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Bitalo, Daphne Nyachaki. "Implementation of molecular markers for triticale cultivar identification and marker-assisted selection." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71670.
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Thesis (MSc)--Stellenbosch University, 2012.Triticale is an amphidiploid that consists of wheat (A and B) and rye (R) genomes. This cereal is fast becoming important on a commercial basis and warrants further assessment for the better management and breeding of the hybrid. The assessment of the genetic diversity among the wheat and rye genomes within triticale can be obtained by using molecular markers developed in both donor genomes. Simple sequence repeats markers (SSRs) and amplified fragment length markers (AFLPs) have been previously used to assess the genetic diversity among triticale lines. SSRs are highly polymorphic markers that are abundant and which have been shown to be highly transferable between species in previous studies while AFLP markers are known to generate plenty of data as they cover so many loci. Thus, the aim of this study was to develop a marker system suitable to assess the genetic diversity and relationships of advanced breeding material (and cultivars) of the Stellenbosch University’s Plant Breeding Laboratory (SU-PBL). Therefore, both AFLP and SSR markers were initially analysed using eight triticale cultivars (with known pedigrees) to facilitate cultivar identification. Fourty-two AFLP primer combinations and 86 SSR markers were used to assess the genetic diversity among the Elite triticale cultivars. The AFLP primer combinations generated under average polymorphism information content (PIC) values. Furthermore, these markers generated neighbour-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) dendograms that displayed relationships that did not correspond with the available pedigree information. Therefore, this marker system was found not to be suitable. A set of 86 SSRs previously identified in both wheat and rye, was used to test the genetic diversity among the eight cultivars. The markers developed in wheat achieved 84% transferability while those developed in rye achieved 79.3% transferability. A subset of SSR markers was able to distinguish the cultivars, and correctly identify them by generating NJ and UPGMA dendograms that exhibited relationships that corroborated the available pedigree data. This panel of markers was therefore chosen as the most suitable for the assessment of the advanced breeding material. The panel of seven SSR markers was optimised for semi-automated analysis and was used to screen and detect the genetic diversity among 306 triticale entries in the F6, Senior and Elite phases of the SU-PBL triticale breeding programme. An average PIC value of 0.65 was detected and moderate genetic variation was observed. NJ and UPGMA dendograms generated showed no clear groupings. However, the panel of markers managed to accurately identify all cultivars within the breeding program. The marker panel developed in this study is being used to routinely distinguish among the advanced breeding material within the SU-PBL triticale breeding programme and as a tool in molecular-assisted backcross.
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Rantapää, Dahlqvist Solbritt. "Genetic markers in rheumatoid arthritis." Doctoral thesis, Umeå universitet, Reumatologi, 1985. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-101305.
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Genetic as well as environmental factors are believed to be of importance in the etiology of rheumatoid arthritis (RA). There are a number of previous studies of genetic markers in RA, but so far no genetic linkage and only a few associations have been found. Of the associations only one (with the HLA antigen DR4) appears to be well documented. In most previous association studies the patients have not been divided according to sex and family history of RA. In this investigation the HLA antigens A, B and DR and five serum protein systems (Bf, C3, Pi, Hp and Tf) were studied in patients with erosive rheumatoid arthritis (RA), from northern Sweden. Special attention was paid to variations in the strength of associations according to sex and family history of polyarthritis. The following results were found: The frequency of the HLA antigen B27 was significantly increased in the North-Swedish population (16.6%) and among patients with a family history of polyarthritis (42.6%). In agreement with previous investigations a significantly increased frequency of the DR4 antigen was found in the RA patients. In the properdin factor B (Bf) system the S phenotype was found to be significantly increased in male patients and in patients with a family history of polyarthritis, more severe form of RA and high titres of rheumatoid factor. No significant differences with respect to phenotype or gene frequencies were found in the C3 complement system. Thus, the association between RA and C3 found in previous investigations was not confirmed. A significant increase of rare alpha-1-antitrypsin (Pi) types (MS, MZ, MF and SZ) was found among RA patients. However, the increase concerned mainly Z heterozygotes and was more strongly pronounced among male patients. In the haptoglobin system a significant increase of the Hp^ gene and the Hp2-2 type was found among patients with a family history of polyarthritis, more pronounced among males. A significant increase of the transferrin gene and of the 2 type was found among male RA patients, more pronounced among patients with a family history of polyarthritis. In 6 out of 8 gene loci studied significant associations were found, which is in agreement with a multifactorial etiology of RA. The results were largely in agreement with the hypothesis that associations would be expected to be stronger in males and in patients with a family history of polyarthritis. A notable finding was the high frequency of first degree relatives (around 40%) with symmetric peripheral polyarthritis of which more than 70% had a diagnosis of RA verified by hospital records.Diss. (sammanfattning) Umeå : Umeå universitet, 1985, härtill 6 uppsatser.
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Baldwin, Samantha, and n/a. "Models for genetic analysis of polyploid plant species." University of Otago. Department of Biochemistry, 2008. http://adt.otago.ac.nz./public/adt-NZDU20090826.092431.
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A number of major crop species, such as allohexaploid wheat and autotetraploid potato are polyploid. Potato is the fourth most important crop in terms of production and has become an important food source in many countries. Therefore, the molecular analysis was directed towards investigating ways to develop markers to assist the potato breeding process; for example breeding for powdery scab disease resistance, and tolerance to cold induced sweetening. Polyploids have more possible genotypes per population, allele dosage effects and increased marker complexity compared to diploids. Potato is also outcrossing and therefore highly heterozygous.
Various methods for detecting marker-trait associations including, linkage, quantitative trait locus (QTL) and association mapping were studied and protocols developed. A mapping population was produced and a number of traits were measured including powdery scab resistance. Powdery scab disease assays were carried out over six seasons and markers associated with disease resistance were identified. Markers associated with resistance to powdery scab were identified on chromosomes I, IV, V, VI, VIII and IX using analysis of variance (ANOVA). Linkage maps were produced for each parent of the population and QTL associated with resistance and susceptibility to disease were identified using interval mapping, which revealed QTL on chromosomes II, V, VII , VIII, IX and an unanchored linkage group. QTL were detected across years on regions of chromosomes VIII and IX. These QTL results had some overlap with the marker-trait associations that were identified using ANOVA analysis. Another marker identification technique was tested, known as association or linkage disequilibrium mapping. Alleles of candidate genes were tested for association with cold-induced sweetening using a germplasm collection. The alleles identified as important were of the apoplastic invertase and UGPase genes and a unique interaction between alleles of the apoplastic invertase and apoplastic invertase inhibitor was also detected.
This thesis describes the first study into the genetics of powdery scab resistance and the markers identified as associated with resistance will be validated for use in a marker-assisted selection (MAS) programme. The tools and resources developed as part of this thesis are vital to the potato breeding programme that requires the identification of associated molecular markers.
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Valdman, Alexander. "Molecular genetic markers of prostate cancer development /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-618-9/.
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Manganaris, Athanasios Georgiou. "Isoenzymes as genetic markers in apple breeding." Thesis, Imperial College London, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389070.
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Usha, A. P. "Microsatellite markers in genetic improvement of livestock." Thesis, University of Edinburgh, 1995. http://hdl.handle.net/1842/11490.
