Biomedical research have been revolutionized by recent technological advances, both in the fields of molecular biology and computer science, turning the biomolecular and genetic research into “big data science”. One of the main objectives have been to improve our understanding of complex human diseases. Among those diseases, multiple sclerosis (MS) is considered as one of the most common. MS is a chronic autoimmune disease that cause inflammation and damage to the central nervous system. In this study, a set of bioinformatics analyses have been conducted on SNP data, as an initial step to gain more information prior to an upcoming genotyping project. The results showed extensive regulatory properties for the 761 selected SNPs, which is consistent with current scientific knowledge, and also identified another 332 SNPs in linkage to these. However, during the study some issues have also been identified, which need to be addressed going forward.

Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage disequilibrium parameter (LD), which is frequently used in association analysis to identify functional mutations. My results showed no considerable effect of different transition to transversion ratios on LD. I also studied the distribution of allele frequencies of biallelic SNPs from the Genome Database. My results showed that the most common SNPs are normally distributed with mean allele frequency of 0.7520 and standard deviation of 0.1272. These results can be useful in future studies for simulating SNP behavior. I also studied the simulated data provided by the Genetic Analysis Workshop 12 to identify functional SNPs in candidate genes by using the genotype-specific linkage disequilibrium method.

<p>A major challenge in human genetics is to understand the genetic variation underlying common diseases. In this thesis, I focus on forces creating differences between individuals and genomic regions, methods for characterizing genomic variation, and the association between genomic and phenotypic variation. Genetic markers are widely used to locate genes associated with different phenotypes. In my first paper, I describe novel algorithms for automatic genotype determination of microsatellite markers, a procedure which is currently both time-consuming and error prone. </p><p>The co-segregation of genetic markers in a population leads to non-random association of alleles at different loci - linkage disequilibrium (LD). LD varies throughout the genome and differs between populations due to factors such as their demographic history. In my second paper, I discuss the increased power, for mapping of human traits, that results from studying a population with appreciable levels of LD such as is found in the Swedish Sami population. </p><p>Lately, large-scale analyses of single nucleotide polymorphisms (SNPs) have become available and efforts have been made to identify a set of SNPs, which captures most of the genome variation in a population (tagSNPs). In my third paper, I describe the limitations of this approach when applied to data from an independent population sample of randomly ascertained SNPs. The transferability of tagSNPs between populations is poor, presumably due to variation in allele frequencies and the bias towards common SNPs used in most studies. </p><p>The level of genomic variation is influenced by population structure, recombination and mutation rate, as well as natural selection. During the exodus from Africa, humans have adapted to new environmental conditions. In my fourth paper, I describe a new method for identifying genomic regions carrying signatures of recent positive selection and apply this to an available dataset of millions of SNPs.</p>

No description available.

A major challenge in human genetics is to understand the genetic variation underlying common diseases. In this thesis, I focus on forces creating differences between individuals and genomic regions, methods for characterizing genomic variation, and the association between genomic and phenotypic variation. Genetic markers are widely used to locate genes associated with different phenotypes. In my first paper, I describe novel algorithms for automatic genotype determination of microsatellite markers, a procedure which is currently both time-consuming and error prone. The co-segregation of genetic markers in a population leads to non-random association of alleles at different loci - linkage disequilibrium (LD). LD varies throughout the genome and differs between populations due to factors such as their demographic history. In my second paper, I discuss the increased power, for mapping of human traits, that results from studying a population with appreciable levels of LD such as is found in the Swedish Sami population. Lately, large-scale analyses of single nucleotide polymorphisms (SNPs) have become available and efforts have been made to identify a set of SNPs, which captures most of the genome variation in a population (tagSNPs). In my third paper, I describe the limitations of this approach when applied to data from an independent population sample of randomly ascertained SNPs. The transferability of tagSNPs between populations is poor, presumably due to variation in allele frequencies and the bias towards common SNPs used in most studies. The level of genomic variation is influenced by population structure, recombination and mutation rate, as well as natural selection. During the exodus from Africa, humans have adapted to new environmental conditions. In my fourth paper, I describe a new method for identifying genomic regions carrying signatures of recent positive selection and apply this to an available dataset of millions of SNPs.

No description available.

Maize production is limited agronomically by the availability of water and nutrients during the growing season. Of these two limiting factors, water availability is predicted to increase in importance as climate change and the growing urban landscape continue to stress limited supplies of freshwater. Historically, efforts to breed maize for water-limited environments have been extensive; especially in the areas of root architecture and flowering physiology. As progress has been made and new traits have been discovered and selected for, the different responses to drought stress at specific developmental stages of the maize plant have been selected as a whole when drought tolerance is evaluated. Herein we attempt to define the characteristics of the maize drought response during different developmental stages of the maize plant that can be altered through plant breeding. Towards breeding for drought tolerance, 400 inbred lines from a diversity panel were amplified and sequenced at the ZmLOX4 and ZmLOX5 loci in an effort to characterize their linkage disequilibrium and genetic diversity. Understanding these characteristics is essential for an association mapping study that accompanies this project, searching for novel and natural allelic diversity to improve drought tolerance and aflatoxin resistance in maize. This study is among the first to investigate genetic diversity at important gene paralogs ZmLOX4 and ZmLOX5 believed to be highly conserved among all Eukaryotes. We show very little genetic diversity and very low linkage disequilibrium in these genes, but also identified one natural variant line with knocked out ZmLOX5, a variant line missing ZmLOX5, and five line variants with a duplication of ZmLOX5. Tajima's D test suggests that both ZmLOX4 and ZmLOX5 have both been under neutral selection. Further investigation of haplotype data revealed that ZmLOX12, a member of the ZmLOX family, showed strong LD that extends much further than expected in maize. Linkage disequilibrium patterns at these loci of interest are crucial to quantify for future candidate gene association mapping studies. Knockout and copy number variants of ZmLOX5, while not a surprising find, are under further investigation for crop improvement.

As a large number of single nucleotide polymorphisms (SNPs) and microsatellite markers are available, high resolution mapping employing multiple markers or multiple allele markers is an important step to identify quantitative trait locus (QTL) of complex human disease. For many complex diseases, quantitative phenotype values contain more information than dichotomous traits do. Much research has been done on conducting high resolution mapping using information of linkage and linkage disequilibrium. The most commonly employed approaches for mapping QTL are pedigree-based linkage analysis and population-based association analysis. As one of the methods dealing with multiple alleles markers, mixed models are developed to work out family-based association study with the information of transmitted allele and nontransmitted allele from one parent to offspring. For multiple markers, variance component models are proposed to perform association study and linkage analysis simultaneously. Linkage analysis provides suggestive linkage based on a broad chromosome region and is robust to population admixtures. One the other hand, allelic association due to linkage disequilibrium (LD) usually operates over very short genetic distance, but is affected by population stratification. Combining both approaches plays a synergistic role in overcoming their limitations and in increasing the efficiency and effectiveness of gene mapping.

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within &lt; 50 kb indicating that &gt; 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

Thesis (MSc)--Stellenbosch University, 2015. / 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.