This work deals with statistical tests of association between genetic markers and disease phenotypes. The main criterion used for comparing the tests is statistical power. First we consider animal models and then data from association studies of humans. For the animal section, we analyse a dataset from a prominent mouse experiment which developed a heterogeneous stock of mice via multiple crosses. This stock is characterised by small distances between recombinants which allows fine mapping of genetic loci, but also by uncertainty in haplotypes. We start by highlighting the disadvantages of the currently used approach to deal with this uncertainty and suggest a method that has greater statistical power and is computationally efficient. The method applies the EM algorithm to the broad class of exponential family distributions of phenotypes. We also develop a Bayesian version of the method, for which we extend the widely used IRLS algorithm to maximisation of the weighted posterior. Then we move on to genome-wide association studies (GWAS), where two situations are considered: known and unknown minor allele frequency. First we develop an innovative Bayesian model with the optimal prior for the known population MAF. We demonstrate that not only it is more powerful than any frequentist test considered (the size of the advantage depends on prevalence of the disease and MAF), but also that the frequentist tests change ranking in terms of power. A remarkable property of the frequentist tests, the advantage of discarding part of the data to gain power, is highlighted. The second chapter on GWAS considers the currently more common situation of the unknown MAF, when the Armitage test is known to be the most powerful frequentist method. We show that the suggested model is more powerful in the broad selection of settings considered, including the three different allele effect models: additive, dominant and recessive. For both known and unknown MAF cases we point out that the parameters are constrained and demonstrate how to gain power by taking this constraint into account.

Made available in DSpace on 2014-06-11T19:26:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-02-20Bitstream added on 2014-06-13T19:33:13Z : No. of bitstreams: 1 000749021.pdf: 7313633 bytes, checksum: dc4dc6a1a08c8f19e48f5fd99e1e3305 (MD5) / Complexos de espécies crípticas são grupos de espécies estreitamente relacionadas, dificilmente distinguíveis por características morfológicas. Estes complexos são conhecidos em uma significativa variedade de organismos, principalmente plantas, insetos, fungos e peixes. Em peixes, complexos de espécies já foram identificados para representantes de diferentes ordens, como Characiformes, Gymnotiformes e Synbranchiformes. No presente estudo, foram analisadas amostras de S. marmoratus coletadas em oito localidades brasileiras distintas com o uso de técnicas citogenéticas clássicas (coloração convencional com Giemsa, localização das regiões organizadoras de nucléolo pela marcação com nitrato de Prata – AgNO3 e bandamento C) e moleculares (hibridação in situ fluorescente com sondas de DNAr 5S e 18S, DNAhis H3, elemento transponível Rex3 e sondas teloméricas). Além disso, análises moleculares foram realizadas utilizando dados de sequências de três genes mitocondriais (Citocromo B - CytB, Citocromo oxidase 1 - COI e DNAr 16S) de indivíduos com cariótipo conhecido. Considerando as amostras analisadas, números diploides distintos foram encontrados (42, 44 e 46 cromossomos) que, combinados com as fórmulas cariotípicas, resultam na distinção de cinco cariomorfos em S. marmoratus. A análise filogenética realizada confirma o status de complexo de espécies e revela que eventos múltiplos, possivelmente bidirecionais, seriam responsáveis pelo surgimento da variabilidade cariotípica neste grupo. O mapeamento físico do DNAr 5S revela que estes sítios se mantiveram conservados durante a história evolutiva de Synbranchus, enquanto que, de forma oposta, os sítios para DNAr 18S estão distribuídos de maneira polimórfica, com variações intrapopulacionais significativas, indicando que mecanismos evolutivos distintos estão agindo sobre a dispersão destas sequências. O mapeamento de... / Cryptic species complex are groups of species straightly related but hardly distinguished by morphological traits. These complexes are known to occur in a great variety of organisms, mainly plants, insects, yeasts and also fishes. Considering the fish group, species complex had already been identified in representatives from different orders, such as Characiformes, Gymnotiformes e Synbranchiformes. In the present study, samples of S. marmoratus collected at eight different Brazilian sites were analyzed, using classical cytogenetic techniques (conventional staining with Giemsa, localization of nucleolar organizer regions with Silver nitrate staining - AgNO3 and C-banding) and molecular (Fluorescence in situ hybridization with 5S and 18S rDNA, H3 DNAhis, transposable element Rex3 and telomeric probes). Besides that, molecular analyses were carried out using sequence data from three mitochondrial genes (Cytochrome B – CytB, Cytochrome oxidase 1 – COI and 16S) obtained for each individual with known karyotype. Considering the analyzed samples, distinct diploid numbers were found (42, 44 and 46 chromosomes) and, associated with karyotype formulae, resulted in the distinction of five karyomorphs in S. marmoratus. The phylogenetic analyses confirmed the status of a species complex and revealed that multiple and, possibly bidirectional events were responsible the karyotypic variability found in this group. The physical mapping of 5S rDNA reveals that these sites kept conserved during the evolutionary history of Synbranchus, contrary to 18S rDNA sites which are distributed in a polymorphic way, with sigficant intrapopulational variability, indicating that distinct evolutionary mechanisms may be acting upon the dispersion of these sequences. The mapping of H3 hisDNA revealed a dispersed pattern of distribution of these sites on the genome of all karyomorphs, frequently found as little clusters accumulated ...