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Genome mapping is in the forefront of interest among both plant and animal breeders, enabling the relationship between genes, genome structure and function to be investigated in addition to identifying the location of genes. The prerequisite of a linkage map of the genome is the availability of a large number of highly polymorphic and informative marker loci which are evenly distributed throughout the genome. Microsatellite loci provide the unique class of markers which overcome many of the difficulties associated with the other market types. The availability of a detailed genetic map of the bovine genome could enhance the genetic progress in cattle breeding programmes through the identification of loci affecting traits of economic importance. Other potential applications of genetic markers include their use in confirmation of parentage, individual identification, germplasm evaluation and identification of disease loci. In this thesis, microsatellite markers are investigated in three areas, a) parentage verification and individual identification b) study of phylogenetic relationship and c) mapping a lethal defect in Dexter cattle. a) Five highly polymorphic microsatellite markers CYP21, DRB3, FSHB, ETH131 and HEL6 were evaluated for parentage verification using 275 animals belonging to 15 breeds of cattle. Some breeds were found not be in Hardy Weinberg Equilibrium (HWE), the deviation being greatest in those breeds which had an excess of homozygotes. A new approach was developed for calculating the Probability of RAndom Sire Exclusion (PRASE) taking into account the deviation from HWE and linkage between markers, using observed genotype frequencies. Taken together, the linked markers, DRB3 and CYP1 gave a PRASE of 0.88 in all breeds with success ranging from 0.75-0.96. Including a third marker the PRASE was increased to 0.97, and with all five markers 0.99 or better was achieved for all the 15 breeds.
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Johns, Neil. "Phenotypes and genetic markers of cancer cachexia." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/23392.
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Cancer cachexia is a chronic wasting syndrome characterised by loss of weight, composed principally of muscle and fat. Patients with advanced cachexia demonstrate loss of appetite, early satiety, severe weight loss, weakness, anaemia and fluid retention. Affected individuals are also likely to report/experience decreased quality of life, decreased levels of physical performance, increased levels of fatigue, increased risks of treatment failure (be it chemotherapy, radiotherapy or surgery), increased risks of treatment side effects, and an increased mortality rate. Cachexia is therefore an extremely important, yet often underappreciated cause of cancer patient morbidity and mortality which requires urgent attention. Weight loss is significantly associated with cancer morbidity and mortality. It has been observed that half of all cancer patients experience weight loss and one-third lose more than 5% of their original body weight. Skeletal muscle loss appears to be the most significant event in cachexia and is associated with a poor outcome. However it is not known why some patients with the same tumour lose weight and muscle mass whilst others do not. The main aim of this thesis was to determine if the genetic makeup of individual patients might contribute to their propensity to lose weight or skeletal muscle. Previous studies had suggested an association between weight loss and SNPs on genes concerned with innate immunity and particularly the cell adhesion molecule Pselectin, however the strength of any gene association study depends on the precision with which it is possible to characterise the phenotype in question. A second aim of this thesis was to explore refining the clinical phenotyping of patients to discriminate those with evidence of muscle fibre atrophy versus those without. Phenotype The conventional phenotype for cachexia is weight loss (WL) but it is unknown the extent to which loss of body mass reflects loss of muscle or fat mass. Recent progress in cross sectional imaging analysis means that it is now possible to gain a direct measure of muscle mass from routine diagnostic CT scanning. However, in the absence of a longitudinal series of scans it is not possible to estimate whether low muscularity (LM) is longstanding or not. By combining a measure of active weight loss with low muscularity it was hoped that such a composite measure would reflect actual muscle loss/fibre atrophy. Compared with non-cachectic cancer patients, patients with LM or LM+ > 2%WL, mean muscle fibre diameter was reduced by about 25% (p = 0.02 and p = 0.001 respectively). No significant difference in muscle fibre diameter was observed if patients had WL alone. Regardless of classification, there was no difference in fibre number or proportion of fibre type across all myosin heavy chain isoforms. Mean muscle protein content was reduced and the ratio of RNA/DNA decreased in patients with either > 5%WL or LM+ > 2%WL. These findings support the use of composite measures (WL and LM) to try and identify those patients with evidence of active muscle fibre atrophy. This novel clinical phenotyping provides an accurate method to enable the conduct of candidate gene studies in the investigation of the genetics of cancer cachexia where the primary focus is on muscle wasting rather than overall weight loss. Genotype In an ideal world it would be possible to explore the entire genome and look for associations with the different phenotypes of cachexia. However, to do so would require considerable resource in terms of the cost of genome wide analysis and the cost of phenotyping large enough cohorts of patients (3000-10000). To address these issues I therefore adopted a candidate gene approach. A total of 154 genes associated with cancer cachexia were identified and explored for associated polymorphisms. Of these 154 genes, 119 had a combined total of 281 polymorphisms with functional and/or clinical significance in terms of cachexia associated with them. Of these, 80 polymorphisms (in 51 genes) were replicated in more than one study with 24 polymorphisms found to influence two or more hallmarks of cachexia (i.e. inflammation, loss of fat mass and/or lean mass and reduced survival). Such election of candidate genes and polymorphisms is a key element of multigene study design. The systematic review provides a contemporary basis to select genes and/or polymorphisms for further association studies in cancer cachexia, and to develop their potential as susceptibility biomarkers of cachexia. Phenotype – genotype associations A total of 1276 patients were recruited, phenotyped and genotyped. There were 545 new patients and 731 patients from a previous study. In our new cohort and in keeping with the previous literature, patients who carried the C allele of the rs6136 SNP in the SELP gene, were at a reduced risk of developing cachexia defined by WL. This association applied to all degrees of weight loss ( > 5%, > 10% or > 15%), and not just at the > 10% level as described previously in the literature. When examining newly identified SNPs in a stage 1 analysis for the weight loss phenotype that included 1276 cancer patients, twelve new candidate SNPs were significant. Six of these SNPs are associated with muscle metabolism in five genes (IGF1, CPN1, FOXO1, FOXO3, and ACVR2B), three are associated with adipose tissue metabolism in two genes (LEPR and TOMM40 (APOE on the reverse strand)), two with corticosteroid signalling in one gene (IFT172 (GCKR on the reverse strand)) and one with the immune response in one gene (TLR4). Two polymorphisms (rs1935949 and rs4946935) in the gene encoding for FOXO3 were consistently associated with WL of increasing severity ( > 5% and > 10%). On the basis that WL is a continuum in the cachectic process, the observation that both SELP and FOXO3 associate with the higher degrees of WL suggests that these genetic signatures may be of particular significance. The role of P-selectin in the genesis of cachexia remains to be determined. When examining all SNPs in a stage 1 analysis for the LM phenotype, 5 SNPs were associated significantly with the cachexia phenotype: (i) rs4291 in the angiotensin converting enzyme (ACE) gene in chromosome 17; this gene has been associated with muscle function and metabolism; (ii) rs10636 in chromosome 16 in the metallothionein 2a gene; this gene has been shown to be involved in zinc dyshomeostasis which may contribute to cancer cachexia; (iii) rs1190584 in chromosome 14 in the WDR20 gene; this gene encodes a WD repeat-containing protein that functions to preserve and regulate the activity of the USP12-UAF1 deubiquitinating enzyme complex; (iv) rs3856806 in the peroxisome proliferator-activated receptor gamma (PPARG) gene in chromosome 3 which has been demonstrated to be involved in fatty acid and glucose metabolism; and (v) rs3745012 in chromosome 18 in the lipin 2 (LPIN2) gene; this gene represents a candidate gene for human lipodystrophy, characterised by loss of body fat, fatty liver, hypertriglyceridemia, and insulin resistance. When examining all SNPs in a stage 1 analysis for the LM + > 2%WL phenotype 4 SNPs were associated significantly with the cachexia phenotype. rs12409877 in the leptin receptor (LEPR) located on chromosome 3, LEPR binds leptin and is involved in adipose tissue regulation. rs2268757 located in the activin receptor type-2B (ACVR2B) gene on chromosome 3, ACVR2B is a high affinity activin type 2 receptor which mediates signalling by a subset of TGF-β family ligands including myostatin, activin, GDF11 and others. SNPs in the tumour necrosis factor (TNF) (rs1799964) and ACE (rs4291) genes were also significantly associated with the phenotype. Whether genes demonstrating significant associations with the cachexia phenotypes had altered transcript expression in muscle from cancer patients with or without those phenotypes was also investigated.
