nie. Navorsing wat fokus op die genetika van Perlemoen sal grootliks die plase steun om die volhoubare produksie van hierdie spesie voort te sit, sowel as hul teling doeltreffendheid te verbeter. Hierdie studie fokus op die ontwikkeling van 'n genetiese koppelingskaart vir H. midae, wat die toekomstige identifisering van die merkers wat verband hou met die gene wat belangrik is vir die produksie, soos groei en weerstand teen siektes sal verbeter. Identifisering van hierdie gene sal toelaat dat telers genetiese voortreflike Perlemoen kan kies vir teelprogramme waartydens die fenotipe van die nageslag sal verbeter word. Vir die ontwikkeling van 'n genetiese koppelingskaart is dit nodig om genoeg informatiewe merkers vir die kartering te hê. In hierdie studie, is geen-gekoppelde mikrosatelliet-merkers ontwikkel deur ‘contig’ data van H. midae se transkriptoom te ondersoek. Agt en negentig inleier pare kon ontwikkel word uit die ‘contigs’ en 60 loki kon ‘n amplifiseringsproduk lewer. Ses-en-twintig mikrosatelliete was polimorfies (27% suksessyfer). Bykomend tot hierdie ontwikkelde merkers is 239 voorheen ontwikkelde mikrosatelliete en 48 geen-gekoppelde SNPs gebruik om geslagsgemiddelde en geslagspesifieke koppelingskaarte in vier volsib families, wat uit ongeveer 100 nageslag elk bestaan, te ontwikkel. Van hierdie merkers was 99 informatief in familie DS1 (31%), 81 in die familie DS2 (26%), 77 in die familie DS5 (24%) en 71 in die familie DS6 (23%). Hierdie merkers is gebruik vir 'n koppelingsanalise (LOD>3). Die gemiddelde aantal koppelingsgroepe vir die geslagsgemiddelde kaarte het gewissel van 17-19. Die gemiddelde genoom lengte vir hierdie kaarte het gewissel van 700cM tot 1100cM met 'n gemiddelde merker spasiëring van 8cm. Die koppelingsgroepe van die geslagspesifieke kaarte het gewissel van 13-17 met 'n gemiddelde genoom lengte van 600cM tot 1500cM. Die gemiddelde merker spasiëring was ongeveer 16cm. Die geïntegreerde kaart is saamgestel deur die samesmelting van die geslagsgemiddelde kaarte. Die kaart toon 25 koppelingsgroepe met 'n gemiddelde berekende genoom lengte van 1700cM en' n gemiddelde merker spasiëring van 9.3cM. Die genetiese koppelingskaarte wat in hierdie studie ontwikkel is, is die eerste om SNPs te gebruik in H. midae. Verdere insluiting van SNPs in koppelingskaarte sal die digtheid verhoog. Die kaarte wat in hierdie studie ontwikkel is, is van medium digtheid (65%) en bied 'n stap nader aan die ontwikkeling van hoë digtheid koppelingskaarte om fenotipiese eienskappe met sekere merkers te assosieer, vir kwantitatiewe kenmerk lokus kartering. Hierdie inligting kan gebruik word vir merker bemiddelde seleksie om geneties verbeterde Perlemoen te produseer.

An understanding of species specific water quality requirements is essential for efficient production of aquaculture products, an aspect not well documented for the land-based culture of the South African abalone, Haliotis midae. In order for the industry to remain competitive in international markets, efficient use of water supplies and the development of water reuse technology is needed. This study assessed the changes in water quality between tanks in a tiered serial-use raceway in relation to accumulated biomass and water flow and estimated the flow index (FI) (L h⁻¹ kg⁻¹) at which growth becomes significantly affected. The effect of dietary protein level, supplementation of pure oxygen and addition of sodium hydroxide (NaOH⁻) on water quality and fundamental production parameters in the serial-use raceways was also assessed. The serial-use raceways were used as a tool to create a range of water quality conditions at which the growth, feed conversion ratio (FCR) and condition factor (CF) of "cocktail" size (60 – 70 mm) H. midae could be monitored. The metabolic activity of the abalone resulted in a deterioration in water quality between tanks in series. pH (r² = 0.99; p < 0.001) and dissolved oxygen concentration (r² = 0.99; p < 0.001) were positively correlated with flow index (pH = 7.38 FI°·°² ; dissolved oxygen = 6.92 FI°·°⁴), while free ammonia nitrogen (FAN) (r² = 0.99, p < 0.001) and nitrite (NO²⁻ - N) (r² = 0.93, p < 0.001) were negatively correlated with flow index (FAN = 8.02 FI⁻°·⁷¹). Nitrite concentrations increased over time indicating colonisation of Nitrosomonas bacteria on the basket surfaces. A flow index of 7.2 – 9.0 L h⁻¹ kg⁻¹ was estimated as the minimum to avoid significant reductions in weight and shell length gain and increases in FCR values. Total ammonia nitrogen (TAN) and FAN concentrations were significantly correlated to dietary protein (P) (t = 6.63, p < 0.0001 and t = 6.41, p < 0.0001, respectively) and flow index (t = 5.42, p < 0.0001 and t = 3.9, p < 0.0002, respectively) and could be estimated using the models TAN = 9.73 P – 110.3 log (FI), and FAN = 0.132 P – 1.10 log (FI). Mean FAN concentrations were 67 and 41 % lower in tanks fed a diet containing 22 and 26 % protein respectively, when