Thesis (MSc)--Stellenbosch University, 2008. / ENGLISH ABSTRACT: Haliotis midae, is the only commercially important species of the six abalone species
found in South African coastal waters and has become a lucrative commercial
commodity. Wild stocks of H. midae are, however, no longer commercially sustainable
due to a combination of environmental factors and poaching. The solution to the crisis is
artificial production systems in the form of abalone farms. An abalone enhancement
programme was initiated in South Africa in 2006, funded by industry and government.
This programme focuses on the elucidation of the abalone genome and genetic factors
contributing to increased productivity, thereby aiding the commercial production of
abalone.
The aims of this study, the first of its kind concerning H. midae, were to develop AFLPbased
markers (specifically fluorescent AFLP analysis); to monitor the segregation of
these markers in a single full-sib family and to use the markers and additional
microsatellite markers to generate the first preliminary linkage map for H. midae.
Genomic DNA of sufficient quality and purity for fluorescent AFLP analysis was
obtained from 3.5-month-old H. midae juveniles. Preliminary linkage maps were
constructed using AFLP and microsatellite markers segregating in an F1 family following
a pseudo-testcross mapping strategy. Twelve AFLP primer combinations, producing 573
segregating peaks, and 10 microsatellite markers were genotyped in the parents and 108
progeny of the mapping family. Of the 573 segregating AFLP peaks genotyped, 241
segregated in a 1:1 ratio and 332 in a 3:1 ratio. Of these AFLP markers, 90 segregated
according to the expected 1:1 Mendelian ratio and 164 segregated according to the
expected 3:1 Mendelian ratio at the P = 0.05 level and were used for linkage analysis. Of
the 10 microsatellite markers genotyped, nine were informative for linkage mapping
analysis.
Preliminary male and female genetic linkage maps were developed using markers
segregating in the female or male parent. A total of 12 and 10 linkage groups were
detected for the female and male maps respectively. The female map covered 1473.5cM
and consisted of 56 markers, and the male map covered 738.9cM consisting of 30
markers. Markers with segregation distortion were observed as previously reported in
other abalone species and potential homology between one of the linkage groups of the male map and two of the linkage groups of the female map were identified using the 3:1
segregating AFLP markers.
In conclusion, the genetic linkage map presented here, despite the fact that it has relatively
low genome coverage and low marker density, forms an ideal starting point for more
detailed study of the H. midae genome and will provide a scaffold for basic and applied
studies in abalone. A high-density linkage map of H. midae should in future be developed
with additional co-dominant molecular markers, such as microsatellites, to improve the
transferability of the linkage map between different laboratories and among populations.
A high-density linkage map will facilitate the mapping of QTL of commercially important
traits (i.e. growth) and future MAS breeding programmes. / AFRIKAANSE OPSOMMING: Perlemoenspesie, Haliotis midae, is die enigste spesie van kommersiële belang van die
ses wat in die kuswater van Suid-Afrika aangetref word en het ‘n winsgewende
handelskommoditeit in Suid-Afrika geword. Die ontginning van natuurlike H. midae
populasies is egter, as gevolg van ‘n kombinasie van omgewingsfaktore en stropery nie
meer kommersieel volhoubaar nie. Die perlemoenkrisis kan die hoof gebied word deur
kunsmatige produksiesisteme op perlemoenplase tot stand te bring. ‘n Perlemoen
verbeteringsprogram is in 2006 in Suid-Afrika geïnisieer en word deur die industrie en
regering befonds. Die program focus op die ontrafeling van die perlemoen genoom en die
genetiese faktore wat bydrae tot verhoogde produksie. Sodanige inligting kan gebruik
word om kommersiële perlemoenproduksie te bevorder.
Die doel van hierdie studie, die eerste met H. midae, is om AFLP-gebaseerde merkers
(spesifiek fluoresserende AFLP analise) te ontwikkel; die segregasie van hierdie merkers
te monitor in ‘n enkel volledige verwante familie en die merkers en addisionele
mikrosatelliet merkers te gebruik om die eerste voorlopige koppelingskaart vir H. midae
te genereer.
Genomiese DNS van genoegsame kwaliteit en suiwerheid vir fluoresserende AFLP
analise is ge-ekstraeer uit 3.5-maand-oue H. midae individue. Voorlopige
koppelingskaart is gekonstrueer deur van segregerende AFLP en mikrosatelliet merkers in
‘n F1 familie gebruik te maak deur ‘n pseudo-kruistoets karteringstrategie te volg. Twaalf
AFLP inleier kombinasies, wat 573 segregerende fragmente geproduseer het, en 10
mikrosatelliet merkers is gegenotipeer in die ouers en 108 individue van die nageslag van
die karteringsfamilie. Van die 573 segregerende AFLP merkers wat gegenotipeer is, het
241 in ‘n 1:1 verhouding en 332 in ‘n 3:1 verhouding gesegregeer. Van hierdie AFLP
merkers, het 90 volgens die verwagte 1:1 Mendeliese verhouding en 164 volgens die 3:1
Mendeliese verhouding by die P = 0.05 gesegregeer vlak en is vir die koppelingsanalise
gebruik. Van die 10 mikrosatelliet merkers gegenotipeer, was 9 informatief vir koppeling
karteringsanalise.
Voorlopige manlike en vroulike genetiese koppelingskaarte is ontwikkel met gebruik te
maak van merkers wat in die manlike of vroulike ouer segregeer het. ‘n Totaal van 12 en
10 koppelingsgroepe is onderskeidelik in die vroulike en manlike karate gegenereer. Die vroulike kaart dek 1473.5cM and bestaan uit 56 merkers, terwyl die manlike kaart
738.9cM beslaan het met 30 merkers. Merkers wat segregasie distorsie toon is
waargeneem soos voorheen in ander perlemoenspesies gerapporteer. Potensiële
ooreenstemming tussen een van die koppelingsgroepe van die manlike kaart en twee van
die koppelingsgroepe van die vroulike kaart is aangetoon deur van die 3:1 segregerende
AFLP merkers gebruik te maak.
Die genetiese koppelingskaarte verskaf wel ‘n relatiewe lae genoomdekking en ‘n lae
merkerdigtheid, maar is ‘n ideale vertrekpunt vir meer gedetailleerde studie van die H.
midae genoom en dien as ‘n raamwerk vir toekomstige basiese en toegepaste studies in
perlemoennavorsing. ‘n Hoëdigtheid koppelingskaart van H. midae moet in die toekoms
ontwikkel word met gebruik van bykomstige ko-dominante molekulêre merkers, soos
mikrosatelliete. Dit sal die oordraagbaarheid van die koppelingskaart tussen verskillende
laboratoria asook tussen populasies verbeter. ‘n Hoëdigtheid koppelingskaart sal die
kartering van kwantitatiewe kenmerk loki (KKL) vir kommersieel belangrike kenmerke
(onder andere groeikrag) en toekomstige merker bemiddelde seleksie (MBS)
teelprogramme moontlik maak.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:sun/oai:scholar.sun.ac.za:10019.1/21525 |
| Date | 12 1900 |
| Creators | Badenhorst, Daleen |
| 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 | viii, 148 leaves : ill. |
| Rights | Stellenbosch University |
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