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Gunn, Melissa Rose School of Biological Earth & Environmental Science UNSW. "The use of microsatellites as a surrogate for quantitative trait variation in conservation." Awarded by:University of New South Wales. School of Biological, Earth and Environmental Science, 2003. http://handle.unsw.edu.au/1959.4/22457.
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Conservation biologists are interested in maintaining genetic variation in small populations, with a view to maintaining fitness and the ability of the species to adapt to changing environmental conditions. The most important type of genetic variation is therefore that which affects fitness and reproduction, and is therefore subject to natural selection. Such fitness traits are often quantitative, i.e. are the result of a suite of loci, and are continuously variable. Microsatellite markers are a popular method of determining the level of variation present in a species??? genome. The assumption is made that microsatellites, which are neutral markers, behave in the same manner as quantitative traits. If this assumption were proved incorrect, then the use of neutral markers in conservation monitoring would have to be re-evaluated. In this study, experiments have been conducted using Drosophila melanogaster to test the assumption that variation in quantitative traits under stabilising selection declines at the same rate as heterozygosity in microsatellite markers, during a population bottleneck. Experimental population bottlenecks were of two effective population sizes (Ne), Ne=2 for one generation and Ne=60 for 35 generations. Based on the effective population size, we expected both types of bottlenecks to lose 25% of neutral genetic variation. Ten replicates of each bottleneck were maintained, along with four large control populations with Ne=320. In each population, heterozygosity (He) for eight microsatellite loci was compared with the heritability and additive genetic variance of two quantitative traits subject to balancing selection: fecundity and sternopleural bristle number. Microsatellite heterozygosity decreased in accordance with neutral predictions, whereas additive genetic variation in quantitative traits altered more than expected in both large and in bottlenecked populations relative to the initial sampling values, indicating that variation in quantitative traits was not being lost at the same rate as predicted by neutral theory. For most traits, the changes in additive genetic variance were congruent in all populations, large or bottlenecked. This congruence suggests that a common process was affecting all populations, such as adaptation. A mite infestation in early generations is a possible source of selective pressure. When bottlenecked populations were compared to the contemporaneous large populations (Ne = 320), the additive genetic variance of most traits was seen to have been lost in accordance with predictions from the loss of microsatellite heterozygosity. Loss of variation in microsatellites can thus be used to predict the loss of variation in quantitative traits due to bottlenecks, but not to predict the potentially much larger changes due to other processes such as adaptation. The effects of concurrent environmental stress and reduced population size were also evaluated. Endangered populations are often subject to environmental stress in addition to reduced population size, but the effect of stress on the additive genetic variance of fitness traits in organisms undergoing population bottlenecks is unknown. If the presence of stress alters the level of additive genetic variance in fitness traits, the viability of such populations could be substantially affected. The loss of microsatellite heterozygosity was not affected by the presence of a stress agent during a bottleneck. I found some significant effects of stress on the additive genetic variance of sternopleural bristles and fecundity; there was also a significant interaction between stress and the response to directional selection in sternopleural bristles. There was also an increase in the coefficient of variation of VA for sternopleural bristles. Stress may therefore affect the manner in which populations respond to selective pressures.
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Appleyard, Sharon Anne. "The application of genetic markers to Fijian Tilapia stock improvement." Thesis, Queensland University of Technology, 1998.
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Badenhorst, Daleen. "Development of AFLP markers for Haliotis midae for linkage mapping." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/21525.
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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.
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Butterfield, Michael Keith. "Marker assisted breeding in sugarcane : a complex polyploid." Thesis, Link to the online version, 2007. http://hdl.handle.net/10019.1/1203.
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Carter, Deidre Anne. "DNA polymorphisms as genetic markers in Phytophthora infestans." Thesis, Imperial College London, 1991. http://hdl.handle.net/10044/1/46699.
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Sarela, Abeezar Ismail. "Molecular genetic markers of prognosis in colorectal carcinoma." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438485.
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Dudley, Roy. "Genetic mapping of Armillaria ostoyae using RAPD markers." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0004/MQ44087.pdf.
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Dudley, Roy 1972. "Genetic mapping of Armillaria ostoyae using RAPD markers." Thesis, McGill University, 1998. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=20796.
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We report here the use of RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) to identify segregating loci in the haploid progeny of an Armillaria ostoyae basidiocarp and the construction of the first genetic linkage map of this fungus, one of the causal species of Armillaria Root Disease. Upon screening 75 RAPD primers, 18 were found to identify a total of 43 loci segregating with a 1 : 1 Mendelian ratio. These loci were analysed for linkage among 58 monospore progeny. The map constructed with Mapmaker (LOD = 3.0, r = 0.38) was confirmed by GMendel (LOD = 1.5, r = 0.38). This map arranged 30 loci into 6 linkage groups and 4 linkage pairs. Thirteen markers remained unlinked. Using the Kosambi mapping function the linked loci accounted for approximately 450 cM and the genome was estimated to be 1600 cM. This preliminary map covers approximately 28% of the A. ostoyae genome.
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Whiteside, Michael C. R. "Genetic markers for prognostic prediction in colorectal cancer." Thesis, Queen's University Belfast, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387972.
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Wynne, Ian R. "Population studies on farmland insects using genetic markers." Thesis, University of Nottingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387677.
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McGinley, Susan, and Kingdon Lorraine. "Improving Dairy Bull Selection: Genetic Markers Reduce Guesswork." College of Agriculture and Life Sciences, University of Arizona (Tucson, AZ), 2000. http://hdl.handle.net/10150/622278.
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Kennedy, Amy. "Genetic Markers, Birth Characteristics, and Childhood Leukemia Risk." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/992.
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The cause for childhood acute lymphoblastic leukemia (ALL) remains unknown, but male gender is a risk factor, and among ethnicities, Hispanics have the highest risk. In this dissertation, we explored correlations among genetic polymorphisms, birth characteristics, and the risk of childhood ALL in a multi-ethnic sample in 161 cases and 231 controls recruited contemporaneously (2007-2012) in Houston, TX. We first examined three lymphoma risk markers, since lymphoma and ALL both stem from lymphoid cells. Of these, rs2395185 showed a risk association in non-Hispanic White males (OR=2.8, P=0.02; Pinteraction=0.03 for gender), but not in Hispanics. We verified previously known risk associations to validate the case-control sample. Mutations of HFE (C282Y, H63D) were genotyped to test whether iron-regulatory gene (IRG) variants known to elevate iron levels increase childhood ALL risk. Being positive for either polymorphism yielded only a modestly elevated OR in males, which increased to 2.96 (P=0.01) in the presence of a particular transferrin receptor (TFRC) genotype for rs3817672 (Pinteraction=0.04). SNP rs3817672 itself showed an ethnicity-specific association (Pinteraction=0.02 for ethnicity). We then examined additional IRG SNPs (rs422982, rs855791, rs733655), which showed risk associations in males (ORs=1.52 to 2.60). A polygenic model based on the number of polymorphic alleles in five IRG SNPs revealed a linear increase in risk (OR=2.00 per incremental change; P=0.002). Having three or more alleles compared with none was associated with increased risk in males (OR=4.12; P=0.004). Significant risk associations with childhood ALL was found with birth length (OR=1.18 per inch, P=0.04), high birth weight (>4,000g) (OR=1.93, P=0.01), and with gestational age (OR=1.10 per week, P=0.04). We observed a negative correlation between HFE SNP rs9366637 and gestational age (P=0.005), again, stronger in males (P=0.001) and interacting with TFRC (PPinteraction=0.05). Our results showed that (i) ALL risk markers do not show universal associations across ethnicities or between genders, (ii) IRG SNPs modify ALL risk presumably by their effects on iron levels, (iii) a negative correlation between an HFE SNP and gestational age exists, which implicates an iron-related mechanism. The results suggest that currently unregulated supplemental iron intake may have implications on childhood ALL development.
