Linkage disequilibrium in the South African abalone, Haliotis midae

Dale Kuys, Ruth (2015-12)

Thesis (MSc)--Stellenbosch University, 2015.

Thesis

ENGLISH ABSTRACT: Linkage disequilibrium (LD) is defined as the non-random association of alleles at two or more loci within a population. It is sensitive to a variety of locus-specific- and demographic factors, and can thus provide much insight into the micro-evolutionary factors that have shaped species of interest. It can also be exploited to identify the genomic regions determining complex traits of interest, which can then be applied as performance evaluation markers in marker-assisted selection (MAS). The South African abalone, Haliotis midae, supports a rapidly developing aquaculture production industry, in which genetic improvement potential is high. This species also represents an opportunistic model for studying the effects of early domestication in a shellfish species. The aim of this study was therefore to quantify and characterise levels of genome-wide LD within the South African abalone, and to demonstrate its utility within population genetic investigations and the characterisation of complex traits. Estimates of LD between 112 mapped microsatellite markers within wild and cultured H. midae revealed that levels of LD in abalone are high relative to other aquaculture species. This was attributed primarily to small effective population sizes produced by a combination of natural- and anthropogenic factors. The decay of LD with genetic distance was evident in both cultured cohorts, but almost absent in wild cohorts, likely reflecting the differences in size, age and sampling of wild populations relative to cultured. Putative evidence for the effects of recombination, selection, and epistasis were also evident in distinctive locus-specific patterns of LD on some of the linkage groups, many of which could represent the effects of domestication. The effects of selection associated with the domestication event were further investigated using a candidate locus LD mapping approach to determine the proportion of candidate loci under selection associated with artificial selection for faster growth rate in cultured abalone. Two loci (15%) were found to be significantly associated with differences in size of individual animals, both of which could be linked with genes potentially involved in growth and development. These markers could therefore find application in MAS programmes for abalone. Several promising candidates for natural selection were also identified based on similarity with known genes. As the latter represented the majority, natural selection, rather than artificial selection, appears to be predominant during the early stages of domestication in abalone. While some conclusions within the current study were speculative, both the direct and indirect applications of LD were clearly demonstrated. Linkage disequilibrium data can provide a unique perspective on many of the commonly used population genetic estimates, and is therefore of great value in population genetic investigations. Furthermore, these results also highlighted the effectiveness of the candidate locus approach in species with both limited molecular resources and extensive LD.

AFRIKAANSE OPSOMMING: Koppelingsonewewig (KO) word gedefinieer as die nie-lukrake assosiasie van allele by twee of meer lokusse binne 'n populasie. Koppelingsonewewig is sensitief vir 'n verskeidenheid van lokus-spesifieke- en demografiese faktore, en kan dus insiggewend wees m.b.t. mikro-evolusionêre faktore wat spesies van belang beïnvloed het. Dit kan ook benut word om die genoom-gebiede onderligend tot komplekse eienskappe te bespeur; wat dan aangewend kan word vir prestasie-evaluering m.b.v. merkerbemiddelde seleksie (MBS). Die Suid-Afrikaanse perlemoen, Haliotis midae, ondersteun 'n vinnig ontwikkelende akwakultuur produksie bedryf, waarin genetiese verbeteringspotensiaal hoog is. Hierdie spesie verteenwoordig ook 'n opportunistiese model vir die bestudering van die gevolge van vroeë domestiseering in 'n skulpvis spesie. Die doel van hierdie studie was dus om vlakke van genoom-wye KO binne die Suid-Afrikaanse perlemoen te kwantifiseer en te karakteriseer, en om die toepassing hiervan binne populasiegenetiese ondersoeke en die karakterisering van komplekse eienskappe te demonstreer. Ramings van KO tussen 112 gekarteerde mikrosatelliet-merkers binne wilde en gekultiveerde H. midae het aan die lig gebring dat die vlakke van KO in perlemoen hoog was, in vergelyking met ander akwakultuur spesies. Dit word hoofsaaklik toegeskryf aan klein effektiewe populasiegroottes wat deur 'n kombinasie van natuurlike- en antropogeniese faktore teweeg gebring word. Die verval van KO met genetiese afstand was duidelik waarneembaar in gekultiveerde kohorte, maar amper afwesig in die wilde kohorte, waarskynlik a.g.v. verskille in populasiegrootte, ouderdom, en streekproef-neemings metodieke van die verskeie populasies. Vermeende bewyse vir die gevolge van rekombinasie, seleksie en epistase kon ook gesien word a.g.v. lokus-spesifieke patrone van KO op sommige van die koppelingsgroepe, moontlik ‘n gevolg van domestisering. Die gevolge van seleksie wat verband hou met die domestiseringsgebeurtenis is verder ondersoek m.b.v 'n kandidaat-lokus KO karteringsbenadering om die verhouding van kandidaat lokusse wat geassosieer is met kunsmatige seleksie (vir vinniger groeikoers in perlemoen) te bepaal. Twee lokusse (15%) was beduidend geassosieer met verskille in grootte tussen individuele diere. Beide van die lokusse was gekoppel met gene wat potensieel betrokke is by groei en ontwikkeling. Hierdie merkers kan dus moontlik aangewend word in MBS programme vir perlemoen. Verskeie belowende kandidaat lokusse vir natuurlike seleksie is ook geïdentifiseer gebaseer op ooreenkoms met bekende gene. Gegewe dat die laasgenoemde die meerderheid van die merkers verteenwoordig, kan daar afgelei word dat natuurlike seleksie, eerder as kunsmatige seleksie, oorheersend is in die vroeë stadia van domestisering in perlemoen. Terwyl sommige gevolgtrekkings binne die huidige studie spekulatief was, is beide die direkte en indirekte toepassings van KO duidelik gedemonstreer. Koppelingsonewewig-data kan 'n unieke perspektief gee op baie van die algemeen gebruikte populasie genetiese skattings, en is dus van groot waarde in populasie genetiese ondersoeke. Verder demonstreer hierdie resultate ook die doeltreffendheid van die kandidaat lokus benadering in spesies met beide beperkte molekulêre hulpbronne en uitgebreide KO.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/97991
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