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Pita, Fabiano Veraldo da Costa. "Construction of the gametic covariance matrix for quantitative trait loci analyses in outbred populations." Universidade Federal de Viçosa, 2003. http://www.locus.ufv.br/handle/123456789/10501.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
A aplicação de análises de “Quantitative Trait Loci” (QTL) em populações exogâmicas é desafiadora porque pressuposições simplificadoras não podem ser aplicadas (por exemplo, os alelos QTL não podem ser assumidos fixados em diferentes famílias, o número de alelos QTL segregantes não é conhecido a priori, não há desequilíbrio de ligação entre um dado alelo marcador e um dado alelo QTL). Quando o efeito genotípico do QTL é assumido aleatório no modelo de análise, a matriz de covariância gamética deve ser calculada para a realização das análises em populações exogâmicas. A acurácia dessa matriz é importante para a obtenção de estimativas confiáveis da posição ou efeito do QTL em análises de mapeamento, ou de valores genotípicos em avaliação genética assistida por marcadores. O objetivo do primeiro estudo foi avaliar diferente estratégias já implementadas em programas computacionais (SO- LAR, LOKI, ESIP e MATVEC) para calcular a matriz de coeficientes Idênticos por Descendência (IBD), que é necessária para o mapeamento de QTL em populações exogâmicas. SOLAR utiliza um método baseado em regressão linear, LOKI e ESIP são ambos baseados em “reverse peeling” e o amostrador implementado em MAT VEC amostra indicadores de segregação. Um pedigree com estrutura F2 típica foi simulado com uma família F2 pequena (2 indivíduos) ou grande (20 indivíduos) e marcadores flanqueadores localizados a 2 cM, 5 cM ou 10 cM de distância um do outro, com o QTL localizado no meio do intervalo. A habilidade dessas estratégias em lidar com informações de marcadores perdidas foi avaliada assumindo um dos pais da geração F2 com ou sem informação de marcador. SOLAR nao estimou os coeficientes IBD corretamente para a maior parte das situações simuladas, enquanto que LOKI apre- sentou problemas quando o tamanho da família F2 era grande. ESIP e o amostrador em MATVEC apresentaram bom desempenho em todas as situacões simuladas, com estimativas de coeficientes IBD próximas aos coeficientes verdadeiros. Portanto, ESIP e MATVEC são os softwares mais indicados quando analises genéticas são realizadas em pedigrees com estruturas complexas. O objetivo do segundo estudo foi avaliar o efeito da utilização de uma melhor aproximação da inversa da matriz de covariância gamética para a avaliação genética de grandes populações de animais domésticos. Algoritmos eficientes, baseados no rastreamento dos alelos QTL de um indivíduo em relação aos de seus avós (Probabilidade de Descendência de um QTL - PDQ), podem ser usados para construir a inversa da matriz de covariância gamética diretamente. Mas essa inversa é uma aproximação quando há informação incompleta de marcador. Também, o calculo exato de PDQºs torna-se difícil quando a informação de marcador é incompleta. Nesse estudo, a inversa da matriz de covariãncia gamética para uma pop- ulação exogãmica simulada foi calculada usando o algoritmo eficiente, mas as PDQ's foram calculadas usando um algoritmo Monte Carlo Cadeia de Markov (MCMC). Essa inversa foi utilizada para predizer o valor genético dos indivíduos através de BLUP assistido por marcadores (MABLUP). O efeito dos cálculos de PDQ usando o algoritmo MCMC sobre a acurãcia da MABLUP foi avaliado com base na resposta a seleção realizada, calculada para o pedigree simulado. Os resultados mostraram que quando as PDQ’S foram estimadas usando MCMC a perda em resposta devido ao uso da inversa aproximada pode ser reduzida em aproximadamente 20%, enquanto que em estudos anteriores essa redução foi de 50%. Ainda, quando quatro marcadores bi-alélicos foram utilizados a resposta para MABLUP foi maior e a perda em re- sposta devido a marcadores com informação perdida foi menor, quando comparadas a situação onde apenas dois marcadores bi-alélicos foram utilizados.
The application of Quantitative Trait Loci (QTL) analyses in outbred population is challenging because simplified assumptions do not hold for these populations (e.g., the QTL alleles cannot be assumed fixed in different families, the number of QTL alleles segregating is not known a priori, there is not gametic phase disequilibrium between a given genetic marker allele and a QTL allele). When the QTL genotypic effect is assumed random, the gametic covariance matrix must be calculated to per- form QTL analyses in outbred populations. The accuracy of this matrix is important to obtain reliable estimates of QTL position or effect when applying QTL mapping, or QTL genotypic values when applying Marker Assisted Genetic Evaluation. The objective of the first study was to evaluate the different strategies already imple- mented in softwares (SOLAR, LOKI, ESIP and MATVEC) to calculate the matrix of identical by descent (IBD) coefficients, which is required for QTL mapping anal- ysis in outbred populations. SOLAR uses a regression method, LOKI and ESIP are both based on reverse peeling, and the MAT VEC sampler samples segregation in- dicators. A typical F2 pedigree was simulated with a small (2 offspring) or a large (20 offspring) F2 family, and the flanking markers were simulated 2 CM, 5 CM, or 10 CM apart, with the QTL located in the middle. The ability of these strategies to deal with missing genetic marker information was evaluated assuming one of the F2 parents with or without marker information. SOLAR failed to estimate the correct coefficients at almost all situations simulated, while LOKI showed problems when a large family was present in the pedigree. ESIP and MATVEC sampler performed well at all situations, providing IBD coefficients closed to the true ones. Therefore, ESIP and MATVEC are more indicated when genetic analysis are carried out on complex pedigree structures. The objective of the second study was to evaluate the effect of using a better approximation of the inverse of the gametic covariance matrix on the genetic evaluation of large livestock populations. Efficient algorithms, based on trac- ing the QTL alleles of an individual to its grandmother or grandfather (probability of descent a QTL - PDQ’s), can be used to construct the inverse of the gametic covari- ance matrix directly. But this inverse is an approximation when incomplete marker information is available. Also, computing the exact PDQ’s becomes difficult when marker information is incomplete. In this study, the inverse of the gametic covariance matrix for a simulated outbred pedigree was calculated using the efficient algorithm, but the PDQ’s were calculated using a Markov chain Monte Carlo (MCMC) algo- rithm. This inverse was used to calculate the predicted genetic value of individuals through Marker Assisted Best Linear Unbiased Prediction (MABLUP). The effect of PDQ calculations using the MCMC algorithm on MABLUP accuracy was evaluated based on the realized response to selection for the simulated pedigree. The results showed that by estimating the PDQ’s by MCMC the loss in response because of using an approximate inverse could be reduced to about 20%, while in previous studies this reduction was of 50%. Further, response to MABLUP was greater when four bi-allelic markers were used, and the loss in response due to missing markers was smaller in the case with four markers compared to when only two bi-allelic markers were used.