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SUSCA, Roberta Rosa. "Patterns of genetic and linguistic variation. A study of uniparental markers." Doctoral thesis, Università degli studi di Ferrara, 2017. http://hdl.handle.net/11392/2488149.
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This dissertation is divided in three sections and focuses on two of the projects I worked on during my three-years PhD, funded by a European Research Council (ERC) grant LanGeLin.
Both the projects share the uniparental markers as tool used for the investigation of the human evolutionary history, but each of them addresses different scientific questions by means of a different combination of molecular and statistical methods.
Part I is a technical summary on current knowledge about uniparental markers features and on the pros and cons of their usage for addressing questions stemming from the fields of linguistics and archaeology.
Part II summarizes the results of one of the ERC-founded LanGeLin works; here I describe the comparison of patterns of genetic and liguistic diversity in 36 Eurasian populations. The ERC-founded LanGeLin project aims to improve our understanding about the coevolution of language and genes. R. Sokal and L.L. Cavalli-Sforza in 1988 showed that a correlation between genetic and linguistic variation within major language families is actually present, but due to imperfect methods to quantify linguistic variation, it has been difficult to compare populations belonging to distant linguistic groups. Thanks to the newly PCM linguistic method, a new way to compare languages is now available, based on stable linguistic syntax features. It is now possible to test the correlation between genetic and linguistic data in a broad geo-linguistic scale, as this thesis will do, and to interpret in evolutionary terms both the rule and the exceptions. It is also possible to study maternal and paternal lineages separately, to inquire their migrational histories. Two different migrational histories emerged, with women dispersing at a higher rate than men. When comparing genetic and linguistic features a neither obvious nor simple pattern is detectable: correlations between languages and DNA variants depend on the geographical area and the genetic markers considered.
Part III addresses questions related with the analysis of complete mitochondrial sequences from Mesolithic (Ms) times, which allowed us to address questions regarding Neolithic (Ne) and pre-Neolithic (pN) peopling of Sardinia. We investigated the role of two Ms Sardinian mtDNA sequences in the European context. Little is known about the genetic prehistory of Sardinia because of the scarcity of pN human remains. Modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Ne farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here I present the first and oldest complete mtDNA sequences from Sardinia, dated back to 10,000 yBP. These two individuals belong to rare mtDNA lineages never been found before in Ms samples and that are currently present at low frequencies also in the whole Europe. When compared with other European pN data, the Ms Sardinian sequences appeared already well differentiated, and in general more similar to pre-Last Glacial Maximum populations, than to coeval sequences. As a side project, I was also involved in the study of the differences in twinning rate (tr) among human populations of Africa (where the tr is maximum), Europe and Asia (where the tr is minimum). The contact point between these projects was represented by the common bioinformatics and biostatistical tools needed for analysis of large genomic. Although I considered that, for the sake of consistency, this thesis will mostly focus on the ERC-funded project, I am enclosing, in the final Manuscripts section, both papers produced during my doctoral years.Questa tesi riassume l’attività di ricerca da me svolta durante i tre anni di dottorato, sovvenzionato dal progetto ERC LanGeLin, il cui scopo principale è di migliorare le conoscenze sulla co-evoluzione di lingue e geni. I progetti descritti condividono l’uso di marcatori uniparentali usati per gli studi di evoluzione umana, ma differiscono per la combinazione di metodi molecolari e statistici. La Parte I descrive lo stato dell’arte dei marcatori uniparentali e i pro e contro del loro utilizzo in ambito linguistico e archeologico. La Parte II riassume i risultati delle ricerche condotte nell’ambito del progetto LanGeLin che descrive la diversità dei pattern genetici e linguistici in 36 popolazioni Euroasiatiche. Il progetto LanGeLin (Language and Gene Lineages), finanziato dal “European Research Council” ha lo scopo di testare l’ipotesi di Darwin presentata in “Origine delle specie”. Darwin intuì che l’albero filogenetico delle diverse sottospecie umane, potesse sovrapporsi a quello ottenuto a partire dalle diverse lingue, offrendo di fatto la possibilità di studiare la genealogia delle lingue e allo stesso tempo capire come le differenze tra queste avrebbero permesso di far luce sugli aspetti elusivi della storia demografica umana. R. Sokal e L.L. Cavalli-Sforza nel 1988 hanno elucidato come la comparazione dei vocaboli rifletta la correlazione fra variabilità genetica e linguistica nelle maggiori famiglie linguistiche ma, a causa di metodi linguistici, risulta difficile comparare popolazioni derivanti da gruppi linguistici distanti. Il nuovo metodo linguistico PCM si basa sulle caratteristiche linguistiche più stabili della sintassi. È stato dunque possibile, anche in questa tesi, testare su larga scala geo-linguistica la correlazione tra dati genetici e linguistici. Lo studio delle discendenze materne e paterne è stato condotto separatamente per indagarne le relative storie di migrazione: due differenti storie sono emerse dall’analisi del Ychr (discendenza patrilineare) e del mtDNA (discendenza matrilineare). Non ovvie considerazioni sono scaturite dalla comparazione delle caratteristiche genetiche e linguistiche, che ha portato a definire come la correlazione tra lingue e sequenza genetica sia dipendente dall’area geografica e dai marcatori genetici considerati. La Parte III descrive l’analisi di sequenze di mtDNA del Mesolitico (Ms) che ci ha permesso di indagare sul popolamento della Sardegna in periodo Neolitico (Ne) e pre-Neolitico (pN). Lo studio è stato incentrato su due sequenze mitocondriali sarde Ms in relazione al contesto europeo. C’è ancora molta incertezza sulla variabilità genetica della Sardegna preistorica, a causa della scarsità di resti umani Ne. Dal punto di vista genetico, i sardi moderni possono considerarsi un gruppo a se stante rispetto al resto dell’Europa continentale, mostrando alti livelli di diversità interna e una forte vicinanza con i primi coltivatori europei del Ne. Questa tesi riporta le due prime sequenze mtDNA complete sarde, datate circa 10000 anni fa. I due individui confermano un’occupazione mesolitica dell’isola e rappresentano un aplotipo mai trovato prima in Sardegna mesolitica e con basse frequenze nell’intera Europa. Le due sequenze risultano ben differenziate se comparate con altri dati europei pN, e più simili a popolazioni dell’era pre-glaciale che a popolazioni coeve. Analisi di inferenza Bayesiana hanno mostrato come i primi abitanti dell’isola abbiano contribuito poco al popolamento attuale dell’isola, la cui diversità genetica deriva da migrazioni dal continente in tempi neolitici. Un progetto portato avanti parallelamente, ha riguardato lo studio di frequenze alleliche in gemelli dizigotici provenienti da popolazioni umane africane, europee ed asiatiche. Le tecniche bioinformatiche e biostatistiche usate per le analisi genomiche su larga scala, fanno da collante con i precedenti progetti descritti.
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Wilson, James F. "Human population structure and demographic history using genetic markers." Thesis, University of Oxford, 2002. http://ora.ox.ac.uk/objects/uuid:5a4844ff-9347-44b5-999e-64ce5025006f.
