Molecular analysis of genetic variation and relationships within the population of abalone (Haliotis midae) at the Sea Plant Products abalone hatchery, Hermanus, R.S.A.

Slabbert, Ruhan (2004-12)

Thesis (MSc)--University of Stellenbosch, 2004.

Thesis

ENGLISH ABSTRACT: The species Haliotis midae is the only commercially exploitable abalone species of the six found in the South African coastal waters. This species is under substantial pressure from both legal and illegal harvesters, to such an extent that it could be commercially extinct within four years. Efforts to alleviate the pressures on the natural populations of both illegal and legal harvesting are being made. The genetic management systems for abalone farming and ranching activities should be carefully evaluated. The loss of genetic diversity and the risks of contaminating the gene pools of natural populations in the vicinity of a farm should be minimized. Genetic evaluation studies will be at great importance to acquire the necessary data needed for genetic diversity and differentiation analysis. The aim at this study was to develop species-specific microsatellite DNA markers to assess the genetic diversity and differentiation within and between the brood stock and commercial stock of the Sea Plant Products abalone farm (Hermanus, Republic of South Africa) and natural populations related to the brood stock. The species-specific DNA markers were also used for parentage assignments within the tarm population (first for abalone) and preliminary OTL (quantitative trait loci)-discovery analysis studying growth rate segregation. Samples were taken of the farm's brood stock and commercial stock (Rows 2, 3, 4) as well as from two natural populations (Saldanha Bay and Black Rock) related to the brood stock. Various statistical parameters and software packages were used to assess genetic diversity and differentiation, to infer parentage and to look for OTL's. Eight species-specific microsatellite DNA markers were designed and used for data analysis. Data analysis showed a loss at genetic diversity from the brood stock to the commercial stock caused by the subdivision of the original brood stock into rows and the differential contributions of parents to the offspring. No genetic differentiation (Fst) was detected between the farm and natural populations, except for the offspring of Row2. levels of inbreeding (ns) were high for all loci within the populations. Thirty-eight percent of all studied offspring were confidently assigned to a couple. The preliminary QTldiscovery suggested the segregation of a number of alleles and genotypes with growth rate. The study concluded that the commercial abalone population of the Sea Plant Products abalone farm holds no threat to the disruption of the genetic diversity of the natural populations. It is proposed that the farm implement a rotational breeding program to increase the genetic diversity of the commercial population. Any newly acquired brood stock must be profiled before their introduction into the breeding program to assess the influence of the animals on the current levels of genetic diversity within the farm. The accuracy and reliability of parentage assignments and QTl-discovery need to be optimised by adding more loci and sampling more animals or even by trying and developing new methods.

AFRIKAANSE OPSOMMING: Van die ses perlemoen spesies wat langs die Suid-Afrikaanse kus gevind word, is die spesie Haliotis midae die enigste een wat van kommersiële belang is. Wettige, sowel as onwettige versameling, plaas hierdie spesie onder sulke geweldige druk dat dit dalk binne vier jaar verlore kan wees vir die kommersiële bedryf. Verskeie strategieë word tans geïmplimenteer om hierdie druk te verlig. Die genetiese bestuurstrategieë binne perlemoen plase moet deeglik ondersoek word. Die verlies aan genetiese diversiteit en die moontlikheid vir die kontaminering van die natuurlike populasies in die omgewing van die plaas se geenpoel, moet uitgeskakel word. Genetiese evaluasies sal van groot belang wees om die nodige data vir genetiese diversiteit- en differensiasie-analises te verkry. Die doel van die studie was om spesies-spesifieke mikrosatelliet DNA merkers te ontwikkel wat gebruik sou word om die genetiese diversiteit en differensiasie binne en tussen die broei diere en die kommersiële diere van Sea Plant Products se perlemoen plaas (Hermanus, Republiek van Suid- Afrika) en die natuurlike populasies wat verwant is aan die broei diere, te bepaal. Die spesies-spesifieke DNA merkers is ook vir ouerskap-bepalings binne die plaas se populasie gebruik, asook vir voorlopige OTL (quantitative trait locI) - ontdekking met betrekking tot groeitempo segregasie. Monsters van die plaas se broei diere en kommersiële diere (Ry 2, 3, 4) asook van twee natuurlike populasies (Saldanha Baai en Black Rock) wat verwant is aan die broei diere, is geneem. 'n Verskeidenheid van statistiese parameters en sagteware pakette is vir die genetiese diversiteit- en differensiasie-analises, vir ouerskap-bepalings en vir die opspoor van OTL's gebruik. Agt spesies-spesifieke mikrosatelliet DNA merkers is ontwerp en toe gebruik vir die data analises. 'n Verlies aan genetiese diversiteit vanaf die broei diere na die kommersiële diere is deur die data analises uitgewys. Dit is veroorsaak deur die verdeling van die oorspronklike broei diere in rye en die differensiële bydraes deur die ouers na die nageslag. Geen genetiese differensiasie (Fst) is tussen die plaas se populasie en die natuurlike populasies gevind nie, maar die nageslag van Ry 2 het wel differensiasie getoon. Die vlakke van inteling (Fis) was hoog oor alle lokusse binne alle populasies. Agt-en-dertig persent van die nageslag wat bestudeer is, was suksesvol met 'n ouerpaartjie geassosieer. Die voorlopige OTL-ontdekking studie toon die potesiële segregasie van 'n aantal allele en genotipes saam met groeitempo. Die bevindinge van die studie is dat die kommersiële populasie op die Sea Plant Products perlemoen plaas, geen bedreiging vir die versteuring van die natuurlike populasies se genetiese diversiteit inhou nie. Daar is voorgestel dat die plaas 'n rotasie-basis broeiprogram moet implimenteer om sodoende die genetiese diversiteit van die kommersiële populasie te verhoog. Enige nuwe broei diere se genetiese profiel moet ook voor die tyd ondersoek word om te sien wat se effek hierdie diere op die huidige genetiese diversiteit van die kommersiële populasie sal hê. Die akkuraatheid en betroubaarheid van die ouerskap-bepalings en OTL-ontdekking moet optimiseer word deur of meer lokusse te bestudeer, of meer diere in analises te gebruik of selfs om nuwe tegnieke te probeer of te ontwikkel.

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