Tese importada do Alexandria
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Masri, Amer. "Use of quantitative trait loci (QTL) affecting muscling in sheep for breeding." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/9526.
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Breeding programmes that use elite sires with the best estimated breeding values for muscling traits have achieved significant improvement in lamb production in the UK. Further acceleration of the rate of genetic gain for the desirable production traits could be achieved using DNA marker-assisted selection (MAS) breeding strategies. The underlying causal genetic variants associated with improved muscling may be unknown and lying between a cluster of genes known as quantitative trait loci (QTL) or could be single nucleotide polymorphisms (SNP). LoinMAXTM, Texel muscling QTL (TM-QTL) and c.*1232G > A myostatin mutation were genetic variants that reported to be associated with improved muscling characteristics and hence subjected to further analysis in this project. It is essential before incorporating segregating genetic variants in any breeding scheme to comprehensively evaluate their effects on carcass traits. In-vivo scanning (ultrasound scanning (US) and computed tomography scanning (CT)), and carcass video image analyses (VIA) were used in the current studies. Objective VIAprediction weights of the carcass primal cuts could be the backbone of a value-based marketing system that is suggested to replace the current Meat and Livestock Commission (MLC) carcass grades for conformation scores (MLC-C) and fat class (MLC-F). The effect of a single copy of LoinMAXTM QTL (LM-QTL) compared to noncarriers was evaluated in UK crossbred lambs out of Scottish Mule ewes. M. longissimus lumborum (MLL) width, depth and area, as measured by CT scanning, were significantly greater in lambs heterozygous for LM-QTL compared to noncarriers. VIA detected a significant effect of the LM-QTL on the predicted weight of saleable meat yield in the loin primal cut (+2.2%; P < 0.05). The effects of the ovine c.*1232G > A myostatin mutation (MM), found on sheep chromosome 2, on carcass traits in heterozygous crossbred lambs sired by Texel and Poll Dorset rams were studied. Texel crossbred lambs carrying MM had increased loin depth and area. In both crossbred lambs, MM-carriers had significantly higher CT-estimated lean weight and proportion (2 to 4%) and muscle to bone ratios (by ~3%). Poll Dorset heterozygous crossbred animals had higher muscle to fat ratio (28%) and significantly lower fat-related measurements. The c.*1232G > A (MM) mutation as well as TM-QTL effects were evaluated in a different genetic background of Texel x Welsh Mountain crossbreed lambs. Carrying two copies of MM was associated with a significant positive effect on 8 week weight, a negative effect on ultrasound fat depth, a substantial decrease in MLC-fat score, positive impact on VIA-estimated weight of the hind leg, chump and loin primal cuts, as well as the muscularity of the hind leg and loin regions with greater loin muscle width, depth and area. Two copies of MM altered lambs‟ morphological traits with significantly wider carcasses across the shoulders, breast and hind legs and greater areas of the back view of the carcass when measured by VIA. TM-QTL significantly increased US-muscle depth and TM-QTL carriers had significantly greater loin muscle width and area measurements. Comparing TM-QTL genetic groups (homozygote allele carriers (TM/TM), heterozygote carriers of paternal and maternal origin of allele (TM/+ and +/TM, respectively) and homozygote non-carriers (+/+)) and TM-QTL mode of action were then studied. TM/TM carcasses were significantly heavier than non-carriers by 1.6 kg and scored higher conformation values when compared to heterozygote groups only. TM/+ lambs had significantly higher VIA-predicted weight and muscularity in the hind leg and loin, and higher loin dimensions relative to some other genotypic groups. The effect of TM-QTL on some carcass shape measurements was significant. TM-QTL mode of action results on the loin muscling traits supports the earlier reports of polar over dominance. In the light of growing calls to replace the current subjective carcass payment system with the objective VIA system that values the carcass according to the superiority of its cuts, I investigated the ability of US and CT measurements to predict the VIAestimated weights of the carcass primal cuts. Several prediction equations were examined but the best could be achieved when ultrasound measurement, CT linear measurements and live weight were fitted in the model. Since CT scanning information of elite sires is now being used for genetic selection for carcass merit, genetic parameters and genetic relationships between CT scanning measurements and post mortem traits (VIA and MLC-FC) were estimated. However, results were not sufficiently accurate to be of practical use due to lack of data.
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Poon, Fong-Yee. "Genetic architecture of neurogenesis in the adult mouse forebrain : insights from quantitative trait locus analyses." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50395.
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Neural stem cells and their precursors, collectively referred to as neural progenitor cells (NPCs), are present in discrete regions of the mature brain, namely the subgranular zone (SGZ) of the dentate gyrus, the subventricular zone (SVZ), and rostral migratory stream (RMS). These NPCs divide and give rise to new neurons in a process called adult neurogenesis. Genetic influence is a major determinant of adult neurogenesis. However, the genetic architecture underlying NPC proliferation and differentiation is poorly understood. My thesis aims to gain insights into the genes regulating NPC proliferation using a phenotypic-driven, genome-wide approach. I first examined nine inbred mouse strains housed in the same condition and across different ages from 60 days (P60) to 2 years. Wide inter-strain differences and negative impact of age on the number of NPCs were observed in the RMS. Genetic background had a significant effect on NPC proliferation and it also differentially influenced the effect of age on this process. The most dramatic inter-strain difference was detected at P60. Heritability estimated ~50% of the differences in NPC numbers were attributed to the genetic variation among the strains. I used quantitative trait locus (QTL) mapping to survey the entire genome for chromosomal segments referred to as QTLs that contribute to the phenotypic differences. Two panels of recombinant inbred strains, AXB/BXAs and BXDs, were employed for QTL mapping. Genetic variation in QTLs on chromosome (Chr) 6 and 11 were significantly associated with the differences in NPC numbers in the RMS. Additional analyses revealed potential interaction of Chr 6 QTL with other loci. These QTLs are hypothesized to harbor genes important for NPC proliferation and downstream experimentation is required to validate the function of these genes. As proof of concept, a candidate gene called Galanin receptor 2 (Galr2) in the Chr 11 QTL was demonstrated to be a pro-proliferative regulator of NPCs using in vitro techniques manipulating Galr2 expression and Galr2 knockout mice. In summary, I identified novel QTLs underlying NPC proliferation and these loci serve as starting points to identify genes (e.g. Galr2) critical to this process.Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Silva, Franklin Magnum de Oliveira. "Integrative analyses of photosynthesis, plant growth, metabolite levels and enzyme activities in an introgression line population of Solanum pennellii." Universidade Federal de Viçosa, 2016. http://www.locus.ufv.br/handle/123456789/21421.