compared to tanks fed a 33 % protein diet. Supplementation with pure oxygen (103 ± 8 % saturation) improved shell length gain (t = 3.45, p = 0.026) in abalone exposed to high FAN (2.43 ± 1.1 μg L⁻¹) and low pH (7.6 ± 0.13), relative to a treatment with no oxygen supplementation (92 ± 6 % saturation). Addition of a sodium hydroxide solution resulted in elevated mean pH in treatment raceways when compared to control raceways. The increased pH resulted in significantly higher weight gain (g abalone⁻¹) (F₁·₁₂ = 4.51; p = 0.055) and shell length gain (mm abalone⁻¹) (F₁·₁₂ = 4.56; p = 0.054) at an α-error level of < 5.5 %. In two trials, weight gain and shell length gain were significantly correlated to pH (p < 0.001), and multiple regression of pH, dissolved oxygen and FAN consistently revealed pH to be the best predictor of growth. It is therefore suggested that decreasing pH is the first limiting water quality variable for abalone in serial-use raceways. As a decrease in water pH is linked to respiration by the abalone and subsequent increase in dissolved carbon dioxide (CO₂) concentration, future studies should examine the effects of CO₂ on H. midae metabolic rate, calcification rate and health. The results of this study will contribute toward our understanding of the specific water quality requirements for H. midae in commercial aquaculture systems, and influence the design and management procedures for abalone water reuse systems.

The Roe’s abalone (Haliotis roei) fishery near Perth, Western Australia, is uniquely accessible, and highly vulnerable to overexploitation. The sustainability of this intensively utilized fishery requires robust assessment. To facilitate an assessment, this research aimed to provide rigorous and detailed biological information with appropriate interpretation. Four critical aspects of the species’ biology and population dynamics were investigated: (1) the stock structure; (2) the recreational catch; (3) an appropriate growth curve and description of size at age; and (4) abundance measures against which to assess the impact of fishing mortality. Allozyme electrophoresis was used to investigate stock structure across the species’ distribution. Standardized variance in allelic frequencies between 10 sites in south-western Australia indicated high levels of gene flow across the 3000 km sampled (mean FST = 0.009). An isolation-by-distance was evident when pairwise measures of GST were related to geographic distance (r=0.45, P<0.001). The area of complete genetic mixing was estimated from samples within the Perth fishery to be less than the distance between the two nearest sites, or 13 km. Consequently, the Perth fishery comprises numerous discrete stocks, each requiring independent assessment. A possible mechanism for this population structure is the retention of larvae in the wind driven currents oscillating in the near-shore lagoons, with rare pulses of long distance dispersal via the southerly Leeuwin current, running further offshore. The presumed impact of intensive recreational fishing, combined with substantial commercial quotas for the Perth fishery, had led to tight restrictions on fishing effort, without any quantitative measure of the recreational catch. A stratified creel survey was adapted to estimate the effort, catch rate and mean weight of abalone harvested by the recreational sector. Catches were estimated for reef complexes, or stocks, of less than 10 nautical miles (18.5 km) of coast. Between 1997 and 2000 the recreational catch varied from 30 to 45 tonnes whole weight, approximately equivalent to the commercial quota of 36 tonnes. On average 88% of the recreational catch came from two stocks, while 98% of the commercial catch came from these two, and one additional, stocks. The incidental mortality from recreational fishing, measured as the number of abalone left dead on the reef as a proportion of the estimated catch, was approximately 7% and 20% at two sites surveyed. Spatial and temporal patterns of growth were examined on the west coast of Western Australia. Growth increments were measured for abalone larger than about 30 mm from tagging studies at five sites in the Perth fishery, a site at the northern extent of the species’ distribution and a site in the southwest. Mean annual growth increments of the 0+ year class were obtained by fitting components to length frequencies from five sites in the Perth fishery, and combined with growth increments from each Perth tag site for model fitting. A von Bertalanffy growth curve provided a slightly better fit to the tag data, but a Gompertz growth curve was a much better fit when the mean increment from the 0+ to 1+ cohort was included, with the inflection occurring at about 40 mm, the size at sexual maturity. There was no difference in annual growth between the two years studied. There was significant variation in growth between the reef platform and adjacent sub-tidal reef, but this variation