Orientador: Maria Elisabete Jorge Amaral / Coorientador: Nedenia Bonvino Stafuzza / Banca: Paola Jocelan Scarin Provazzi / Banca: Luciane Madureira de Almeida / Resumo: As β-defensinas são as proteínas mais amplamente estudadas dentre as três subfamílias das defensinas, uma vez que possuem extensa atividade antimicrobiana e são produzidas por vários tipos de células epiteliais, fornecendo assim proteção às membranas das células do hospedeiro. Em mamíferos, além de sua atividade antimicrobiana, essas proteínas atuam na maturação do espermatozoide, na capacitação espermática, na proteção do espermatozoide contra a resposta imune da fêmea e na expressão diferenciada e específica nos tecidos reprodutivos, sugerindo assim, uma importante função na reprodução e na fertilidade. O painel de linhagens celulares híbridas irradiadas (painel RH) construído para o genoma do búfalo (BBURH5000) vem sendo utilizado com sucesso nos estudos de mapeamento dos cromossomos bubalinos. A estratégia do mapeamento RH, ou seja, a utilização do painel RH associado a análises estatísticas, determina a ordem linear de marcadores nos cromossomos, sendo uma importante ferramenta para a construção de mapas físicos de alta resolução do genoma, e também na construção de mapas comparativos entre espécies. O presente trabalho teve por objetivo utilizar o painel BBURH5000 para mapear um conjunto de genes das β-defensinas no cromossomo 14 bubalino (BBU14) e a construção de um mapa comparativo in silico entre o BBU14 e seu homólogo em bovino. Para tal, foram testados com DNA bubalino, sequências de iniciadores para PCR provenientes de oito genes das β-defensinas, localizados no cromossomo 13 bovino (BTA13), o qual é homólogo ao BBU14. Do total de marcadores testados, seis amplificaram produtos de PCR adequados ao mapeamento utilizando o painel BBURH5000. No entanto, dois marcadores foram excluídos na etapa de genotipagem. A frequência de retenção dos marcadores no painel apresentou uma variação de 16,66% com o marcador BBD125 a 20,00% com ... / Abstract: The β-defensins are proteins most widely studied of the three subfamilies of defensins, because have extensive antimicrobial activity and are produced by several types of epithelial cells, thereby providing protection to the membranes of host cells. In mammals, in addition to their antimicrobial activity, these proteins act in the maturation of spermatozoa, in sperm capacitation, in protecting the sperm against the female immune response and specific and differential expression in reproductive tissues, thus suggesting an important role in reproduction and fertility. The radiation hybrid panel (RH panel) constructed for buffalo genome (BBURH5000) has been successfully used in mapping studies of buffalo chromosomes. The RH mapping strategy, in other words, use of RH panel associated statistical analysis, determines the linear order of markers on chromosomes and is an important tool for the construction of physical maps of high resolution genome and also in the construction of comparative maps between species. The present study has the purpose to use the BBURH5000 panel to map a set of β-defensins genes on buffalo chromosome 14 and the construction of a comparative map in silico between BBU14 and homologous bovine. To this end, we tested buffalo DNA sequences of primers for PCR from eight genes of β-defensins, located on bovine chromosome 13 (BTA13), which is homologous to BBU14. Of the markers tested, six amplified suitable PCR product to the mapping using BBURH5000 panel. However, two markers were excluded in step genotyping. The retention frequency of markers on the panel presented a variation of 16.66% with a marker BBD125 to 20.00% with markers BBD119 and BBD122. The comparative analysis in silico between the BBU14 RH map and the sequence map of BTA13 allowed to indicate the location of these markers on buffalo chromosome 14 / Mestre