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Fundação de Amparo à Pesquisa do Estado de MInas Gerais
Para identificar regiões genômicas envolvidas na regulação de processos fisiológicos fundamentais, como fotossíntese, respiração e aqueles relacionados, uma população de ILs de Solanum pennellii em fundo genético de S. lycopersicum (M82) foi analisada. Foram estudados parâmetros fisiológicos, metabólicos e de crescimento, que vão desde troca gasosa (por exemplo, taxa de assimilação de CO 2 e condutância estomática), fluorescência da clorofila (por exemplo, taxa de transporte de elétrons e de extinção fotoquímica), bem como parâmetros de crescimento (por exemplo, taxa de crescimento relativo, matéria seca da raiz e parte aérea). Em paralelo, nós também analisamos, por meio de uma plataforma robotizada, os principais intermediários metabólicos (por exemplo, açúcares, amido, nitrato, aminoácidos e proteínas), e a atividade de nove enzimas representativas do metabolismo central do C e N. O objetivo do estudo foi: (1) combinar informações sobre as atividades enzimáticas e os níveis de metabólitos de caule, pecíolo e folha com a biomassa e rendimento de frutos; (2) através do estudo desses três órgãos interligados, examinar o quanto há de conectividade entre a atividade das enzimas e os níveis de metabólitos; (3) fornecer informações preditivas sobre as diferenças de particionamento do C e assimilação N inorgânico; (4) investigar a diversidade genética natural e identificar QTLs relacionados ao metabolimo central e a atividade enzimática no caule, pecíolo e folha. As análises dos dados permitiram a identificação de 67 QTL relacionados à parametros fisiológicos e metabólicos. Além disso, uma anotação abrangente e detalhada destas regiões permitiu apontar um total de 87 genes candidatos que possam controlar as características investigadas. Desses, 70 genes apresentou variantes alélicas relacionadas inserções de elementos transponíveis entre os dois genótipos parentais. As análises metabólicas e enzimática revelaram alta frequência de correlações positivas entre as enzymas, frequência moderada de correlações entre metabólitos relacionados, e baixa correlações entre a atividade das enzimas e os níveis de metabólitos. Tomados em conjunto, vapresentamos o maior estudo de parâmetros de fotossíntese e crescimento em plantas de tomate até à data. Os resultados permitiram a identificação de genes candidatos que podem estar envolvidos na regulação da fotossíntese, metabolismo primário e crescimento da planta, e fornece um recurso genético valioso para a compreensão dos mecanismos bioquímicos envolvidos na regulação do metabolismo primário em tomateiro.
To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis, respiration and underlying traits, a population of 71 Solanum pennellii introgression lines (ILs) in the genetic background of S. lycopersicum (M82) was analyzed. We determined IL phenotypes physiological, metabolic and growth related traits, ranging from gas- exchange parameters (e.g. CO 2 assimilation rates and stomatal conductance), chlorophyll fluorescence parameters (e.g. electron transport rate and photochemical quenching) as well as growth related traits (e.g. relative growth rate, shoot and root dry matter accumulation). In parallel, we also analyzed by robotized platform the major metabolic intermediates (e.g. sugars and starch), and the activities of nine representative enzymes from central C and N metabolism. We aimed: (1) combine information about enzyme activities and metabolite levels from stem, petiole and leaf with biomass and fruit yield; (2) by studying these three interconnected organs, examine how much connectivity exists between enzyme activities and metabolite levels; (3) provide predictive information about differences in C partitioning and inorganic N assimilation; (4) investigate the natural genetic diversity and identify QTL controlling variation of enzyme activities and metabolite levels in stem, petiole and leaf. Data analyses allowed identification of 67 physiological and metabolic QTL. Additionally, a comprehensive and detailed annotation of these regions allowed to point out a total of 87 candidate genes that might control the investigated traits. Out of those, 70 genes showed allelic variants related to differentially transposable element insertions pattern between both parental genotypes. Furthermore, the results revealed high frequency of positive correlations between enzyme activities, moderate frequency of correlations between related metabolites, and few correlations between enzyme activities and metabolite levels. Taken together, we present the largest study of photosynthetic and growth parameters in tomato plants to date. Our results allowed the identification of candidate genes that might be involved in the regulation of photosynthesis, primary metabolismo and plant growth, and provide an valuable genetic resource to understanding of the biochemical mechanisms involved in the regulation of primary metabolism in tomato plants.
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Shimomura, Koichiro. "Quantitative trait locus analysis of agronomic traits in weedy cucumber lines for breeding." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263362.
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Joehanes, Roby. "Multiple-trait multiple-interval mapping of quantitative-trait loci." Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1605.
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Conde-Martinez, F. Victor. "Quantitative trait loci and bulk segregant analysis to identify drought-related traits in maize (Zea mays L.)." Thesis, University of East Anglia, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432430.
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Yao, Ping. "Quantitative trait loci mapping and candidate gene analysis for growth and carcass traits on two bovine chromosomes." Diss., Columbia, Mo. : University of Missouri-Columbia, 2006. http://hdl.handle.net/10355/4576.
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Thesis (M.S.)--University of Missouri-Columbia, 2006.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on May 7, 2009) Includes bibliographical references.
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Marklund, Lena. "Genome analysis of quantitative trait loci in the pig /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1997. http://epsilon.slu.se/avh/1997/91-576-5416-6.gif.
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Atkinson, Jennifer L. "Quantitative trait locus analysis of growth in Arabidopsis thaliana." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/11892.
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Natural genetic variation found among accessions of Arabidopsis thaliana presents the opportunity of locating and identifying novel genes by means of quantitative trait locus (QTL) analysis. In this study, QTL analysis was used to identify loci involved in the genetic control of growth in A. thaliana. Non-destructive methods of analysis were developed and used for the measurements of growth rates in roots and leaves, whilst a simple size measurement of mature petals was used to assess growth in the floral organ. Two putative QTL were identified for primary root length, four for leaf number at day 32 and three for petal size in the Bay-0 x Shahdara recombinant inbred line (RIL) population. The Landsberg erecta x Columbia RIL population was also analysed, but no significant QTL were identified. The analysis suggested that, in all three organs, growth-rate is controlled by multiple small-effect QTL and is a highly plastic trait. Thus, minor environmental fluctuations during the course of experiments can lead to a large environmental variance in measurement of the traits, limiting the power of QTL analyses. Despite minimising these effects by adjusting growth techniques, the numbers and significance of QTL identified in each trait were lower then expected, and for the trait of relative growth rate in leaves no significant QTL were identified.