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The evolutionary history of the human species has generated complex patterns of population structure and linkage disequilibrium (non-random associations of alleles at different loci or LD). The understanding of these patterns is crucial to two of the most important challenges facing biomedical science today: the identification of disease predisposing genes and prediction of variable drug reactions. The genetic variation revealed by these endeavours can also illuminate the underlying population historical processes. Here, I illustrate each of these applications: first, by assessing the demographic context of cultural change in the British Isles. Y chromosome variation indicates that the Viking age invasions left a significant paternal legacy (at least in Orkney), while the Neolithic and Iron Age cultural transitions did not. In contrast, mitochondrial DNA and X chromosome variation indicate that one or more of these pre-Anglo-Saxon revolutions had a major effect on the maternal genetic heritage of the British Isles. Second, I provide conclusive evidence that diverse demographic histories produce strikingly different patterns of association. Elevated LD extends an order of magnitude further in the Lemba, a Bantu-Semitic hybrid population, than in the putative parental populations. A significant relationship between allele-frequency differentials in the parental populations and the Lemba LD demonstrates that it is admixture-generated. Third, I demonstrate that the genetic structure inferred in a heterogeneous sample using neutral markers (a) shows ethnic labels to be inaccurate descriptions of human population structure, and (b) predicts drug metabolising profiles, defined by the distribution of drug metabolising enzyme variants. Thus the trade-off between therapeutic response and adverse drug reactions will differ between different sub-clusters. Assessment of genetic structure during drug trials is therefore, like the empirical evaluation of each population’s pattern of LD, a necessity.
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Mote, Benny Edd. "The use of genetic markers to improve sow productive life and genetic abnormalities." [Ames, Iowa : Iowa State University], 2008.
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Van, Staden Derick. "AFLP and PCR markers for the Ht1, Ht2, Ht3 and Htn1 resistance genes in maize." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52078.
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Thesis (PhDAgric)--University of Stellenbosch, 2001.ENGLISH ABSTRACT: Maize is undoubtedly South Africa's most important field crop. The identification of markers and genes for traits of interest is important to sustain the improvement of maize cultivation. Northern corn leaf blight (NClB) is a disease that occurs worldwide and can dramatically reduce yield. A number of single dominant resistance genes have been identified for NClB and some have been mapped. Currently there are no simple PCR markers for any of these resistance genes, making markerassisted selection (MAS) difficult. The aim of this study was to develop PCR markers for the NClB resistance genes Ht1, Ht2, Ht3 and Htn1 in maize. To accomplish this, the AFlP (amplified fragment length polymorphism) technique was first optimised. The results indicated that the Mlul/Msel restriction enzyme combination produces a higher percentage of polymorph isms when compared to the PstllMsel enzyme combination. It was also shown that the enzyme combination plays an important role in the percentage of polymorphic fragments observed, whereas the number of restriction enzymes used in AFlP analysis only significantly affects the total number of fragments scored. Populations segregating for the different resistance genes were not available for this study. Nearly-isogenic lines (Nils) were used in combination with AFlP technology to identify markers that map close to the genes. AFlP markers common in at least two resistant or susceptible lines were cloned and converted to PCR markers. Two commercially available recombinant inbred line (Ril) populations were then used to map the identified markers. For Htn1 fifteen polymorphic fragments were present in both resistant lines. They were selected for sequence specific marker conversion. Seven of the fifteen sequence characterized amplified region (SCAR) markers were polymorphic on the Nil pairs and five mapped to one region of maize chromosome 8.05/06. Twenty-one AFlP markers were identified for Ht1 and four SCAR markers were polymorphic In the Ht1 Nils. Three of these were mapped to chromosome 2.07. Three AFlP markers were identified for Ht2 of which two were converted to SCAR markers. Both SCAR markers were polymorphic on the Ht2 Nils and mapped to chromosome 8.05/06. On the Ht3 NILs, four AFLP markers were identified and two converted SCAR markers and one microsatellite marker (bnlg1666) were polymorphic. One of the SCAR markers and the microsatellite marker were mapped to chromosome 7.04 using a RIL population. This reports the first tentative mapping position for the Ht3 locus. The next step was to determine if a set of marker alleles could be used in a number of Htn 1 resistance lines to identify a common donor region selected by the breeders. Nine markers consisting of five SCAR markers, three converted RFLP markers and one microsatellite marker were used on 16 Htn1 resistant lines. The marker allele of us3 was in 12 of the 16 lines in coupling with Htn1 resistance. Second was the marker us5 in 11 of the 16 lines. Using this data 14 of the 16 lines shared a common introgressed region between the markers us3 and us5. A further common introgressed region between 11 of the inbred lines was found between the markers us14 and asg17. The last aim of this study was to propose a new marker technique that might be more successful than the AFLP technique in the identification of markers closely linked to genes. A new marker approach was identified where a MITE (Hbr) primer was used as an anchor primer in combination with resistance gene analog primers. This was found to be a highly polymorphic marker technique that could be used to identify markers and possibly candidate genes. It is a robust technique, which is affordable since amplifications occur from undigested genomic DNA and the primers mainly amplify fragments from genic regions.
AFRIKAANSE OPSOMMING: Mielies (Zea mays) is ongetwyfeld Suid Afrika se belangrikste lanbou gewas. Vir volgehoue opbrengs verbetering is die identifisering van merkers en gene vir belangrike eienskappe noodsaaklik. Noordelike blaarskroei (NBS) kan opbrengs wesenlik kan beïnvloed. Tans is daar reeds "n aantal enkel weerstandsgene geïdentifiseer, maar geen PKR-merkers is beskikbaar vir merker gebaseerde seleksie nie. Die doelwit van hierdie studie was om PKR-merkers te ontwikkel vir vier enkel weerstands gene (Ht1, Ht2, Ht3 en Htn1) teen NBS in mielies. Om die doelstelling te bereik is die AFLP-tegniek eers geoptimiseer. Op grond van waargenome aantal polimorfismes, was Mlul/Mse/"n beter restriksie ensiem kombinasie as Pstl/Msel. In die studie is ook bewys dat die aantal (meer as twee) restriksie ensieme wat gebruik word slegs die aantal fragmente, en nie die persentasie polimorfismes, wesenlik beïnvloed nie. Geen segregerende populasie was vir die verskillende gene beskikbaar nie. Naby isogeniese lyne (NILe) is daarom in kombinasie met die AFLP-tegniek gebruik om merkers te identifiseer wat naby die gene karteer. Alleenlik polimorfiese merkers wat in ten minste twee weerstand biedende of vatbare lyne voorgekom het, is gekloneer en omgeskakel na PKR-merkers. Daarna is twee kommersiële rekombinante ingeteelde lyn populasies gebruik om die gene te karteer. Vyftien fragmente is gevind wat gekoppel was met die Htn1 weerstand. Sewe van hierdie merkers is omgeskakel in polimorfiese SCAR-merkers waarvan vyf gekarteer is in een gebied op chromosoom 8.05/06. Een-en-twintig AFLP-merkers is geïndentifiseer vir Ht1 en vier is omgeskakel na polimorfiese SCAR-merkers. Drie hiervan is gekarteer op chromosoom 2.07. Drie AFLP-merkers is geïndetifiseer vir Ht2 waarvan 2 omgeskakel is na polimorfiese SCAR-merkers. Altwee hierdie merkers is gekarteer op chromosoom 8.05/06. Op die Ht3 lyne is vier AFLP-merkers geïdentifiseer waarvan twee omgeskakel is na polimorfiese SCAR-merkers. Een mikrosatelliet merker (bnlg1666) is ook gevind wat die selfde polimorfiese patroon wys op die Ht3 lyne. Die mikrosateliet en een van die SCAR-merkers het gekarteer op chromosomale posisie 7.04. Hierdie is die eerste tentatiewe posisie vir die Ht3 lokus. Die volgende stap was om te bepaal of "n stel polimorfiese merker-allele gebruik kan word om die donor DNA-segment te identifiseer wat die plantteiers geselekteer het. Nege PKR-merkers wat bestaan het uit vyf SCAR-merkers, 3 omgeskakelde RFLP merkers en een mikrosateliet is gebruik op 16 Hnt1 weerstandslyne. Us3 was die merker alleel wat in die meeste gevalle gekoppel was met die Htn1 weerstandslyne (12/16). Tweede was die merker us5 (in 11 van die 16 lyne). Uit die data blyk dit dat 14 van die 16 lyne "n donor segment het wat beide merkers us3 en us5 bevat. Merkers us14 en asg17 het in 11 van die 16 bestande lyne saam voorgekom. Die laaste doelstelling van hierdie studie was om "n nuwe tegniek te ontwikkel wat dalk meer suksesvol as AFLPs kan wees om merkers te identifiseer nabyaan gene. "n Nuwe tegniek word voorgestel waar "n MITE (Hbr) inleier gebruik kan word in kombinasie met weerstandgeen-analoog inleiers. Dit is gevind dat hierdie kombinasie van inleiers "n hoogs polimorfiese band patroon gee en dat die merkers ook dalk kandidaat-gene kan wees. Die tegniek is maklik uitvoerbaar, relatief goedkoop en maak gebruik van onverteerde genomiese DNA. Die fragmente wat geamplifiseer word is hoofsaaklik vanaf geenryke areas.