Primary angle closure glaucoma (PACG) is a chronic optic neuropathy that results in retinal ganglion cell (RGC) degeneration, cupping of the optic nerve head (ONH) and subsequent loss of vision. In humans, PACG occurs as a result of a plateau iris or more commonly, a pupillary block. Increased Intraocular pressure and reduced axial length are some of the predisposing factors to PACG. The condition occurs in several breeds of dogs and the prognosis for affected animals is typically poor. Unlike PACG in humans, the mechanism of PACG in canines involves the gradual collapse of the ciliary cleft with or without complete collapse of the irido-corneal angle. We have identified and examined several Basset Hound (BH) pedigrees with clinically confirmed PACG that segregates in an autosomal recessive manner. The goal of this proposal is to utilize the Basset Hound PACG model in order to characterize the genetics of PACG. In addition to investigating the underlying genetic mechanisms of PACG, a series of functional studies aimed at improving our understanding of the pathophysiology of PACG, were also performed to investigate the disease. Extensive clinical phenotyping of all pedigree members was conducted by a veterinary ophthalmologist. We performed a genome-wide logistic regression test for association using 37 PACG cases and 41 unaffected controls. Population stratification and cryptic relatedness were assessed using a multidimensional scaling analysis. The expression of two candidate genes within the target tissues of the Basset Hound eye was assessed by immunohistochemistry. SNP-chip genotyping was additionally conducted in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1. Targeted exome capture was performed using the Agilent SureSelect exon kit. A primary fibroblast cell culture was established from the sclera of three PACG, two wild type and two obligatory carrier Bassets. Total RNA extracted from fibroblast cells was assayed using the Affymetrix GeneChip Canine Genome 2.0 Array. The Robust Multichip Average expression summary method was used for background adjustment and normalization. A two class, unpaired, Wilcoxon statistical test was conducted to identify differentially expressed genes. qRT-PCR was performed to validate significantly expressed genes. Furthermore, a primary fibroblast cell culture was established from the skin of a PACG and an obligatory carrier BH. Microscope images and cell counts from all cell cultures were established at various time points. Our findings reveal significant associations at two novel loci: BICF2P31912 in COL1A2 on chromosome 14 with a per-allele odds ratio OR(95% CI) 8.95(1.73-6.51); Pgenome = 3.6 x 10-4 and BICF2P893476 residing in proximity to RAB22A on chromosome 24 with a per-allele odds ratio OR(95% CI) = 12.03(1.78-8.66); Pgenome = 4.9 x 10-4. COL1A2 and RAB22A demonstrated wide-spread localization throughout the eye and were prominently noted in the ciliary body, trabecular meshwork and iris. A 1.82Mbp locus was additionally mapped to chromosome 19 with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and shares synteny to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, nonsynonymous variant was found to segregate with PACG in the gene Nebulin (NEB) (g.55885214 A->G, p.2051 K->R), which alters a conserved Lysine. Nebulin, a protein that promotes the contractile function of sarcomeres was found to be prominently expressed in the ciliary muscles of the anterior segment. Primary scleral fibroblast cells derived from PACG animals were found to exhibit severely reduced growth rates when compared to wild type derived cells. Genes with sharply reduced expression levels are of particular interest due to the possible involvement of a loss of- function mutation in PACG. More than 600 genes were found to be significantly under expressed in PACG derived cells. In contrast to unaffected-derived cell, PACG derived cells display significantly altered gene expression patterns for a number of possibly important candidate genes. Furthermore, PACG derived cells display aberrant and reduced motility in PACG versus wild type derived cell cultures. The identification of two genetic associations supports the potential segregation of PACG risk-conferring variants in the Basset Hound. The genetic associations identified may contribute to mechanisms underlying the pathogenesis of PACG, which remain to be elucidated. Moreover, our studies provide the first evidence of a gene directly linked to PACG in the Basset Hound. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG. The findings of our functional studies suggest that cellular dysfunction is an important aspect in the pathophysiology of PACG in the dog. The identification of genes with significantly altered expression levels may provide insight into the molecular pathways associated with the development of the disease and aid in the identification of the genetic defect underlying PACG.