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Randall, Joshua Charles. "Large-scale genetic analysis of quantitative traits." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:addfb69d-602c-43e3-ab18-6e6d3b269076.
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Recent advances in genotyping technology coupled with an improved understanding of the architecture of linkage disequilibrium across the human genome have resulted in genome-wide association studies (GWAS) becoming a useful and widely applied tool for discovering common genetic variants associated with both quantitative traits and disease risk. After each GWAS was completed, it left behind a set of genotypes and phenotypes, often including anthropometric measures used as covariates. Genetic associations with anthropometric measures are not well characterized, perhaps due to lack of power to detect them in the sample sizes of individual studies. To improve power to detect variants associated with complex phenotypes such as anthropometric traits, data from multiple GWAS can be combined. This thesis describes the methods and results of several such analyses performed as part of the Genome-wide Investigation of ANThropemtric measures (GIANT) consortium, and compares various different methods that can be used to perform combined analyses of GWAS. In particular, the comparisons focus on comparing differences between meta-analysis methods, in which only summary statistics that result from within-study association testing are shared between studies, and mega-analysis methods in which individual-level genotype and phenotype data is analysed together. Finally, a brief discussion of technological means that have the potential to help overcome some of the challenges associated with performing mega-analyses is offered in order to suggest future work that could be undertaken in this area.
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Smith, Kelsey. "Identifying Frogeye Leaf Spot Resistance in Two Elite Soybean Populations and Analysis of Agronomic Traits in Resistant Lines." OpenSIUC, 2021. https://opensiuc.lib.siu.edu/theses/2843.
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Soybeans (Glycine max L.) are an important crop globally for its food, feed, and oilpurposes. It is impacted by many diseases, including Cercospora sojina, the causal agent of Frogeye Leaf Spot (FLS). Chemical and cultural controls to this fungal pathogen are insufficient, so genetic resistance must be acquired for adequate control. To this end, two recombinant inbred populations were screened in a greenhouse setting for their relative resistance to FLS, and their genomes were analyzed for contributing quantitative trait loci (QTL). In the Essex ́ Forrest population, one QTL was discovered on chromosome 13, and in the Forrest ́ Williams 82 population, two QTL were identified on chromosomes 6 and 11, respectively. These populations were then also screened in a field setting for agronomic traits. These traits were analyzed to detect one superior line for both FLS resistance and advanced agronomic traits, F ́W 125. This line should be used in future breeding projects to increase FLS resistance and reduce linkage drag for other desired characteristics.
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Purcell, Shaun. "Sample selection and complex effects in quantitative trait loci analysis." Thesis, King's College London (University of London), 2003. https://kclpure.kcl.ac.uk/portal/en/theses/sample-selection-and-complex-effects-in-quantitative-trait-loci-analysis(730a92fb-113b-42c1-8f38-8a085bb37112).html.
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Benyamin, Beben. "Genetic analyses of quantitative traits in human twins." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/10786.
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The aim of this thesis is to understand the genetic basis of the variation of human quantitative traits using data from twins and (to some extent) their families. Traits investigated include behavioural traits (intelligence), clinical traits (the metabolic syndrome) and anthropometric measures (height). The importance of human twins for understanding genetic variation in human quantitative traits is reviewed. The use of a novel finite mixture distribution model to partition phenotypic co(variance) of a trait into underlying genetic and environmental factors from twins of unknown zygosity is presented. The Scottish Mental Surveys of 1st June 1932 and 4th June 1947, respectively, administered the same validated verbal reasoning test (the Moray House Test) to almost everyone born in 1921 or 1936 and attending school in Scotland. Information on zygosity was unavailable. A novel application of a finite mixture distribution model estimated a large and consistent heritability of cognitive ability of about ~0/7. This study is the first to estimate genetic and environmental components of cognitive ability in entire school-attending populations and implies that large (national) data collections can provide sufficient information on twin pairs to estimate genetic parameters, even without known zygosity. The precision and bias of the finite mixture distribution model were assessed using computer simulations and application to IQ measures from a large sample of known zygosity twins (i.e. twins from the UK Twins’ Early Development Studies). It is shown that the mixture distribution is unbiased provided that the twins’ trait values are (bivariate) normally distributed and the sample size is large. However, it the bivariate normality assumption is violated, then the mixture distribution provides biased estimates. The extension of the model to multivariate analysis is discussed. The simulations show that multivariate analysis decreases the standard error of the variance component estimates. Another statistical model, a mixed linear model is used to partition the phenotypic (co)variances of traits into genetic and environmental factors from twins of known zygosity (twins from the Danish Twin Registry). Its application to understand underlying genetic and environmental aetiology showed that endophenotypes associated with the metabolic syndrome do not appear to share a substantial common genetic or familial environmental background. Finally, a genome-wide linkage analysis to identify gene/chromosomal regions associated with adult height reveals several chromosomal regions that showed a modest linkage to adult height. This analysis provides further evidence for the polygenic nature of body height.
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Pearson, Caroline. "Analysis of a hierarchial Bayesian method for quantitative trait loci /." Electronic version (PDF), 2007. http://dl.uncw.edu/etd/2007-2/pearsonc/carolinepearson.pdf.
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Darrah, Chiarina. "Quantitative trait locus analysis of circadian phase in Arabidopsis thaliana." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487036.
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The plant clock is the least well characterized of circadian systems, although mutant screens have identified a number of putative components. Here, an approach using forward genetics is employed which takes advantage of natural allelic variation in Arabidopsis thaliana ecotypes to identify areas ofgenome responsible for variation in clock traits. This means that intact, viable systems are the basis of analysis. Circadian output in transgenic seedlings is monitored by measuring the activity of a cab2::1uc+ transgene. The circadian parameter studied here is 'phase', i.e., the timing of a point of the circadian cycle relative to a fixed point in the external light dark cycle. The timing of the peak of cab2::1uc+ expression after last dawn was used as a phase marker. Initially, a quantitative trait locus ('QTL') analysis attempted to identify QTL for phase. Phase was measured in transgenic Arabidopsis seedlings from a population of recombinant inbred lines (Rll-s), whose genomes are homozygous mosaics derived from two inbred parental genotypes (Ler xCvi). QTL analysis attempts to correlate phenotypic variation with genetic variation within this population; both types of variation arise from the natural allelic variation present in the parents. The analysis was repeated on phase data obtained after entrainment to different photoperiods. Loci were found where Cvi alleles either advanced or delayed the phase relative to Ler alleles in particular environments. The QTL were characterized in near isogenic lines (t\lJLs). The Nll..,s are lines which contain small regions of Cvi alleles in an otherwise homogeneous Ler background, and the lines were transformed with cab2::1uc+ in order to measure their circadian output. This allowed us to evaluate candidates for genes underlying the QTL found.
