Research Articles (Genetics)

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Browsing Research Articles (Genetics) by Author "Bester-Van der Merwe, Aletta"

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    Isolation and validation of microsatellite markers from a depleted South African sciaenid species, the dusky kob (Argyrosomus japonicus), by means of the FIASCO/454 approach
    (Springer Verlag, 2013-04) Mirimin, L.; Ruiz Guajardo, J. C.; Vervalle, J.; Bester-Van der Merwe, Aletta; Kerwath, S.; Macey, B.; Bloomer, P.; Roodt-Wilding, R.
    The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild population structure, assist the effectiveness of broodstock and breeding programmes, and ensure monitoring of potential interactions between wild and farmed fish. The present study uses a recently tested approach that combines the FIASCO enrichment protocol with 454 GS-FLX Next Generation Sequencing, to identify large numbers of microsatellite-containing sequences at a low cost and high discovery rate from the dusky kob genome. Following the FIASCO enrichment (targeting specifically tetranucleotide repeats), 2,355 potential tetranucleotide microsatellites (perfect repeat motifs including eight or more repeat units flanked by regions for primer design) were identified from 1/5th of a single 454 lane. From these sequences, a test panel of 60 potential markers was selected for validation. A total of eight (13 %) markers were successfully amplified from a test sample of wild dusky kob individuals and showed high levels of polymorphism (observed heterozygosity per locus ranging between 0.375 and 0.905). Cross-species amplification of seven of these markers was also successfully carried out in another closely related and commercially important South African sciaenid species, the silver kob (A. inodorus). The microsatellite markers developed in the present study are readily available tools suitable to address genetic variability of Argyrosomus species of southern Africa.
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    Transcriptome-wide single nucleotide polymorphisms (SNPs) for Abalone (Haliotis midae) : validation and application using GoldenGate medium-throughput genotyping assays
    (MDPI, 2013-09) Bester-Van der Merwe, Aletta; Blaauw, Sonja; Du Plessis, Jana; Roodt-Wilding, Rouvay
    Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and single nucleotide (SNPs). Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%−69% conversion rate (percentage polymorphic markers) with a global genotyping success rate of 76%−85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174) were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50) located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.