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Laughlin, Thomas Fain. "Hypervariable DNA markers and population structure in three fish species." Diss., This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-06062008-171854/.
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Liu, Shaolin 1968. "Oligonucleotides applied in genomics, bioinformatics and development of molecular markers for rice and barley." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85569.
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A genome sequence can be conceptualized as a 'book' written with four nucleotide 'letters' in oligonucleotide (oligo) 'words'. These words can be used in genomics, bioinformatics and the development of molecular markers. The whole-genome sequence for rice (Oryza sativa L.) is almost finished and has been assembled into pseudomolecules. For barley ( Hordeum vulgare L.) expressed sequence tags (ESTs) have been assembled into 21,981 tentative consensus sequences (TCs). The availability of such sequence information provides opportunities to investigate oligo usage within and between genomes. For the first of three studies reported in this thesis, a C++ program was written to automatically design oligos that are conserved between two sets of sequence information. In silico mapping between rice coding sequences (CDS) and barley TCs indicated that oligos between 18 and 24 bp provide good specificity and sensitivity (83% and 86%, respectively, for 20mers). Conserved oligos used as PCR primers had a high (91%) success rate on barley lines. Sequencing of PCR products revealed conservation in exon sequence, size and order between barley and rice. Introns were not conserved in sequence but were relatively stable in size. Map locations of eight new markers in barley revealed both genome colinearity and rearrangements between barley and rice. The second study reported in this thesis examined word frequency within the rice genome. A non-random landscape composed of high-frequency and low-frequency zones was observed. Interestingly, high-frequency words seemed to be rice specific while single-copy words were gene specific and conserved across species. As in the first study, oligos of 12 bp or less were not specific, and 18 bp seemed to be a critical length for the specificity of oligos. The third study reported in this thesis involved the development of molecular markers for known genes using public sequence information. Six new polymorphic markers were d
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Kennedy, Aaron P. "Investigations into obesity using anthropometric, serum and genetic markers/." Internet access available to MUN users only. Search for this title in:, 2010.
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Chiu, Kam-hung, and 趙錦鴻. "Genetic aberrations in chronic lymphocytic leukaemia as prognostic markers." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B41290781.
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Topipat, Chutima. "Genetic and metabolic markers of ageing in sheep oocytes." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/22244/.
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Burrows, Kimberley. "Molecular genetic epidemiology studies of quantitative nucleic acid markers." Thesis, University of Bristol, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.761240.
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Gupta, Jayanta. "Genetic and Biological Markers of Atopic Dermatitis in Children." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1204843640.
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Chiu, Kam-hung. "Genetic aberrations in chronic lymphocytic leukaemia as prognostic markers." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B41290781.
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Chalmers, Kenneth James. "The development and utilization of genetic markers for barley." Thesis, University of St Andrews, 1992. http://hdl.handle.net/10023/14402.
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The development of new and novel polymorphic assay methods represents one of the most significant developments in plant and animal biology. The exploitation of these genetic markers is of relevance to both applied and fundamental research. Recombinant DNA technology provides the opportunity to develop phenotypically neutral genetic markers in any organism from which DNA can be extracted. The research described in this thesis has focused on the development, evaluation and exploitation of genetic markers in barley. Both protein and DNA based molecular markers were evaluated as a means of detecting polymorphism in H. vulgare and H. spontaneum. New methods for detecting polymorphisms based on the Polymerase Chain Reaction (PCR) were assessed and successfully applied to barley. The segregation of alleles at morphological, isozyme and RFLP loci were monitored in doubled haploid (DH) populations of barley. In order to detect molecular variability, both clones of known function and anonymous clones were employed. Clones homologous to the- hordein gene complex on chromosome IH were used in conjunction with DHs to intra-chromosomally map various members of this multi-gene family. Allelic variation at the genetic loci segregating in the DH population was evaluated in relation to the expression of quantitative traits. This study established that several isozymes and RFLP loci were significantly associated with quantitative trait loci (QTL) of agronomic importance. Grain isozyme and ribosomal DNA (rDNA) variability was examined in Hordeum spontaneum populations sampled from 27 geographical sites in Israel. Considerable phenotypic variability was observed and isozyme and rDNA variants were identified that were not present in the H. vulgare gene pool. Furthermore, the variability detected was quantified and correlated with a range of ecogeographical factors. The distribution of grain isozyme and rDNA phenotypes was non-random with particular phenotypes being restricted to specific geographical areas of Israel. Information on the spatial distribution of diversity in H. spontaneum is a pre-requisite for the optimization of sampling and germplasm collecting strategies. Opportunities and limitations to the exploitation of genetic markers in barley improvement are considered.
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Brand, Elizabeth Gertruida. "Selectable markers for recombinant poxvirus." Thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/25692.
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Moro-Méndez, José. "Associations between genetic markers and mastitis resistance in Canadian Holsteins." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85943.
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The objective of this thesis was to test for associations between genetic polymorphisms of genes related to immune response (growth hormone (GH), growth hormone receptor (GHR), ornithine decarboxylase (ODC), insuline-like growth factor-1 (IGF-1), adrenocorticotropin hormone (ACTH), corticotrophin releasing hormone (CRH), and prolactin (PRL)) and mastitis resistance traits (incidence of clinical mastitis (ICM), occurrence of clinical mastitis (OCM), culling due to mastitis (CDM), and somatic cell scores (SCS)) in Canadian Holsteins.Using lactation records of cows enrolled in milking recording in Quebec (Programme d'Analyse des Troupeaux Laitiers du Quebec, PATLQ from 1980 to 1994 (411,291 first, 238,432 second, and 130,983 third lactations, respectively) Estimated Transmitting Abilities of traits were generated with a model that included the random effect of sire, and fixed effects of herd-year-season-of calving, age at calving, and genetic group. 721 bulls which had daughters in the phenotypic data sets were genotyped for twenty polymorphisms of the above genes located on autosomes (BTA) 5, 11, 14, 19, 20, and 23.
Two types of analysis of associations were performed: analysis across-population with a model that included the fixed effect of marker and random effect of the son of grandsire, and within-family analysis with a model that included the fixed effects of the grandsire, marker nested within grandsire, and the random effect of son nested within marker and grandsire. Permutation tests were performed to reduce Type I error probability.