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Sebastian, Rachel Louise. "The genetic mapping and quantitative trait analysis of Brassica oleracea." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396237.
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Zhou, Hua, Jin Zhou, Eric Sobel, and Kenneth Lange. "Fast genome-wide pedigree quantitative trait loci analysis using MENDEL." BioMed Central, 2014. http://hdl.handle.net/10150/610091.
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The linkage era left a rich legacy of pedigree samples that can be used for modern genome-wide association sequencing (GWAS) or next-generation sequencing (NGS) studies. Family designs are naturally equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Unfortunately, pedigree likelihoods are notoriously hard to compute, and current software for association mapping in pedigrees is prohibitively slow in processing dense marker maps. In a recent release of the comprehensive genetic analysis software MENDEL, we implemented an ultra-fast score test for association mapping with pedigree-based GWAS or NGS study data. Our implementation (a) works for random sample data, pedigree data, or a mix of both(b) allows for covariate adjustment, including correction for population stratification
(c) accommodates both univariate and multivariate quantitative traits
and (d) allows missing values in multivariate traits. In this paper, we assess the capabilities of MENDEL on the Genetic Analysis Workshop 18 sequencing data. For instance, when jointly testing the 4 longitudinally measured diastolic blood pressure traits, it takes MENDEL less than 51 minutes on a standard laptop computer to read, quality check, and analyze a data set with 959 individuals and 8.3 million single-nucleotide polymorphisms (SNPs). Our analysis reveals association of one SNP in the q32.2 region of chromosome 1. MENDEL is freely available on http://www.genetics.ucla.edu/software webcite.
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Loredo-Osti, J. Concepción. "Analysis of quantitative traits, segregation and conditional linkage." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0015/NQ49278.pdf.
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Keith, Deborah J. "Genetic analysis of quantitative traits in Brassica napus." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296926.
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Olatoye, Olalere Marcus. "Quantitative genomic analysis of agroclimatic traits in sorghum." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/38251.
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Doctor of PhilosophyDepartment of Agronomy
Geoffrey Morris
Climate change has been anticipated to affect agriculture, with most the profound effect in regions where low input agriculture is being practiced. Understanding of how plants evolved in adaptation to diverse climatic conditions in the presence of local stressors (biotic and abiotic) can be beneficial for improved crop adaptation and yield to ensure food security. Great genetic diversity exists for agroclimatic adaptation in sorghum (Sorghum bicolor L. Moench) but much of it has not been characterized. Thus, limiting its utilization in crop improvement. The application of next-generation sequencing has opened the plant genome for analysis to identify patterns of genome-wide nucleotide variations underlying agroclimatic adaptation. To understand the genetic basis of adaptive traits in sorghum, the genetic architecture of sorghum inflorescence traits was characterized in the first study. Phenotypic data were obtained from multi-environment experiments and used to perform joint linkage and genome-wide association mapping. Mapping results identified previously mapped and novel genetic loci underlying inflorescence morphology in sorghum. Inflorescence traits were found to be under the control of a few large and many moderate and minor effect loci. To demonstrate how our understanding of the genetic basis of adaptive traits can facilitate genomic enabled breeding, genomic prediction analysis was performed with results showing high prediction accuracies for inflorescence traits. In the second study, the sorghum-nested association mapping (NAM) population was used to characterize the genetic architecture of leaf erectness, leaf width, and stem diameter. About 2200 recombinant inbred lines were phenotyped in multiple environments. The obtained phenotypic data was used to perform joint linkage mapping using ~93,000 markers. The proportion of phenotypic variation explained by QTL and their allele frequencies were estimated. Common and moderate effects QTL were found to underlie marker-trait associations. Furthermore, identified QTL co-localized with genes involved in both vegetative and inflorescence development. Our results provide insights into the genetic basis of leaf erectness and stem diameter in sorghum. The identified QTL will also facilitate the development of genomic-enable breeding tools for crop improvement and molecular characterization of the underlying genes Finally, in a third study, 607 Nigerian accessions were genotyped and the resulting genomic data [about 190,000 single nucleotide polymorphisms (SNPs)] was used for downstream analysis. Genome-wide scans of selection and genome-wide association studies (GWAS) were performed and alongside estimates of levels of genetic differentiation and genetic diversity. Results showed that phenotypic variation in the diverse germplasm had been shaped by local adaptation across climatic gradient and can provide plant genetic resources for crop improvement.
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Huq, Md Nazmul. "The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour." Thesis, Linköpings universitet, Biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-78393.
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Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.
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Grieve, Ian C. "Quantitative trait analysis in a panel of recombinant inbred rat strains." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/5617.
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Expression quantitative trait loci (eQTLs) are generated by the combined use of microarray technology to measure gene expression and genetic linkage analysis to map the expression traits to the genome. This thesis describes co-expression and quantitative trait transcript (QTT) analysis carried out on a dataset consisting of thousands of cis- and trans-eQTLs. These were mapped in 29 rat Recombinant Inbred strains derived from a cross between the Spontaneously Hypertensive Rat (SHR), a widely used model of the human metabolic syndrome, and the normotensive Brown Norway (BN). Gene expression data from four tissues relevant to the metabolic syndrome and cardiovascular disease were analysed: fat, kidney, adrenal gland and left ventricle. By systematically applying a rigorous statistical methodology to the eQTL dataset, a consistent, distinct correlation structure was observed. Co-expression of groups of transcripts linked to a common region of the genome, referred to as trans-eQTL clusters, was investigated. Some of these cluster-forming groups were found to remain significantly correlated after the effect of genotype was accounted for, and functionally enriched. An example of successful application of QTT analysis to the dataset is described. This contributed to the identification of Ogn as a regulator of left ventricular mass in rodents and subsequent implication of the homologue of Ogn in a related role in humans. Correlation of a further 103 physiological traits with cis-eQTLs in each of the four tissues was also carried out; analysis which potentially informs a wide range of hypotheses concerning relevant phenotypes. Together, the findings described here demonstrate the utility of a systematic computational approach using correlation-based methodologies in combination with appropriate statistical techniques to inform the genetic analysis of complex traits. These findings indicate the importance of understanding potential confounding factors in eQTL analysis, as well as the potential of the eQTL approach to stimulate gene discovery.
