Department of Genetics

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Browsing Department of Genetics by Subject "Abalone culture"

Now showing 1 - 5 of 5
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    Development of gene-linked molecular markers in South African abalone (Haliotis midae) using an in silico mining approach
    (Stellenbosch : University of Stellenbosch, 2010-03) Rhode, Clint; Roodt-Wilding, R.; University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is the only endemic species of commercial value. Aquaculture remains the only avenue for expanding the industry, since the closure of the fishery. The current focus is on implementing a molecular breeding programme; thus the development of molecular markers for linkage mapping and QTL analysis is a priority. Various markers, mainly anonymous, have been developed for H. midae; however emphasis is being placed on the development of gene-linked type I molecular markers. The present study investigates and demonstrates the use of public sequence collections to develop type I markers for a species with limited genomic resources, via three strategies: Surveying anonymous H. midae microsatellite markers’ flanking regions to find homology to gene sequences in public databases, cross-species marker transfer of anonymous markers from H. rubra and H. discus hannai demonstrating putative gene associations and lastly EST marker mining (SNP and microsatellites) from various Haliotids and testing transfer to the target species. Approximately 17% of H. midae anonymous markers showed significant similarity to genes. The current study also reports higher cross-species transferability from both H. rubra and H. discus hannai to H. midae (39% and 20.5%, respectively) than previously demonstrated and 15 EST-microsatellites and 16 EST-SNPs were successfully mined. Furthermore, the non-random distribution of microsatellites and high nucleotide diversity in the H. midae genome was confirmed. This is a low cost and time effective method for marker development and presents a continuous and dynamic resource that could be used for future marker development and characterisation as sequence information in public databases grow exponentially.
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    Microsatellite genotyping of contributing broodstock and selected offspring of Haliotis midae submitted to a growth performance recording scheme
    (Stellenbosch : Stellenbosch University, 2007-12) Ruivo, Nicola Ribeiro; Roodt-Wilding, R.; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.
    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.
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    Microsatellite marker development and parentage assignment in Haliotis midae
    (Stellenbosch : Stellenbosch University, 2008-03) Van den Berg, Nicol-Candice; Roodt-Wilding, R.; Brink, Danie; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: The five leading abalone producers in South Africa have initiated a genetic enhancement program for Haliotis midae in a collaborative effort to improve economically valuable traits. Several independent objective-specific studies were initiated, including the establishment of a Performance Recording Scheme (PRS), utilised in this study, and necessary to monitor the ongoing performance of individuals as the move from mass-selection to marker assisted selection (MAS) is implemented. The primary objective of this study was parentage assignment of F1 offspring mass-selected for size at approximately one year and allocated to either a “faster” or a “slower” growth group. Nine microsatellite markers were used to genotype juveniles and potential parents, with assignment completed using CERVUS 2.0. Average growth results for Abagold and HIK were comparable for both growth groups. Slight environmental effects, although not statistically significant, were evident as growth advantages for juveniles within the faster growth group at two of the five locations and for juveniles within the slower growth group at one of the five rearing locations. Despite measures to standardise environmental influences, variables are difficult to control within the reality of a production environment; and potential genotype x environment interactions may require further investigation and factoring into future breeding programs. The additional costs associated with MAS often make the technology prohibitive to most aquaculture operations, despite the significant genetic gains to be realised from its implementation. Cost-optimising routine processes such as DNA extractions may be one approach to reduce these additional costs. Chelex®100 appears to be a suitable alternative to the CTAB method – being quick and cost-effective to perform. Applying this method in combination with the high throughput of a robotic platform warrants further evaluation. For the microsatellite development, 50% of positive recombinant clones contained inserts. Sequencing of these clones produced 16% perfect repeats and 47% imperfect repeats for which 52 primer sets were designed and tested. In total, 31 polymorphic microsatellite loci of different motifs and composition were developed. Sixty-one percent of sequenced clones were deemed redundant and pre-screening for both uniqueness and the presence of microsatellites would reduce unnecessary sequencing thus improving the efficiency of the FIASCO method and reducing costs. Nine loci were selected for parentage assignments. Null alleles were present for all the selected markers; however, frequencies were below the critical level of 5%. Parentage yielded 91% and 90% successful assignment for Abagold and HIK respectively; however, observations indicate that a measure of relatedness may exist between breeders. Recommendations with regards to future family breeding include, for both Abagold and HIK, retaining selected breeders based on their respective contributions to the F1 progeny while reassessing the potential of remaining breeding stock under more controlled breeding conditions. No obvious trends were observed for growth with most individuals producing both faster and slower growing offspring. Juveniles will be reassessed at two years to determine whether the size advantage or disadvantages were maintained and to ascertain whether growth advantages/disadvantages may be gender specific.
