Department of Genetics

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Browsing Department of Genetics by Subject "Abalone"

Now showing 1 - 4 of 4
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    Growth-related gene expression in haliotis midae
    (Stellenbosch : University of Stellenbosch, 2010-12) Van der Merwe, Mathilde; Roodt-Wilding, R.; Auzoux-Bordenave, S.; Niesler, C.; University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: The slow growth rate of Haliotis midae impedes the optimal commercial production of this most profitable South African aquaculture species. To date, no comprehensive effort has been made to identify genes associated with growth variation in farmed H. midae. The aim of this study was therefore to investigate growth variation in H. midae and to identify and quantify the expression of selected growth-related genes. Towards this aim, molecular methodologies and cell cultures were combined as a time-efficient and economical way of studying abalone transcriptomics and cell biology. Modern Illumina sequencing-by-synthesis technology and subsequent sequence annotation were used to elucidate differential gene expression between two sibling groups of abalone demonstrating significant growth variation. Following transcriptome sequencing, genes involved in growth and metabolism, previously unknown in H. midae, were identified. The expression of selected target genes involved in growth was subsequently analyzed by quantitative real-time PCR (qPCR). The feasibility of primary cell cultures for H. midae was furthermore investigated by targeting embryo, larval and haemolymph tissues for the initiation of primary cell culture. Larval cells and haemocytes could be successfully maintained in vitro for limited periods. Primary haemocyte cultures demonstrated to be a suitable in vitro system for studying gene expression and were subsequently used for RNA extraction and qPCR, to evaluate differential growth induced by bovine insulin and epidermal growth factor (EGF). Gene expression was thus quantified in fast and slow growing abalone and in in vitro primary haemocyte cultures treated with different growth stimulating factors. The results obtained from transcriptome analysis and qPCR revealed significant differences in gene expression between large and small abalone, and between treated and untreated haemocyte cell cultures. Throughout in vivo and in vitro qPCR experiments, the up-regulation of genes involved in the insulin signaling pathway provides evidence for the involvement of insulin in enhanced growth rate for various H. midae tissues. Besides the regulation of target genes, valuable knowledge was also gained in terms of reference genes, during qPCR experimentation. By quantifying the stable expression of two genes (8629, ribosomal protein S9 and 12621, ornithine decarboxylase) in various tissues and under various conditions, suitable reference genes, that can also be used in future H. midae qPCR studies, were identified. By providing evidence at the transcriptional level for the involvement of insulin, insulin-like growth factors (IGFs) and insulin-like growth factor binding proteins (IGFBPs) in improved growth rate of H. midae, the relevance of investigating ways to stimulate insulin/IGF release in aquaculture species was again emphasized. As nutritional administration remains the most probable route of introducing agents that can stimulate the release of insulin-related peptides, continuous endeavours to stimulate abalone growth through a nutritional approach is encouraged. This is the first time next generation sequencing is used towards the large scale transcriptome sequencing of any haliotid species and also the first time a comprehensive investigation is launched towards the establishment of primary cell cultures for H. midae. A considerable amount of sequence data was furthermore annotated for the first time in H. midae. The results obtained here provide a foundation for future genetic studies exploring ways to optimise the commercial production of H. midae.