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Ye, Chun. "Statistical methods for the analysis of expression quantitative traits." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3386752.
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Thesis (Ph. D.)--University of California, San Diego, 2009.Title from first page of PDF file (viewed February 11, 2010). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 156-169).
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Morrill, Benson H. "Quantitative Genetic Analysis of Reproduction Traits in Ball Pythons." DigitalCommons@USU, 2011. https://digitalcommons.usu.edu/etd/1005.
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Although the captive reproduction of non-avian reptiles has increased steadily since the 1970’s, a dearth of information exists on successful management practices for large captive populations of these species. The data reported here come from a captive population of ball pythons (Python regius) maintained by a commercial breeding company, The Snake Keeper, Inc. (Spanish Fork, UT). Reproductive data are available for 6,480 eggs from 937 ball python clutches. The data presented suggest that proper management practices should include the use of palpation and/or ultrasound to ensure breeding occurs during the proper time of the female reproductive cycle, and that maintenance of proper humidity during the incubation of eggs is vitally important.
Ball python reproduction traits (clutch size, clutch mass, relative clutch mass, egg mass, hatch rate, egg length, egg width, hatchling mass, healthy offspring per clutch, week laid, and days of incubation) were recorded for the clutches laid during this study. For the 937 clutches, the identity of the dam and sire were known for 862 (92%) and 777 (83%) of the clutches, respectively. A multivariate model that included nine of the 11 traits listed above was compiled. Heritability and genetic and phenotypic correlations were calculated from the multivariate analysis. The trait that showed the most promise for use in artificial selection to increase reproduction rates was clutch size due to considerable genetic variation, high heritability, and favorable genetic correlations with other reproduction traits.
Although large datasets have been published for twinning in avian species, relatively few are available for non-avian reptiles. Reported here are 14 sets of twins produced from 6,480 eggs from 937 ball python clutches. The survival rate for twins during the first 3 months of life in our study was 97%. Interestingly, 11 of the sets of twins were identical in sex and phenotype, and additional genetic data suggested the rate of monozygotic twinning within this captive population of ball pythons was higher than that of dizygotic twinning. Further, using microsatellite analysis we were able to generate data that shows three sets of python twins were genetically identical.
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Lam, Alex C. "Design and analysis of genetical genomics studies and their potential applications in livestock research." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3950.
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Quantitative Trait Loci (QTL) mapping has been widely used to identify genetic loci attributable to the variation observed in complex traits. In recent years, gene expression phenotypes have emerged as a new type of quantitative trait for which QTL can be mapped. Locating sequence variation that has an effect on gene expression (eQTL) is thought to be a promising way to elucidate the genetic architecture of quantitative traits. This thesis explores a number of methodological aspects of eQTL mapping (also known as “genetical genomics”) and considers some practical strategies for applying this approach to livestock populations. One of the exciting prospects of genetical genomics is that the combination of expression studies with fine mapping of functional trait loci can guide the reconstruction of gene networks. The thesis begins with an analysis in which correlations between gene expression and meat quality traits in pigs are investigated in relation to a pork meat quality QTL previously identified. The influence on power due to factors including sample size and records of matched subjects is discussed. An efficient experimental design for two-colour microarrays is then put forward, and it is shown to be an effective use of microarrays for mapping additive eQTL in outbred crosses under simulation. However, designs optimised for detecting both additive and dominance eQTL are found to be less effective. Data collected from livestock populations usually have a pedigreed structure. Many family-based association mapping methods are rather computationally intensive, hence are time-consuming when analysing very large numbers of traits. The application of a novel family-based association method is demonstrated; it is shown to be fast, accurate and flexible for genetical genomics. Furthermore, the results show that multiple testing correction alone is not sufficient to control type I errors in genetical genomics and that careful data filtering is essential. While it is important to limit false positives, it is desirable not to miss many true signals. A multi-trait analysis based on grouping of functionally related genes is devised to detect some of the signals overlooked by a univariate analysis. Using an inbred rat dataset, 13 loci are identified with significant linkage to gene sets of various functions defined by Gene Ontology. Applying this method to livestock species is possible, but the current level of annotations is a limiting factor. Finally, the thesis concludes with some current opinions on the development of genetical genomics and its impact on livestock genetics research.
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Bassoi, Manoel Carlos. "Quantitative trait analysis of grain dormancy in wheat (Triticum aestivum L. Thell)." Thesis, University of East Anglia, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.251389.
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Zur, Lage Petra. "Molecular analysis of a gene affecting a quantitative trait in Drosophila melanogaster." Thesis, University of Edinburgh, 1993. http://hdl.handle.net/1842/13260.
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During an artificial selection experiment by T.F.C. Mackay for high and low abdominal bristle number in lines of Drosophila melanogaster which had been exposed to P element mutagenesis, a new allele of the smooth gene exhibiting an extremely low number of bristles on the abdomen was isolated. The molecular cloning and characterisation of the smooth gene is described here. Genomic cloning of the P element insertion in the new mutant allele was carried out and sequences immediately adjacent to either side of the P element insertion were subcloned. These were used to screen a cDNA library from which a 2.6 kb cDNA clone was isolated. Northern analysis using the cDNA as a probe confirmed the presence of a single transcript of equivalent size showing varying levels of expression during development. The 2.6 kb cDNA clone was completely sequenced and the genomic organisation of smooth was established revealing that the gene consists of ten exons differing in size from 64 bp to 590 bp and introns from 60 bp to more than 20 kb. The smooth gene extends over a genomic region more than 74 kb in length. The predicted gene product is a 53 kD protein that shows a high degree of sequence similarity to a group of RNA-binding proteins and in particular to the human heterogeneous nuclear ribonucleoprotein L. The possible role of smooth in RNA metabolism and the way in which mutations in this gene give rise to alteration in bristle number are discussed.
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Nagy, Réka. "Genetic analysis using family-based populations." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/28978.