Significant associations were found within families for markers of IGF-1 (BTA5), ODC (BTA11), GH (BTA 19), GHR (BTA 20), and PRL (BTA 23) for ICM, OCM, CDM, and SCS in different lactations. Some of these putative quantitative trait loci (QTL) are located on BTA where other authors have reported QTL affecting SCS and udder conformation. The results from this study may contribute to efforts to dissect the genetic basis of mastitis resistance in dairy cattle.
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Lambert, Carol-Ann. "A novel marker technique : using miniature inverted-repeat transposable elements (MITEs) in combination with resistant gene analogues (RGAs)." Thesis, Stellenbosch : Stellenbosch University, 2001. http://hdl.handle.net/10019.1/52117.
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Thesis (PhD)--Stellenbosch University, 2001.ENGLISH ABSTRACT: Given the organisation of the maize genome as well as demands placed on the saturation of molecular linkage maps it would be desirable to identify informative molecular markers that is located or linked to genic rich areas. Sequences of gene products from different gene classes were investigated. Proteins containing a nucleotide binding site (NBS) and leucine-rich repeat (LRR) region comprise the largest class of disease resistance proteins. Resistant gene analogue (RGA) primers belonging to this specific class were derived from previous published literature studies. By means of similarity studies of short stretches of conserved amino acid and DNA sequences, primers were developed that belonged to the peroxidase and reductase gene classes. A novel class of transposable element was identified, that occurred in the gene rich areas of a diverse range of grass genomes. Of all the MITE families described so far, the Heartbreaker (Hbr) and Hb2 family elements were of particular interest. The unique properties of MITEs, especially their high copy number, polymorphism, stability and preference for genic areas together with the RGA primers, were exploited to develop a new marker technique for the isolation of a class of molecular marker with a strong preference for genic areas. Using the publicly available recombinant inbred population, Tx303 x C0159, 196 MITE/RGA markers were added to the existing recombinant inbred linkage map consisting of ±1033 already established markers. It became apparent that just like loci for disease resistance, the 196 MITE/RGA fragments were not randomly distributed across the maize genome but occurred in clusters spread across the ten maize chromosomes. Ninety-two (92) of the MITE/RGA fragments showed significant correlation to previously mapped maize resistance genes. To establish the conservation and specificity of both the Hbr and Hb2 elements, sequences of 19 MITE/RGA fragments were ascertained. When comparing the partial MITE element sequences from these fragments, a high degree of element conservation was observed. One fragment showed good sequence correlation to a NADPH He Toxin reductase protein product and mapped to the same chromosomal location as the hm1 gene locus in maize. This fragment can be considered a candidate gene for resistance against the pathogen, Helminthosporium carbonum. The Hbr primer used proved to be very specific for the Heartbreaker MITE element, this was in contrast to the non-specificity of the Hb2 primer. The applicability of this technique was tested on two maize diseases that cause immense damage in the maize production industries in South Africa. Fourteen MITE/RGA markers were used to fine map the putative chromosomal locations for the HtN1, Ht1, Ht2 and Ht3 genes that confer resistance. against Setosphaeria turcica, the northern corn leaf blight (NelS) pathogen in maize. Three MITE/RGA fragments were identified that aided in the saturation of the linkage map for quantitative trait resistance (QTl) against gray leaf spot (GlS) in maize. This novel MITE/RGA technique presented a unique opportunity to search for additional candidate genes by using polymerase chain reaction (peR) analysis. When compared to the conventional amplified fragment length polymorphism (AFLP) technique, the MITE/RGA technique proved to be just as efficient but was more cost effective and less time consuming.
AFRIKAANSE OPSOMMING: Die organisasie van die mielie genoom as ook die vereistes wat daar geplaas word op die versadiging van koppelingskaarte, vereis dat daar meer klem geplaas word op die ontwikkeling van molekulêre tegnieke wat merkers in geenryke areas identifiseer. Die volgordes van geenprodukte, wat behoort tot verskillende geenklasse, is deeglik bestudeer. Proteïenprodukte wat bestaan uit 'n nukleotiedbindingsarea (NBA) en 'n leusienryke herhalende (LRH) area is een van die grootste klasse waaronder siekteweerstandsproteïene sorteer. Polimerase kettingreaksie (PKR) inleiers wat behoort tot hierdie spesifieke klas, is verkry vanuit vorige publikasies. Deur kort gekonserveerde aminosuur en DNS volgordes te vergelyk is inleiers ontwikkel wat behoort tot die peroksidase en reduktase gene klasse. 'n Nuwe klas transponeerbare elemente wat voorkom in die geenryke areas van diverse gras genome, is geïdentifiseer. Van al die miniatuur inversie herhalende transponeerbare elemente (MITE) wat al geïdentifiseer is, is die twee elemente, Heartbreaker (Hbr) en Hb2, van groot belang. Unieke eienskappe van die MITEs, veral hul hoë kopie aantal, polimorfiese-indeks, stabiliteit asook voorkeur vir geenryke areas, tesame met die weerstandsgeen analoë (WGA) inleiers, is gebruik om 'n nuwe merker tegniek te ontwikkel. Hierdie nuwe tegniek identifiseer 'n klas merker wat 'n sterk voorkeur het vir geenryke areas. Deur gebruik te maak van die openbare beskikbare rekombinante ingeteelde (RI) populasie, Tx303 x C0159, is 196 MITE/WGA-merkers gekarteer op die bestaande RIL koppelingskaart, wat alreeds bestaan uit ±1033 gevestigde merkers. Net soos die lokusse vir siekteweerstand het dit geblyk dat hierdie 196 merkers in groepe voorkom wat verspreid is oor die tien mielie chromosome. Twee-en-negentig (92) van die 196 gekarteerde MITE/WGA-merkers het betekenisvolle korrelasie gewys met reeds gekarteerde mielie weerstandsgene. Die volgordes van 19 MITE/WGAfragmente is bepaal om sodoende die spesifisiteit en mate van konservering van die Hbr and Hb2 elemente te bereken. 'n Hoë mate van element konservering is waargeneem. Een fragment het In baie goeie volgorde korrelasie gewys met In NADPH HG toksien reduktase proteïen produk en karteer op dieselfde chromosomale posisie as die hm1 geen lokus. Hierdie fragment kan gesien word as In kandidaatgeen vir weerstand teen die mielie patogeen, Helminthosporium carbonum. Die toepasbaarheid van hierdie tegniek is getoets op twee siekte toestande, wat lei tot groot verliese in die mielie industrie, in Suid-Afrika. Veertien van die MITE/WGAmerkers is gebruik om die waarskynlike chromosomale posisies van die HtN1, Ht1, Ht2 en Ht3 gene, wat weerstand bied teen Setosphaeria turcica, die noordelike mielie blaarvlek (NMBV) patogeen, fyner te karteer. Drie MITE/WGA fragmente is geïdentifiseer wat gehelp het in die versadiging van die koppelingskaart vir die kwantitatiewe kenmerk weerstandbiedenheid (KKW) teen grys blaarvlek (GBV) in mielies. Deur gebruik te maak van polimerase kettingreaksie (PKR) analise, verskaf hierdie tegniek die moontlikheid om te soek vir addisionele kandidaatgene. Hierdie tegniek is ook vergelyk met die konvensionele geamplifiseerde fragment lengte polimorfisme (AFLP) tegniek. Daar is gevind dat die nuwe tegniek net so informatief is, maar wel meer koste effektief en tyd besparend.
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Hibbets, Eric Matthew. "Molecular Characterization of Hybridization Between Magellanic (Spheniscus magellanicus) and Humboldt (Spheniscus humboldti) Penguins in the Wild." Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1562071641076803.
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Persson, Maj-Liz. "Suicide attempt and genes : psychiatric and genetic characteristics of suicide attempters /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3760-5/.
