Department of Genetics

Permanent URI for this community

https://scholar.sun.ac.za/handle/10019.1/21

Browse

Browsing Department of Genetics by Subject "Abalone -- Genetics -- South Africa"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    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.
  • Thumbnail Image
    Item
    Linkage mapping in Haliotis midae using gene-lnked markers
    (Stellenbosch : Stellenbosch University, 2012-03) Jansen, Suzaan; Roodt-Wilding, R.; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    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.
  • Thumbnail Image
    Item
    Microsatellite markers as a tool in genetic enhancement and husbandry of Haliotis midae : a South African case study
    (Stellenbosch : Stellenbosch University, 2012-03) Swart, Liana; Roodt-Wilding, R.; Slabbert, R.; Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics.
    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.