was site specific and faster growth rates were not consistently associated with either habitat. There was no latitudinal trend in growth rate. Growth at the Perth sites was the fastest and similar at all five sites with growth increments greater in summer than in winter. Size and abundance of abalone were measured using fixed transects and quadrats. Abalone densities were highest on the outer edge of the platform, intermediate in the middle of the reef platform, and lowest on both the inner platform and the sub-tidal reef. The pattern of mean lengths of abalone was the inverse of the density. Mean length and abundance were driven by the presence of post-settlement juveniles on the outer and middle reef habitats. There was a high spatial variation in abundance, with densities varying between transects at the same site, but the trend between years for each transect at a site was not significantly different. Abalone abundances, by size class, were examined from sites sampled between 1996 and 2002. A low density of post-settlement juveniles at all sites in 1997 was reflected in low densities of the 1+ and 2+ year classes in subsequent years. Abalone abundances at an unfished site were steady over the seven years. Two sites were located within each of the main stocks utilised by the recreational fishery. Abundance was stable or increasing in one stock, corresponding to a stable total catch. In the second stock the total catch increased over time and abundances declined. Perth is the focus of the Roe’s abalone fishery, with recreational and commercial fishers take about equal shares of the annual catch. Stocks are highly subdivided, with most of this catch coming from only 3 stocks occupying about 20 nautical miles of coast. Growth rates were found to be lower than previous estimates, and more similar to other commercial species of abalone. All life history stages are highly habitat specific, particularly the recruits, and the distribution and abundance through time indicate that the main stocks are near, or slightly over, the limit of sustainable fishing.

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2009. / An 84-day study was conducted to find a suitable diet and feeding level for the culture of South African abalone (Haliotis midae) in Namibia. Two experimental diets, namely, a seaweed diet (SWD) Laminaria pallida (macrophytic algae) and a formulated diet (FD) (macro-algae), for use in abalone (Haliotis midae) feed development, were evaluated. The animals used in this study were juveniles (24.33 ± 3.14 mm shell length; 2.72 ± 0.83 g live weight, mean ± SE) and sub-adults (58.07 ± 10.33 mm shell length and 41.96 ± 20.61 g live weight, mean ± SE). The nutrient profile of the SWD and FD displayed no differences in the protein and carbohydrate levels. Crude protein levels ranged from 4.91 to 17.68% (dry matter (DM) basis). The lipid levels in the FD (0.25%) were almost 0.56% lower than that in the SWD (0.76%). The feed conversion ratio (FCR) and protein efficiency ratio (PER) for the sub-adult abalone ranged from 2.80 to 10.90 and 0.10 to 0.40, respectively. The juvenile abalone fed on the FD yielded significantly lower (P < 0.05) FCRs (0.8) and higher PERs (1.20) than their counterparts fed on the SWD. A similar trend was observed for the sub-adult abalone although the differences were not significant (P > 0.05). The relative growth rate (RGR) of juvenile fed on the FD was 25% lower compared to those fed on the SWD, while that of the sub-adult abalone fed on the FD was 29% lower compared to the abalone fed on the SWD. From the daily growth rate (DGR) in terms of daily body weight (DGRBW) calculated after the 84-day period, repeated-measures ANOVA (RANOVA) indicated no interaction between time period and diet. Although slightly lower, the DGRBW for the juvenile abalone fed on the SWD diet (0.033 g/day) did not differ significantly from the DGRBW of abalone fed on the FD (0.079 g/day). In contrast, sub-adult abalone fed on the SWD exhibited significantly higher DGRBW compared to those fed on the FD. Although the abalone fed on the FD was slightly higher in nutritional content, there was no significantly difference (P > 0.05) in the nutritional profile of the abalone soft body tissue fed on either the SWD or FD. There was no significant (P > 0.05) difference in preference when comparing the aroma of the abalone meat samples fed on either the SWD or FD. However, there was a significant difference (P < 0.05) in the consumers’ preference in terms of flavour for the abalone sample fed on the FD. The trained taste panel results indicated that there was no difference in the aroma and flavour of the abalone fed on the different diets (P > 0.05). This study showed that cultured juvenile H. midae, readily accepted a FD, producing high consumption and survival rates. The FD still warrants further refinement and testing for it to become a more effective mariculture feed with commercial potential.