Recent studies show polymorphisms in the leptin gene significantly impact milk production in dairy cattle. If the leptin gene were to have a similar impact on beef cattle, calf weaning weights would be expected to increase from the increased milk production in the cows. Since weaning weight is a key component of profitability in a cow-calf operation, leptin genotyping may prove to have an economic impact in breeding cattle. However, no research has been done to link the economic impact of increased milk production to breeding cattle. Using 595 observations from genotyped cows spanning 11 years (1995-2005), calf weaning weight by genotype is estimated as a function of calf and dam characteristics and environmental effects. A MIXED procedure, utilizing data from 89 culled cows, is used to determine statistical differences in average cull age by genotype. A simulation model calculates mean annualized equivalent return by genotype and breed using the regression coefficients and residuals and 16 years of price data. results show that at least one T-allele in breeding cows increases calf weaning weight, average cull age, and annualized equivalent return compared to cows with homozygous C-alleles. These results indicate that there may be future premiums and discounts for breeding cattle based on genotype. Seedstock producers could potentially begin to segregate herds based upon genotype so that they could sell genotypic registered products. Cow-calf producers may also benefit from this knowledge by increasing the amount of TT genotype breeding cattle in their herd to maximize profits.

Orientador: Fausto Foresti / Resumo: Cromossomos B são componentes aparentemente dispensáveis encontrados nos genomas de inúmeras espécies, compostos basicamente de sequências repetitivas de DNA. Dentre uma variedade de questões a respeito destes elementos, a busca pelo conhecimento de sua origem tem sido amplamente estudada. Em peixes, a ocorrência destes cromossomos foi relatada em cerca de 60 espécies, incluindo espécies do gênero Characidium, no qual estes elementos aparentam não ter uma origem única. Com o objetivo de investigar a origem e conteúdo molecular dos cromossomos B em Characidium, nós analisamos duas espécies, Characidium gomesi e Characidium alipioi, portadoras de cromossomos B, utilizando a combinação de técnicas citogenéticas moleculares, análises de sequências e sequenciamento massivo. Nossos resultados mostraram que i) em ambas as espécies os Bs tiveram origem intraespecífica, no entanto, em C. alipioi se originaram de forma independente em relação aos Bs de outras duas espécies do gênero, assim, não compartilham os mesmos cromossomos ancestrais; ii) em C. gomesi as duas variantes compartilham DNA repetitivos, sendo cinco distribuídos nos cromossomos A, B e ZW, e um restrito aos cromossomos B e ZW, confirmando a origem dos Bs a partir dos cromossomos sexuais; iii) os supranumerários em C. alipioi provavelmente surgiram a partir do par de cromossomos autossômicos submetacêntrico 19; iv) Bs em C. alipioi se tornaram um cenário propício para acumulação de DNAs repetitivos após seu surgimento... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: B chromosomes are apparently dispensable components found in the genomes of many species, mainly composed of repetitive DNA sequences. These elements have been reported in approximately 60 fish species, including the genus Characidium, in which these elements do not appear to have a single origin. In order to investigate the origin and molecular content of B chromosomes in Characidium, we analyzed two species bearing B chromosomes, Characidium gomesi and Characidium alipioi, using a combination of molecular cytogenetic techniques, DNA sequence analysis and massive sequencing. Our results showed that i) the B chromosomes of both species had an intraspecific origin, but from different chromosomes; ii) the two B-variants of C. gomesi share the same repetitive DNA sequences, five distributed on the elements of the A set, and on B and ZW chromosomes, and one restricted to B and ZW chromosomes, reforcing its origin from the sex chromosomes; iii) the supernumerary in C. alipioi probably arose from the chromosomes of the submetacentric pair 19; iv) B chromosomes in C. alipioi became a conducive setting for repetitive DNAs accumulation after its emergence; v) the sequence of H3 histone gene isolated from the chromosomes of the A set and B chromosomes of C. gomesi presented identical aminoacid sequences and the rates of dN/dS were lower for those from the B genome, suggesting the action of a positive selection and possible transcription of the supernumerary copies. The results reveals the importance of multiple approaches of chromosomal and molecular methods to understand issues related to evolutionary biology of supernumerary chromosomes, once allowed to increase knowledge about the structure, composition and origin of B chromosomes in representatives of the genus Characidium. These observations reinforce the proposition of this fish group as an interesting model for studies on the origin and... (Complete abstract click electronic access below) / Doutor

The human genome contains ~1.5% coding sequence, with the remaining 98.5% being non-coding. The functional potential of the majority of this non-coding sequence remains unknown. Much of this non-coding sequence is derived from transposable element (TE) sequences. These TE sequences contain their own regulatory information, e.g. promoter and transcription factor binding sites. Given the large number of these sequences, over 4 million in the human genome, it would be expected that the regulatory information that they contain would affect the expression of nearby genes. This dissertation describes research that characterizes that alternation of and contribution to the human transcriptome by non-coding elements, including TE sequences.

