Thesis (MSc)--Stellenbosch University, 2012. / 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. / AFRIKAANSE OPSOMMING: Haliotis midae (ook bekend as perlemoen) is die enigste van vyf inheemse spesies in
Suid-Afrika wat noemenswaardige kommersiële waarde toon plaaslik sowel as
internasionaal. Ongelukkig het kommersiële uitbuiting, wildstropery en natuurlike
bedreiging (bv. die Weskus kreef Jasus lalandii), wilde perlemoen populasies
noemenswaardig verminder. Dus, om natuurlike diversiteit en die voortbestaan van beide
wilde en kommersiële populasies te beskerm, is genetiese bestuur en verbetering
absoluut noodsaaklik. Genetiese bestuur vereis die gebruik van molekulêre merkers as ’n
hulpmiddel in die opstellingvan koppelingskaarte, en die identifisering van die relevante
kwantitatiewe eienskap loki (QTL) tipies geassosieer met ekonomies belangrike
eienskappe. Die laasgenoemde beoog om kommersiële voorraad bestuur te verbeter,
kragtens deur broeidier seleksie sowel as om insig te verskaf m.b.t. wilde bevolking
dinamika.
Enkel Nukleotied Polimorfismes (SNPs) is gekies as die toepaslike merker vanweë die
omvattende toepaslikheid van hierdie merkers binne die genome van verskeie mariene
spesies. Hierdie studie fokus op die karakterisering van nuwe SNPs vanuit transkript
volgordes ontwikkel deur middel van Volgende Generasie Volgordebepaling (“Next
Generation Sequencing”). ’n Beraamde 40% van transkripte het gelei tot die ontwikkeling
van 105 potensiëlemerkers, aanduidend van ’n SNP frekwensie van ~1% binne die H.
midae genoom.
’n Sub-versameling van 24 merkers, tesame met 24 bestaande merkers, is
gekarakteriseer deur die Illumina GoldenGate genotiperings toets met die VeraCode
tegnologie, ’n medium tot hoë deurvloei genotiperingstegnologie. Hierdie is die eerste
berig van medium tot hoë deurvloei karakterisering van SNPs in H. midae. Die
geselekteerde merkers is gebruik om die doeltreffendheid van die GoldenGate platform te
bepaal. Merker karakterisering is uitgevoer in beide wilde en kommersiële bevolkings om
die effektiewe bruikbaarheid van hierdie merkers m.b.t. genetiese diversiteit, en bevolking
struktuur bepaling, te ondersoek. Die platform het ’n 85% genotiperingsukses syfer
getoon. Statistiese analise dui daarop dat merkers ontwikkel tydens hierdie studie
toepaslik is vir bevolking genetiese struktuur bepaling, genetiese diversiteitberaming en
moontlik ook genetiese koppelingskartering. Hierdie merkers word bestempel as
onmisbaar vir toekomstige navorsing in genetiese bestuur en bewaring van H. midae.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/19976 |
| Date | 03 1900 |
| Creators | Blaauw, Sonja |
| Contributors | Roodt-Wilding, R., Van der Merwe, A. E., Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | English |
| Type | Thesis |
| Format | 141 p. : ill. |
| Rights | Stellenbosch University |
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