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    An integrated linkage map of perlemoen (haliotis midae)
    (Stellenbosch : University of Stellenbosch, 2010-12) Hepple, Juli-ann; Roodt-Wilding, R.; University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: Haliotis midae, or Perlemoen, is the only cultured species of abalone in South Africa and is under great international demand. This species is considered endangered, making sustainable farming practises and law enforcement against poaching essential for maintaining wild stocks. A limited amount of broodstock animals are provided to each farm from which thousands of offspring are grown and exported. The prevention of inbreeding and preservation of genetic diversity within farmed stocks is necessary for future sustainable farming and production of genetically stable offspring. Further research into the genetic dynamics of Perlemoen will provide the knowledge for advanced management programs for optimal farming practises and essentially sustainable production. This study focuses on genetic linkage map development with the intention of future identification of markers associated with genes of economic importance, such as growth rate. Identification of markers linked to genes responsible for such phenotypic traits will ultimately allow farming practises to select naturally genetically superior animals for breeding, thereby enhancing production. For the construction of a genetic linkage map of H. midae, microsatellite markers were developed using two strategies: FIASCO and screening of next generation sequence-bysynthesis contig data. The FIASCO-derived markers were characterised by genotype screening in 32 individuals from a full-sib family and analysed using Mendelian segregation expectations. The Illumina-derived markers were characterised by genotype screening in 32 individuals from wild populations and analysed against Hardy-Weinberg expectations. Forty four microsatellite-family combinations were obtained from FIASCO of which 28 provided informative genotype results (32% success). Twenty two markers were developed from sequence-by-synthesis screening. Fourteen provided reliable genotypes (37%) and six conformed to Hardy-Weinberg expectations. These markers were used, in addition to 156 previously developed markers, to develop sex-specific and sex-average linkage maps in two full-sib families consisting of approximately 100 offspring each. One hundred and six polymorphic loci were used for linkage analysis (LOD>3) in both families. The number of linkage groups obtained from sex-specific maps ranged from 13-16. The average genome length ranged from 500 cM to 800 cM with an average marker spacing of 10 cM. The sex-average linkage map provided 18 linkage groups with an average genome length calculation of 1800 cM and average marker spacing of approximately 13 cM. The linkage maps created in this study are preliminary but provide a stepping stone towards a high density map incorporating high throughput markers. This also provides a base for QTL mapping studies, in which phenotypic traits of interest can be identified and associated to specific locations in the H. midae genome for marker-assisted selection.
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    Reproduction of the South African abalone, Haliotis midae
    (Stellenbosch : Stellenbosch University, 2011-12) Visser-Roux, Adelle; Roodt-Wilding, R.; Lambrechts, Helet; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.; Roux, Adelle
    ENGLISH ABSTRACT: Currently, South African aquaculture is dominated by the cultivation of Haliotis midae, which is estimated as the most lucrative sector of the industry, with 934 t being export in 2008, totalling an income of ZAR 268 million (40 million USD) in 2008. This represents 81% of the total rand value of the aquaculture sector. Abalone was the highest aquaculture commodity exported during the last two years from South Africa, representing 24% of the total tonnage exported. Employment in the aquaculture sector increased by approximately 80% between 2005 and 2008, and was highest in the abalone sector where the number of people employed increased by 234%. Despite these high production rates, no hatchery procedures have been developed specifically for H. midae. Most procedures and protocols currently used in South African abalone hatcheries have been adopted from cultivation methods used for foreign species. Although certain aspects of reproduction are universally conserved between abalones, it is important to consider the physiology and the origin of the species studied. To date, no scientific research has been conducted on the reproduction of H. midae, except for a few studies in the early 1990s, which focused on the basic reproduction of this species. No further studies have been done on H. midae reproduction under intensive culture. Currently, hatch-out rates obtained by most abalone farms in South Africa averages 80%, with a 50% settlement rate, and a final hatchery output of only 30%. This study reports on various aspects of H. midae reproduction that can influence its commercial culture. A detailed histological characterisation of gametogenesis was developed. Findings indicated that cultured H. midae reaches 50% sexual maturity at a shell width of between 25 mm and 30 mm. During fertilisation trials, a sperm concentration of 50 000 sperm mL-1 and egg concentrations lower than 50 eggs mL-1 produced the highest hatch-out rates. Whilst fertilisation volume did not influence fertilisation success, fertilisation potential of the eggs did decrease with time. Eggs older than 100 minutes showed a lower fertilisation potential than eggs fertilised earlier. A larval stress test was developed to evaluate larval resistance against chemical stress. It was determined that 50% of resultant larvae would exhibit morphological abnormalities after fertilised eggs were incubated in 0.7% dimethyl sulfoxide (Me2SO) for a 24 hour period. If larvae exhibited fewer abnormalities at this concentration, it could be deduced that the larvae had a high resistance to the negative effect of the toxicant, and could thus be seen as good quality larvae. When evaluating hybridisation potential between H. midae and H. spadicea, it was found that it was possible to fertilise spawned H. midae eggs with biopsied H. spadicea sperm. By incorporating the results obtained from the present study into current hatchery systems on South African abalone farms, higher hatchery yield could be achieved, which in turn would lead to an increase in commercial revenue.
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    SNP screening and validation in Haliotis midae
    (Stellenbosch : Stellenbosch University, 2012-03) Blaauw, Sonja; Roodt-Wilding, R.; Van der Merwe, A. E.; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    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.