Seven years into the postgenomic era, we sit atop a mountain of data whose generation was enabled by gene sequencing. The creation, integration, and analysis of these large scale data sets allow us to move forward toward the complementary goals of determining the individual roles of the thousands of uncharacterized mammalian genes and understanding how they work together to produce a healthy human being -- or, perhaps more importantly, how their malfunction results in disease. Collapsing the results of large-scale assays into gene networks provides a useful framework from which we can glean information that advances both of these goals. However, the utility of networks is limited by the quality of the data that goes into them. This study offers seeks to shed some light on the quality and breadth of protein interaction networks, describes a new experimental technique for functional genetic assays in mammalian cell lines, and ultimately suggests a strategy for how to improve the overall utility of the output generated by the systems biology community. / text

Hepatitis C virus is a pathogen causing severe hepatic diseases. Though HCV genotype 6a circulated prevalently in Hong Kong, its sequence information is greatly in deficient. The molecular characteristics and epidemiology of HCV 6a were thus extensively investigated in this thesis. The distribution of HCV genotypes in Hong Kong was analyzed from 1055 samples by the Ohno's method. HCV 6a accounted for 23.6% HCV infections in the general population and 58.5% in the injecting drug-users. It is prevalent in Hong Kong, associated with younger age, injecting drug-user status and the male gender. Fourteen independent HCV 6a isolates were sequenced for their full-genomes. They share a sequence homology of 94.5% between each other. HCV 6a had undergone high frequency of recombination. Four (28.5%) of 14 isolates were found having recombination with other strains in different genomic regions. Evolutionary pressure on HCV 6a genomes was analyzed by evaluating dS/dN ratio. NS4A, NS4B and NS3 showed higher dS/dN ratios (16.94-29.30) indicating a purification effect, whilst NS2, E2 and p7 showed lower dS/dN ratios (2.35-7.33) indicating a positive selection effect. This pattern of evolutionary pressure distribution alongside genomic regions was similar to the observations in HCV 1b. However HCV 6a eISDR experienced less extent of positive selection than HCV 1b eISDR (dS/dN = 12.82 vs 4.96) did. Evolutionary history of HCV 6a was inferred by Bayesian coalescent analysis. Twenty-six heterochronic, 513-bp HCV 6a partial-NS5A sequences and 63 HCV 1b sequences were analyzed. The time of exponential growth of HCV 6a in Hong Kong was postulated as during 1986 to 1994, overlaps with the time 1987 to 1997 when the second Vietnamese Boat People influx event occurred. Rooted phylogenetic analysis showed that Vietnamese HCV 6a strains were ancestors of the Hong Kong strains. Hence, a hypothesis was raised that HCV 6a outbreak in Hong Kong may be related to the Vietnamese Boat People influx event. The sequence variations within the eISDR of HCV 6a and HCV 1b were explored for correlation with the outcome of IFN-alpha/ribavirin combination treatment. Twenty-five HCV 6a patients and 37 HCV 1b patients were recruited. Three amino acid variations I2160V, V2256I, and I2292V were significantly correlated with the treatment outcome (P < 0.05) for HCV 6a. Three variations R2260H, V2268I and S2278T (P = 0.023-0.076) were weakly correlated with the outcome for HCV 1b. None of correlated variations located within the previously defined ISDR. These pieces of information can be helpful for predicting the outcome before the commencement of treatment. / Zhou Xiaoming. / "May 2006." / Adviser: Paul K. S. Chan. / Source: Dissertation Abstracts International, Volume: 69-01, Section: B, page: 0207. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 178-186). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Thesis (PhD (Agric)) -- Stellenbosch University, 2001. / ENGLISH ABSTRACT: Chromosome arm 7DL of common wheat carries genes for agronomically important traits such as leaf rust, stem rust, Russian wheat aphid and eye spot resistance. Some of these genes occur on introgressed foreign chromatin, which restricts their utility in breeding. The 7DL genetic maps are poorly resolved, which seriously hampers attempts to manipulate the genes and introgressed regions in breeding. This dissertation represents an attempt to improve our knowledge of the relative map positions of three resistance genes that have significant potential for use in local breeding programmes. The leaf rust resistance gene, Lr19, is located on a Thinopyrum ponticum-derived translocation which occupies a large part of the terminal end of 7DL. The translocation also carries genes for less favourable traits such as yellow flour colour. Attempts have been made to reduce the size of the translocation through allosyndetic pairing induction; the primary aims being to remove deleterious genes and to minimise the amount of foreign chromatin associated with Lr19 so it can be recombined with other useful 7DL genes. Twenty-nine 'Indis'-derived Lr 19 deletion mutants were previously produced by gamma irradiation and a physical map was constructed. In this study, the set of mutant lines were further analysed using 144 Sse8387I/Msei and 32 EcoRI/Msel amplified fragment length polymorphism (AFLP) primer combinations. The previous physical map, which was based on five restriction fragment length polymorphism (RFLP) markers and five structural gene loci, was extended and now includes 95 novel AFLP markers (86 Sse8387I/Msei and 9EcoRI!Msel markers), of which seven map close to Lr 19. Most of the deletions could be ordered according to size and the improved map has already been used to characterise shortened recombinant forms of the Lr 19 translocation. An unsuccessful attempt was made to convert one of the seven markers closest to Lr 19 into a sequence-specific marker. However, an AFLP marker located distally from Lr 19 was successfully converted into a sequence-specific marker in collaboration with other researchers. An attempt was also made to map and tag the Russian wheat aphid (RWA) resistance gene, Dn5. A doubled haploid mapping population consisting of 94 lines was created and typed for Dn5, four microsatellite loci and the endopeptidase locus, Ep-Dl. The Dn5 locus mapped 25.4 cM and 28.6 cM distally from Xg.vm111 and Xg.vm437, respectively, but was not linked to Xgwm428, Xgwm3 7 or Ep-Dl. Tagging of Dn5 was attempted by screening twelve homozygous resistant and seven homozygous susceptible F2 lines from a cross between 'Chinese Spring' and 'PI 294994' with 70 Sse8387IIi\1sei AFLP primer combinations. Only two potentially useful polymorphisms (one in coupling and one in repulsion phase) were identified. Conversion of the coupling phase marker to a sequence-specific marker was not successful. The eyespot resistance gene, Pchl , was derived from Triticum ventricosum and is present in the wheat VPM-1. Close association between Pchl and the endopeptidase Ep-Dlb allele has been reported previously. Pchl/Ep-Dl was tagged by screening ten wheat genotypes (each homozygous for the confirmed presence or absence of Pchl and/or Ep-Dl b) with 36 Sse83 87I/ Msei AFLP primer combinations. Three AFLP markers were closely associated with Pchl I Ep-D 1, one of which was targeted for conversion into a sequence-specific marker. The sequence-specific marker contained a microsatellite core motif and was found to be useful for tagging Pchl!Ep-Dl. A genetic distance of 2 cM was calculated between the novel microsatellite marker and Ep-Dl. The microsatellite marker was also polymorphic for the Lr 19 translocation and it was possible to map it between the Wsp-Dl and Sr25 loci. In this dissertation, mapping and/or tagging of three important resistance genes were achieved. Due to the fact that all markers used in these studies were not polymorphic between all of the targeted regions, it was not possible to fully integrate the data obtained for the three regions. / AFRIKAANSE OPSOMMING: Chromosoom arm 7DL van broodkoring dra gene vir