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Most human traits are influenced by a combination of genetic and environmental effects. Heritability expresses the proportion of trait variance that can be explained by genetic factors, and the 1980s heralded the beginning of studies that aimed to pinpoint genetic loci that contribute to trait variation, also known as quantitative trait loci (QTLs). Subsequently, the availability of cheap, high-resolution genotyping chips ushered in the era of genome-wide association studies (GWAS). These genetic studies have discovered many associations between single-nucleotide polymorphisms (SNPs) and complex traits, but these associations do not explain the genetic component of these traits entirely. This is known as the ‘missing heritability’ problem. Within this thesis, 40 medically-relevant human complex traits are studied in order to identify new QTLs. These traits include eye biometric traits, blood biochemical traits and anthropometric traits measured in approximately 28,000 individuals belonging to family-based samples from the general Scottish population (the Generation Scotland study) or from population isolates from Croatian (Korčula, Vis) or Scottish (Shetland, Orkney) islands. These individuals had been genotyped using commercially-available arrays, and unobserved genotypes were imputed using the Haplotype Reference Consortium (HRC) dataset. In parallel to standard GWAS, these traits are analysed using two other statistical genetics approaches: variance component linkage analysis and regional heritability (RH) mapping. Each study is analysed separately, in order to detect study-specific genetic effects that may not generalise across populations. At the same time, because most traits are available in several studies, this also enables meta-analysis, which boosts the power of discovery and can reveal cross-study genetic effects. These methods are a priori complementary to each other, exploiting different aspects of human genetic variation, such as the segregation of variants within families (identity by descent, IBD), or the presence of the same variant throughout the general population (identity by state, IBS). The strengths and weaknesses of these methods are systematically assessed by applying them to real and simulated datasets.
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Nadesalingam, Jeyakumary. "Mapping and detection of quantitative trait loci (QTL) for milk production traits based on linkage analysis using microsatellite markers in Canadian Holstein cattle." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0019/NQ47403.pdf.
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Wambach, Tina. "Effects of epistatic interaction on detection and parameter analysis of quantitative trait loci." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33039.
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Recent scientific support for the involvement of genetic locus interaction in quantitative trait variation and the widespread use of quantitative trait locus (QTL) mapping has resulted in the need to examine those aspects concurrently. Computer software was written to simulate interacting quantitative trait loci (QTLs) in plant populations. Using this software, interacting QTLs were simulated to examine effects of epistasis on the detection of QTLs and the quality of QTL parameter estimates. Simulations involved doubled haploid populations exhibiting two non-epistatic traits and seven epistatic traits, each trait at four levels of heritability. Detection efficiency of QTL main and interaction effects decreased with decreasing heritability. At a given level of broad-sense heritability, traits differed with respect to the relative quality of main-effect detection and interaction-effect detection. Main-effect detection was notably poor for one epistatic locus that has a relatively small additive effect. Position estimates were accurate but their precision deteriorated with decreasing heritability. The quality of QTL effect estimates declined consistently with decreasing heritability, and loss in the accuracy was associated with losses in power of detection.
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Saint, Pierre Aude. "Méthodes d'analyse génétique de traits quantitatifs corrélés : application à l'étude de la densité minérale osseuse." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00633981.
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La plupart des maladies humaines ont une étiologie complexe avec des facteurs génétiques et environnementaux qui interagissent. Utiliser des phénotypes corrélés peut augmenter la puissance de détection de locus de trait quantitatif. Ce travail propose d'évaluer différentes approches d'analyse bivariée pour des traits corrélés en utilisant l'information apportée par les marqueurs au niveau de la liaison et de l'association. Le gain relatif de ces approches est comparé aux analyses univariées. Ce travail a été appliqué à la variation de la densité osseuse à deux sites squelettiques dans une cohorte d'hommes sélectionnés pour des valeurs phénotypiques extrêmes. Nos résultats montrent l'intérêt d'utiliser des approches bivariées en particulier pour l'analyse d'association. Par ailleurs, dans le cadre du groupe de travail GAW16, nous avons comparé les performances relatives de trois méthodes d'association dans des données familiales.
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Lisec, Jan. "Identification and characterization of metabolic Quantitative Trait Loci (QTL) in Arabidopsis thaliana." Phd thesis, Universität Potsdam, 2008. http://opus.kobv.de/ubp/volltexte/2008/2590/.
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Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach.
This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL).
Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis.
The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.
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Jayawardena, Mahen. "An e-Science Approach to Genetic Analysis of Quantitative Traits." Doctoral thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-111597.
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Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.eSSENCE
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Jayawardena, Mahen. "Parallel algorithms and implementations for genetic analysis of quantitative traits." Licentiate thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-85815.
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Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be regulated by multiple genetic loci. Standard computational tools for analysis of quantitative traits use linear regression models for relating the observed phenotypes to the genetic composition of individuals in a population. However, using these tools to simultaneously search for multiple genetic loci is very computationally demanding. The main reason for this is the complex nature of the optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms and implementation techniques for such optimization problems. The new computational tools will eventually enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the algorithm used for global optimization in the standard, serial software is parallelized and implemented on a grid system. Then, we also describe a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be deployed on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithms such as DIRECT. Finally, a pilot implementation of a grid portal providing a graphical front-end for our code is implemented. After some further development, this portal can be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.
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Gale, Joanne. "Statistical Methods for the Analysis of Quantitative Trait Data in Genetic Association Studies." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504345.
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Vaezi, Kakhki Mohammad Reza. "Quantitative trait locus and insertional mutant analysis of abiotic stress-tolerance in Arabidopsis." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437572.
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Goddard, Katrina Blouke. "Study design issues in the analysis of complex genetic traits /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/9565.
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Linney, Yvonne. "A quantitative genetic analysis of schizotypal personality traits and neuropsychological functioning." Thesis, King's College London (University of London), 2001. http://kclpure.kcl.ac.uk/portal/en/theses/a-quantitative-genetic-analysis-of-schizotypal-personality-traits-and-neuropsychological-functioning(cdce6371-4dd0-401e-873d-75fc5571afc1).html.
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Gan, Siou Ting. "The development and application of molecular markers for linkage mapping and quantitative trait loci analysis of important agronomic traits in oil palm (Elaeis guineensis Jacq.)." Thesis, University of Nottingham, 2014. http://eprints.nottingham.ac.uk/14197/.
