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Growth-Related Gene Expression in Haliotis Midae

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GROWTH‐RELATED GENE EXPRESSION IN HALIOTIS MIDAE Mathilde van der Merwe Dissertation presented for the degree of Doctor of Philosophy (Genetics) at Stellenbosch University Promoter: Dr Rouvay Roodt‐Wilding Co‐promoters: Dr Stéphanie Auzoux‐Bordenave and Dr Carola Niesler December 2010 Declaration By submitting this dissertation, I declare that the entirety of the work contained therein is my own, original work, that I am the authorship owner thereof (unless to the extent explicitly otherwise stated) and that I have not previously in its entirety or in part submitted it for obtaining any qualification. Date: 09/11/2010 Copyright © 2010 Stellenbosch University All rights reserved I Acknowledgements I would like to express my sincere gratitude and appreciation to the following persons for their contribution towards the successful completion of this study: Dr Rouvay Roodt‐Wilding for her continued encouragement, careful attention to detail and excellent facilitation throughout the past years; Dr Stéphanie Auzoux‐Bordenave for valuable lessons in abalone cell culture and suggestions during completion of the manuscript; Dr Carola Niesler for setting an example and providing guidance that already started preparing me for a PhD several years ago; Dr Paolo Franchini for his patience and greatly valued assistance with bioinformatics; Dr Aletta van der Merwe and my fellow lab‐colleagues for their technical and moral support; My dear husband Willem for his love, support and enthusiasm, for sitting with me during late nights in the lab and for making me hundreds of cups of tea; My parents for their love and encouragement and for instilling the determination in me to complete my studies; All my family and friends for their sincere interest. II 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 signalling 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 III 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. IV Opsomming Die stadige groeitempo van Haliotis midae belemmer die optimale kommersiële produksie van hierdie mees winsgewende Suid‐Afrikaanse akwakultuur spesie. Tot op hede is geen omvattende poging aangewend om gene verwant aan groeivariasie in H. midae te identifiseer nie. Die doel van hierdie studie was dus om groeivariasie in H. midae te ondersoek en om spesifieke groei‐gekoppelde gene te identifiseer en hul uitdrukking te kwantifiseer. Ter bereiking van hierdie doel is molekulêre metodes en selkulture gekombineer as ‘n tydsbesparende en ekonomiese manier om perlemoen transkriptomika en selbiologie te bestudeer. Moderne Illumina volgordebepaling‐deur‐sintese tegnologie en daaropvolgende annotasie is gebruik om verskille in geenuitdrukking tussen naby‐verwante groepe perlemoen, wat noemenswaardige groeivariasie vertoon, toe te lig. Na afloop van die transkriptoom volgordebepaling is gene betrokke by groei en metabolisme, vantevore onbekend in H. midae, geïdentifiseer. Die uitdrukking van uitgesoekte teikengene betrokke by groei is vervolgens ge‐analiseer deur kwantitatiewe “real‐time PCR” (qPCR). Die lewensvatbaarheid van primêre selkulture vir H. midae is ook ondersoek deur embrio, larwe en hemolimf weefsels te teiken vir die daarstelling van primêre selkulture. Larweselle en hemosiete kon in vitro suksesvol onderhou word vir beperkte periodes. Primêre hemosietkulture het geblyk ‘n gepaste in vitro sisteem te wees om geenuitdrukking te bestudeer en dit is vervolgens gebruik vir RNS ekstraksie en qPCR, om differensiële groei, geïnduseer deur insulien en epidermale groeifaktor (EGF), te evalueer. Geenuitdrukking is dus gekwantifiseer in vinnig‐ en stadiggroeiende perlemoen en in in vitro primêre hemosiet selkulture wat behandel is met verskillende groei stimulante. Die resultate wat verkry is van transkriptoomanalise en qPCR het noemenswaardige verskille in geenuitdrukking tussen groot en klein perlemoen, en tussen behandelde en onbehandelde hemosiet selkulture uitgelig. Die op‐regulering van gene betrokke by die insulien sein‐padweg, tydens in vivo en in vitro qPCR eksperimente, bied getuienis vir die betrokkenheid van insulien in die verhoogde groeitempo van verskeie H. midae weefsels. Benewens die regulering van teikengene is waardevolle kennis ook ingewin in terme van verwysingsgene tydens qPCR eksperimentering. Deur die stabiele uitdrukking van twee gene (8629, ribosomale proteïen S9 en 12621, ornitien dekarboksilase) te kwantifiseer in verskeie weefsels en onder verskeie kondisies is gepaste verwysingsgene, wat ook in toekomstige H. midae qPCR eksperimente aangewend kan word, geïdentifiseer. Deur getuienis vir die betrokkenheid van insulien, insuliensoortige groeifaktor en insuliensoortige groeifaktor‐bindingsproteïene by verbeterde groei van H. midae op transkripsievlak te bied, is die toepaslikheid van bestudering van maniere om insulienvrystelling in akwakultuurspesies te stimuleer, V beklemtoon. Aangesien voeding die mees waarskynlike roete is om middele wat insuliensoortige peptiedvrystelling stimuleer daar te stel, word vogehoue pogings om perlemoengroei deur die regte voeding te stimuleer, aangemoedig. Hierdie is die eerste studie wat volgende generasie volgordebepaling (“next generation sequencing”) gebruik vir die grootskaalse transkriptoom volgordebepaling van enige haliotied spesie. Dit is ook die eerste keer dat ‘n omvattende ondersoek geloods word na die daarstelling van primêre selkulture vir H. midae. ‘n Aansienlike hoeveelheid volgorde data is ook vir die eerste keer geannoteer in H. midae. Die resultate wat hier verkry is bied ‘n basis vir toekomstige genetiese studies wat maniere ondersoek om die kommersiële produksie van perlemoen te optimiseer. VI Publications and conference proceedings resulting from this PhD An article reporting a large portion of the content of chapter three was accepted for publication: Van der Merwe, M., Auzoux‐Bordenave, S., Niesler, C and Roodt‐Wilding, R. 2010. Investigating the establishment of primary cell culture from different abalone (Haliotis midae) tissues. Cytotechnology 62 (3): 265‐277. Results from chapter two were presented at the 10th International Symposium on Genetics
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