agronomies-belangrike kenrnerke soos blaarroes, stamroes, Russiese koringluis en oogvlek weerstand. Sommige van hierdie gene kom voor in blokke spesie-verhaalde chromatien wat hul bruikbaarheid in teling beperk. Die genetiese kaarte van 7DL is swak ontwikkel en dit maak dit baie moeilik om hierdie gene en spesie-verhaalde streke tydens teling te manipuleer. Hierdie proefskrif verteenwoordig 'n paging om kennis van die relatiewe kaart liggings van drie weerstandsgene, met betekenisvolle potensiaal in plaaslike tee! programme, te verbreed. Die blaarroes weerstandsgeen, Lr 19, kom voor op 'n Thinopyrum ponticum-verhaalde translokasie wat 'n groot terminale gedeelte van 7DL beslaan. Die translokasie dra ook gene vir minder gewensde kenrnerke soos gee! meelkleur. Pogings is aangewend om die translokasie deur homoeoloe parings-induksie te verkort. Die doe! was om nadelige gene te verplaas en die hoeveelheid vreemde chromatien geassosieer met Lr 19 te minimiseer sodat dit met ander nuttige gene op 7DL gerekombineer kan word. Nege-en-twintig 'Indis'-verhaalde Lr 19 delesie mutante is vroeer met gamma bestraling geproduseer en gebruik om 'n fisiese kaart op te stel. Teenswoordig is die stel mutante verder ontleed met behulp van 144 Sse8387I!Msei en 32 EcoRII Msel amplifikasie-fragment-lengte-polimorfisme (AFLP) inleier kombinasies. Die bestaande fisiese kaart, wat gebaseer was op vyf restriksie-fragment-lengte-polimorfisme (RFLP) merkers en vyf strukturele geen loki, is uitgebrei en sluit nou 95 unieke AFLP merkers (86 Sse8387I/Msel en 9EcoRI/Msel merkers) in, waarvan sewe naby aan Lr19 karteer. Die meeste van die delesies kon op grond van hulle grootte gegroepeer word en die verbeterde fisiese kaart is alreeds gebruik om verkorte rekombinante vorms van die Lr 19 translokasie te karakteriseer. 'n Onsuksesvolle paging is aangewend om een van die sewe merkers naaste aan Lr 19 om te skakel na 'n volgorde-spesifieke merker. 'n AFLP merker wat distaal van Lr 19 karteer is egter wel suksesvol in samewerking met ander navorsers omgeskakel na 'n volgordespesifieke merker. 'n Paging is ook aangewend om die Russiese koringluis (RKL) weerstandsgeen, Dn5, te karteer en merkers gekoppel aan die geen te identifiseer. 'n Verdubbelde-haplo!ede karteringspopulasie van 94 lyne is geskep en getipeer vir Dn5, vier mikrosatelliet loki en die endopeptidase lokus, Ep-D1. Die Dn5 lokus karteer 25.4 cM en 28.6 cM distaal van Xgwml11 en Xgwm437, respektiewelik, maar was me gekoppel met Xgwm428, Xgwm37 of Ep-D1 me. Twaalf homosigoties weerstandbiedende en sewe homosigoties vatbare F2 lyne uit die kruising: 'Chinese Spring' I 'PI 294994' is met 70 Sse8387VMsel AFLP inleier kombinasies getoets in 'n poging om merkers vir Dn5 te identifiseer. Slegs twee moontlik bruikbare polimorfismes (een in koppelings- en een in repulsie fase ), is ge'identifiseer. Omskakeling van die koppelingsfase merker na 'n volgorde-spesifieke merker was onsuksesvol. Die oogvlek weerstandsgeen, Pch1, is uit Triticum ventricosum oorgedra en kom voor in die koringlyn, VPM-1. Noue koppeling van Pch1 en die endopeptidase alleel, Ep-D1 b, is vantevore gerapporteer. Merkers is vir P chl I Ep-D 1 gevind deur tien koring genoti pes ( elkeen homosigoties vir die bevestigde teenwoordigheid of afwesigheid van Pch1 en/of Ep-D1 b) te toets met 36 Sse83871/kfsel AFLP inleier kombinasies. Drie AFLP merkers is gevind wat nou koppel met Pchl!Ep-D1 , waarvan een gekies is vir omskakeling na 'n volgorde-spesifieke merker. Die volgorde-spesifieke merker het 'n mikrosatelliet kernmotief bevat en was nuttig as merker vir Pch1/Ep-D1. 'n Genetiese afstand van 2 cM is tussen die unieke mikrosatelliet merker en Ep-D1 bereken. Die mikrosatelliet merker was ook polimorfies vir die Lr 19 translokasie en dit is tussen die Wsp-D1 en Sr25 loki gekarteer. Kartering en/of identifikasie van merkers vir drie belangrike weerstandsgene was suksesvol in hierdie studie. Omdat al die merkers wat gebruik is, nie polimorf was tussen al die streke van belang nie, was dit nie moontlik om die data vir elk van die drie streke ten volle te integreer nie.