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    Molecular markers to assist the South African abalone industry
    (Academy of Science for South Africa, 2006) Roodt-Wilding, R.; Slabbert, Ruhan
    HALIOTIS MIDAE (PERLEMOEN) IS THE ONLY southern African species of abalone to be commercially exploited. Commercial farms are currently producing 750 tons per annum, making this an economically viable enterprise. Increasing world demand and dwindling natural populations have, however, necessitated the adoption of genetic management practices on South African abalone farms to remain sustainable. This can be done by means of DNA markers, which are employed to investigate various phenomena from genetic diversity, parentage and broodstock contributions to linkage mapping and marker-assisted selection for genetic enhancement of the commercial species. The use of microsatellite markers for various abalone aquaculture applications is highlighted in this review.
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    Population genetic structure and demographical history of South African abalone, Haliotis midae, in a conservation context
    (Stellenbosch : University of Stellenbosch, 2009-03) Van der Merwe, Aletta Elizabeth; Roodt-Wilding, R.; D'Amato, M. E.; Volckaert, F.; Bester, Aletta Elizabeth; University of Stellenbosch. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: South African abalone, Haliotis midae, has been the subject of major concern regarding its survival and conservation over the last decade or more. Being the only one of five endemic species with commercial value, there is considerable interest and urgency in genetic management and improvement of this species. Limited genetic information and the increasing conservation concern of this species are considered the key motivations for generating information on the micro- and macro-evolutionary processes of H. midae, the overall objective of this study. This study reported the first microsatellite and Single Nucleotide Polymorphism (SNP) markers developed specifically for Haliotis midae. Both these marker types were applied to elucidate the degree of gene flow in nine natural abalone populations whilst testing for two contrasting hypotheses; panmixia versus restricted gene flow. Data was analysed using a series of methodological approaches ranging from traditional summary statistics to more advanced MCMC based Bayesian clustering methods with and without including spatial information. Using only microsatellite data, the historical demography of the species was also examined in terms of effective population size and population size fluctuations. Finally, the evolutionary positioning and origin of Haliotis midae with regards to other Haliotis species was investigated based on mitochondrial and nuclear sequence data. Both microsatellite and SNP data gave evidence for subtle differentiation between West and East coast populations that correlates with a hydrogeographic barrier in the vicinity of Cape Agulhas. Population substructure was supported by AMOVA, FCA and Bayesian clustering analysis. Clustering utilizing spatial information further indicated clinal variation on both sides of the proposed barrier with a region in the middle coinciding with a secondary contact zone, indicating possible historical isolation during glacial periods. Overall, the similar degree of substructure observed with both microsatellites and SNPs supported the existence of contemporary and/or historical factors with genome-wide effect on gene flow. The population expansion measured with the microsatellites was inconsistent with the known recent decline but taking the species’ life cycle and large effective population size into account, a shrinkage in population size will probably only be apparent in a few generations time. On a macro-evolutionary scale, this study presents the first classification of South African abalone as a monophyletic group within the Haliotidae family. The topology based on the combined mitochondrial and nuclear dataset is highly suggestive of a relatively recent radiation of the SA species from the Indo-Pacific basin. The study concludes by describing the most likely factors that could have affected overall population structure and makes suggestions on how the given genetic information should be incorporated into strategies aimed towards the effective management and conservation of Haliotis midae.