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Oil palm (Elaeis guineensis) produces over five times more oil/year/hectare than oil seed rape and accounted for 33% of world vegetable oil production in 2011. Being a cross-pollinated perennial tree crop with long breeding cycles (typically 12 years) and a large planting area requirement (usually 143 palms/hectare), utilization of molecular technology could greatly improve the efficiency of oil palm breeding. In the present study, various approaches were used to develop molecular markers for genetic linkage mapping and QTL analysis, with the ultimate goal of marker-assisted selection in oil palm. Firstly, Representational Difference Analysis (RDA) and Amplified Fragment Length Polymorphism (AFLP) were coupled with Bulked Segregant Analysis (BSA) to try to identify marker(s) closely linked to the important shell-thickness gene. A novel combination of RDA with Roche 454 pyrosequencing enabled a more comprehensive study of the enrichment profiles compared to Sanger sequencing. Identification of >35% redundant sequences, repetitive sequences and organelle DNA suggested that subtractive hybridization and target enrichment of RDA were inefficient here, with the lack of elimination of common sequences masking the real difference products. The use of the AFLP method identified 29 primer pairs that yielded 49 putative shell-thickness related-polymorphic bands. A detailed analysis will need to be carried out to fully evaluate and validate these markers. The use of the relatively new Diversity Array Technology “Genotyping-By-Sequencing” (DArTSeq) platform through genotyping of two closely-related tenera self-pollinated F2 populations, 768 (n=44) and 769 (n=57), generated a total of 11,675 DArTSeq polymorphic markers of good quality. These markers were used in the construction of the first reported DArTSeq based high-density linkage maps for oil palm. Both genetic maps consist of 16 major independent linkage groups (total map length of 1874.8 and 1720.6 cM, with an average marker density of one marker every 1.33 and 1.62 cM, respectively), corresponding well with the 16 homologous chromosome pairs of oil palm (2n = 2x = 32; 14/16 chromosomes were confirmed by known location SSR markers). Preliminary quantitative trait loci (QTL) mapping of the yield and vegetative growth traits detected four significant and 34 putative as well as two significant and 30 putative QTLs for these small 768 and 769 populations, respectively. No common significant QTL were detected between the two closely-related controlled crosses which could have allowed combination of QTL across the two populations. Saturation of the shell-thickness (Sh) region with all available DArTSeq markers, as well as map integration around the Sh regions for both populations, identified 32 Single Nucleotide Polymorphism (SNP) and DArT markers mapped within a 5 cM flanking region of the Sh gene. Homology search of the DArTSeq marker sequence tag (64 bp) against the recently published oil palm genome assembly confirmed that 23 out of the 32 (72%) DArTSeq markers were located on the p5_sc00060 scaffold in which the SHELL gene was identified. The identified shell-thickness markers could be useful as molecular screening tools. This study demonstrated the potential and feasibility of using genomic resources available for genetic improvement of oil palm breeding programmes.
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Thumma, Bala Reddy. "QTL analysis of physiological and biochemical traits contributing to drought resistance in stylosanthes /." [St. Lucia, Qld.], 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16386.pdf.
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Dierks, Claudia. "Molecular genetic analysis of quantitative trait loci (QTL) for osteochondrosis in Hanoverian warmblood horses." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980656702.
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Park, Hee-Bok. "Genetic Analysis of Quantitative Traits Using Domestic Animals : A Candidate Gene and Genome Scanning Approach." Doctoral thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4582.
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Domestication has led to genetic changes that affect quantitative traits in farm animals. Both candidate gene analysis using association tests and genome scans based on linkage analysis have been performed to understand the molecular basis underlying quantitative genetic variation in horses, pigs and chickens. To test a possible association of polymorphisms in the PRKAG3 gene, previously found to be associated with excess glycogen content in pig skeletal muscle, with quantitative traits in the horse, the major coding part of the equine PRKAG3 sequence was identified. Bioinformatic characterization of the equine PRKAG3 gene was conducted. A single nucleotide polymorphism (SNP) causing a missense mutation (Pro258Leu) was found. Screening this SNP showed that the Leu258 allele was more frequent in breeds with heavy muscularity. To assess previously reported associations between polymorphisms in the MC4R gene and obesity-related traits further, we conducted linkage analysis between the MC4R locus and fatness-related traits using a Wild BoarxLarge White intercross. No significant association between segregation at the MC4R locus and fatness was detected in this pedigree. A genome scan of quantitative trait loci (QTLs) has been performed in an intercross between chicken lines divergently selected for growth. Divergent parental lines have been established by selecting for high and low 56-day body weight for over 40 generations. The selection has led to approximately a 9-fold difference in 56-day body weight between lines and resulted in correlated responses for a number of traits including appetite, immune response, body composition and metabolic traits. Phenotypic data on growth and other correlated traits were collected from more than 800 F2 individuals. Genome scans using 145 markers on 26 linkage groups have identified QTLs affecting growth and correlated responses to selection for 56-day body weight. No major QTL explaining a large portion of phenotypic variation in growth was revealed in this study.
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Tinker, Nicholas Andrew. "Studies on the analysis of genetic markers and quantitative trait loci in plant breeding populations." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=41774.
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Laboratory experiments, genetic simulation, and theoretical analyses were performed to address several objectives related to the use of genetic markers in plant breeding programs. Two software packages were developed: GREGOR provides flexible and efficient computer algorithms for performing genetic simulation experiments, and KIN provides improved methods for estimating coancestry from known pedigrees. Random amplified polymorphic DNA (RAPD) markers were investigated in elite barley lines, and estimates of genetic distance based on RAPD markers were compared to estimates based on coancestry. Both types of estimate can provide information that is useful to breeders and geneticists. Genetic simulation was used to investigate the power, accuracy and precision of several methods that are available for analyzing quantitative trait loci (QTL). In most cases, simplified methods of QTL analysis based on linear regression were similar or superior to more complex methods based on mixture models. Methods for genetic analysis using selective genotyping and pooled DNA were also investigated. These methods may allow precise estimates of the positions of markers and QTL to be made.
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Santos, Laura Viviana [Verfasser]. "Quantitative genetic analyses for dairy cow behavior traits and traits reflecting human-animal-technic interactions / Laura Viviana Santos." Gießen : Universitätsbibliothek, 2018. http://d-nb.info/1161339450/34.
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Santos, Laura [Verfasser]. "Quantitative genetic analyses for dairy cow behavior traits and traits reflecting human-animal-technic interactions / Laura Viviana Santos." Gießen : Universitätsbibliothek, 2018. http://d-nb.info/1161339450/34.
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Gutierrez, Rojas Libardo Andres. "Quantitative trait loci analysis to identify modifiers genes of the gene opaque2 in maize endosperm." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-2551.
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George, Andrew Winston. "A Bayesian analysis for the mapping of a quantitative trait locus given half-sib data." Thesis, Queensland University of Technology, 1998.
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Maniatis, Nikolaos. "Quantitative genetic analyses of growth traits in sheep under different models of inheritance." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.341920.
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Zhu, Guohua. "Ascertainment in two-phase sampling designs for segregation and linkage analysis /." Connect to text online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1112844349.
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Thesis (Ph. D.)--Case Western Reserve University, 2005.[School of Medicine] Department of Epidemiology and Biostatistics. Includes bibliographical references. Available online via OhioLINK's ETD Center.