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Larsson, Lena C. "Disentangling small genetic differences in large Atlantic herring populations: comparing genetic markers and statistical power." Doctoral thesis, Stockholms universitet, Zoologiska institutionen, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-8338.
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Genes are the foundation of evolution and biodiversity. The genetic structure of natural populations needs to be understood to maintain exploited resources rationally. This thesis focuses on genetic variability and methods to determine spatial and temporal genetic heterogeneities. Intense human exploitation generates particular challenges to conserve genetic diversity of fishes since it has genetic effects. My research concerns one of our most valuable fish species: the Atlantic herring (Clupea harengus). I analyzed Atlantic herring samples from the North and Baltic Seas. The objectives were to determine: 1) spatial genetic structure, 2) whether allozymes and microsatellites provide similar descriptions of the differentiation pattern, or 3) if they are influenced by selection, 4) factors affecting statistical power when testing for genetic differentiation, and 5) the temporal stability of the genetic structure. The results show: 1) very low levels of spatial genetic differentiation in Atlantic herring; a major component is a difference between the Baltic and North Seas, 2) a concordant pattern with allozymes and microsatellites, 3) that selection influences a microsatellite locus, which can be a low salinity adaptation, 4) that statistical power is substantial for frequently used sample sizes and markers; the difference in power between organelle and nuclear loci is partly dependent on the populations’ stage of divergence, and 5) no changes in amount of genetic variation or spatial genetic structure over a 24-year period; the selection pattern in one microsatellite locus remained. The notion that the large population sizes make herring unlikely to lose genetic diversity may be disputed. I found small local effective population sizes, and the evidence of selection hints of a distinct evolutionary lineage in the Baltic. When Atlantic herring is managed as very large units, there can be detrimental genetic effects if certain population segments are excessively harvested.
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Luan, Shi-Lu. "Molecular epidemiology of Streptococcus agalactiae : mobile elements as genetic markers /." Doctoral thesis, Umeå : Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-877.
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Marinou, Ioanna. "Identification of genetic markers influencing rheumatoid arthritis susceptibility and severity." Thesis, University of Sheffield, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.505786.
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Rheumatoid Arthritis (RA) is a chronic inflammatory disease characterized by progressive joint inflammation that results in bony erosions and cartilage damage. Until recently only 2 genes were unambiguously correlated with disease risk: the HLA-DRB1 and the protein tyrosine phosphatase non-receptor 22 (PTPN22). Several genome wide scans conducted in populations from UK, USA and Sweden have suggested other risk loci including TNFAIP3-OLIG3, TRAF1-C5 and STAT4. The search for genetic regions associated with complex diseases such as RA is an important challenge that could lead to better diagnosis and treatment directed at the cause of the disease.
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Gartland, J. S. "Introduction and use of selectable markers in plant genetic manipulation." Thesis, University of Nottingham, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.233705.
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Mazhar, Kehkashan. "Molecular genetic markers for selection and genome mapping in cattle." Thesis, University of Reading, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260797.
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Sasse, Juergen. "The development of genetic markers for the Trypanosoma brucei genome." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624805.
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Drasar, Emma Rachel. "Genetic and biological markers of severity in sickle cell disease." Thesis, King's College London (University of London), 2014. https://kclpure.kcl.ac.uk/portal/en/theses/genetic-and-biological-markers-of-severity-in-sickle-cell-disease(7c1f16a0-0862-4311-ae7f-7842a85e915e).html.
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Sickle cell disease (SCD) is remarkable for the variability of its phenotype despite its genetic simplicity, with family and population studies indicating a strong genetic influence. The best characterised genetic modifiers are genes controlling HbF levels and co-inheritance of alpha-thalassaemia. Other genetic and biological factors may also influence disease severity and the development of complications. King’s Health Partners have the largest adult cohort of SCD patients in the United Kingdom, approximately 2400 patients. Characterising this group (using laboratory variables, evidence of clinical complications and admission data) has formed the basis for my studies. Telomere length and Duffy antigen receptor for chemokines (DARC) status and two complications, sickle nephropathy and sickle hepatopathy were investigated. Relative telomere length (measured using qPCR) was significantly longer in patients with SCD than controls and positively correlates with white blood count. Shorter telomeres were found in patients on hydroxycarbamide treatment and those with Hb SC. We hypothesise that longer telomeres result from up-regulation of telomerase due to inflammation. Polymorphisms in DARC have a high prevalence in people of African ancestry and explain benign ethnic neutropenia. We found positive associations with Duffy positive phenotype and a reduced time to readmission and the development of leg ulcers. We investigated if sickle-related renal impairment was associated with the APOL1, DARC and HMOX1 genes. Duffy positive phenotype was associated with the development of macroalbuminuria and the presence of 1 or more APOL1 risk alleles was associated with the development of renal impairment (as measured by MDRD eGFR). We assessed the prevalence of liver disease in our population using Enhanced Liver Fibrosis score (a combination of serum markers associated with liver fibrosis) and transient elastography (Fibroscan®). Using this approach we found that transfusional iron overload and haemolysis appear to play a key role in the pathogenesis of sickle hepatopathy.
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Sant, V. J. "Genetic diversity and linkage analysis in chickpea using DNA markers." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2001. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2852.
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Campino, Susana Gomes. "Genetic analysis of murine malaria /." Umeå : Univ, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-124.
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Gupta, Manu. "Autoimmune markers in autoimmune diabetes /." Stockholm, 2003. http://diss.kib.ki.se/2004/91-7349-756-8/.
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Boersma, Jeffrey George. "Contributions to the molecular genetics of the Narrow-leaf Lupin (Lupinus augustifolius L.) : mapping, marker development and QTL analysis." University of Western Australia. School of Earth and Geographical Sciences, 2007. http://theses.library.uwa.edu.au/adt-WU2008.0001.
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[Truncated abstract] Narrow-leaf lupin (Lupinus angustifolius L.) was first recorded as having been introduced into Germany during the mid-19th century for use as green manuring and as fodder crops. However, it was not until post World-War I that there was any serious attempt to domesticate the species. Since that time several key domestication genes have been incorporated to enable the species to be grown as a crop over a range of climates, harvested as a bulk commodity and, the seed used for both animal and human consumption. However, the recent domestication of this species has seen a rather limited use of wild germplasm largely as a result of the difficulty in retaining these key domestication genes. To make the task of retaining these genes manageable, it was decided to resort to molecular technology. A mapping population of F8 derived recombinant inbred lines (RILs) has previously been established by the Department of Agriculture and Food, Western Australia, from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin. The parents together with 89 RILs (of a population of 115) were subjected to DNA fingerprinting using microsatelliteanchored fragment length polymorphism (MFLP) to rapidly generate DNA markers for construction of a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 8 or more markers. ... Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use this data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula high-lighted. The work presented in this thesis demonstrates the importance of tight linkage between markers and genes of interest. It is especially important when dealing with genetically diverse material as found in the wild. One of the main problems faced by molecular scientists is the phenomenon known as linkage disequilibrium in marker populations caused by either small population size or 4 insufficient opportunity for recombination. This frequently results in the development of markers with little or no application outside of the population in which it was developed. Although the relatively small size of the population used in this study exposes it to such constraints, in this case excellent and valuable results were achieved in developing useful markers to at least 3 of the domestication traits within a relatively short time period of less then 4 years.
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Rae, Stephen J. "Isolation and characterisation of simple sequence repeat markers for Beta vulgaris." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274669.
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Donati, Mauro. "Gene polymorphisms and related cell markers in periodontitis lesions /." Göteborg : Department of Periodontology, Institute of Odontology, The Sahlgrenska Academy at University of Gothenburg, 2009. http://hdl.handle.net/2077/20298.
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