Thesis (PhD (Genetics))--Stellenbosch University, 2010. / ENGLISH ABSTRACT: The South African abalone, Haliotis midae, is a commercially valuable mollusc and is
mostly exported to the Far East. Genetics research on H. midae has increased
substantially since a genetic improvement programme was introduced in 2006 by
collaboration between Stellenbosch University, government and industry partners. The
development of molecular markers, QTL-mapping, gene-expression and genome
manipulations are the main focuses of the research currently being conducted. The end
goal is to create high quality and fast growing animals for the industry. The present study
focused on the development of microsatellite markers and the detection of quantitative trait
loci (QTL) affecting growth traits (shell length, shell width, wet weight) in this species. A
combination of three methods, namely selective genotyping and bulked segregant analysis
(pooling analysis), single marker regression and interval mapping were used to identify
putative QTL in two full-sib families from two different farmed locations. Additional methods
and protocols were developed that can assist the industry in other molecular research
aspects. A total of 125 microsatellite loci were characterised. A total of 82 of these loci
were isolated using second generation sequencing, a first for any abalone species. A
preliminary, low-density framework linkage map was constructed containing 50 loci that
mapped to 18 linkage groups. The observed genome length was 148.72cm with coverage
of ±47%. QTL analyses revealed two putative QTL for shell width and wet weight, with
17% and 15% variance explained, that mapped on one linkage group in the first family and
three putative QTL, for shell length, shell width and wet weight, with 33%, 28.5% and
31.5% variance explained, that mapped on one linkage group in the second family.
Additional methods and protocols developed include an automated high-throughput DNA
isolation protocol, a real-time PCR assay for H. midae x H. spadicea hybrid verification, a
triploid verification microsatellite assay and a pre- and post-PCR multiplex setup and
optimisation protocol. Future studies focussing on QTL and marker assisted selection
(MAS) should verify the QTL found in this study and also utilise additional family structures
and determine QTL-marker phase within the commercial populations. / AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is ’n kommersieel waardevolle
weekdier en word hoofsaaklik na die Verre-Ooste uitgevoer. Genetiese navorsing op H.
midae het aansienlik toegeneem sedert ’n genetiese verbeteringsprogram in 2006 deur
samewerking tussen die Universiteit van Stellenbosch, die regering en industrievennote
ingebring is. Die ontwikkeling van molekulêre merkers, KEL-kartering, geen-uitdrukking en
genoom manipulasies is die hooffokusse van die navorsing wat tans uitgevoer word. Die
einddoel is om hoë kwaliteit en snelgroeiende diere vir die industrie te skep. Die huidige
studie het op die ontwikkeling van mikrosatelliet merkers en die opsporing van
groeiverwante (skulplengte, -breedte en nat gewig) kwantitatiewe eienskap lokusse (KEL)
in hierdie spesie gefokus. ’n Kombinasie van drie metodes, naamlik selektiewe
genotipering en versamelde segregaat analise (samevoegingsanalise), enkel merker
regressie en intervalkartering is gebruik om waarskynlike KEL in twee vol-sibbe families
van twee verskillende produksiegebiede te identifiseer. Aanvullende metodes en protokolle
is ontwikkel wat die industrie in ander molekulêre navorsingsaspekte kan ondersteun. ’n
Totaal van 125 mikrosatelliet lokusse is beskryf. ’n Totaal van 82 van hierdie lokusse is
deur die gebruik van derde generasie volgordebepaling geïsoleer, ’n eerste vir enige
perlemoen spesie. ’n Voorlopige, laedigtheid raamwerkkoppelingskaart is saamgestel met
50 lokusse wat op 18 koppelingsgroepe gekarteer is. Die waarneembare genoomlengte
was 148.72cm met ’n dekking van ±47%. KEL-analises het twee waarskynlike KEL vir
skulpbreedte en nat gewig blootgelê wat 17% en 15% variasie verduidelik en is op een
koppelingsgroep in die eerste familie gekarteer asook drie waarskynlike KEL, vir
skulplengte, -breedte en nat gewig wat 33%, 28.5% en 31.5% variasie verduidelik en is op
een koppelingsgroep in die tweede familie gekarteer. Aanvullende metodes en protokolle
wat ontwikkel is, sluit ’n geoutomatiseerde hoë-deurgang DNS-isolasieprotokol, ’n intydse
PKR-proef vir H. midae x H. spadicea hibried verifikasie, ’n triploïed verifikasie
mikrosatellietproef en veelsoortige pre- en post-PKR opstelling en optimaliseringsprotokol
in. Toekomstige studies wat fokus op KEL en merker ondersteunde seleksie (MOS)
behoort die KEL wat in hierdie studie gevind is te verifieer en ook bykomende familie
strukture te benut om KEL-merker fases binne die kommersiële populasie te bepaal.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/5477 |
| Date | 12 1900 |
| Creators | Slabbert, Ruhan |
| Contributors | Roodt-Wilding, R., Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics |
| Publisher | Stellenbosch : Stellenbosch University |
| Source Sets | South African National ETD Portal |
| Language | en_ZA |
| Detected Language | Unknown |
| Type | Thesis |
| Format | 240 p. : ill. |
| Rights | Stellenbosch University |
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