Dissertations / Theses on the topic 'Quantitative genetics'
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1
Olsson, Charlotta. "Quantitative analysis of disease associated mutations and sequence variants." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5018-0/.
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Souleman, Dima. "Genetic consequences of colonization of a metal-polluted environment, population genetics and quantitative genetics approaches." Thesis, Lille 1, 2017. http://www.theses.fr/2017LIL10006/document.
Abstract:
Les habitats naturels sont de plus en plus détruits et fragmentés par l'expansion urbaine et les activités humaines. La fragmentation des espaces naturels et agricoles par les bâtiments et les nouvelles infrastructures affecte la taille, la connectivité et la qualité des habitats. Les populations d’organismes vivants sur ces territoires anthropisés sont alors plus isolées. Or, la différenciation entre populations d’un même organisme dépend de processus démographiques et génétiques tels que la dérive génétique, le flux génétique, la mutation et la sélection naturelle. La persistance et le développement des populations dans des conditions environnementales modifiées dépendent de mécanismes de tolérance. Dans ce contexte, l'introduction de contaminants tels que des métaux dans l'environnement peut influencer l'évolution des plantes et des animaux en modifiant les forces évolutives et en créant des différences entre populations. Dans ce travail, l’attention a été portée sur les conséquences génétiques de la pollution métallique sur deux espèces, le ver de terre Lumbricus terrestris et une plante modèle Arabidopsis halleri. Deux approches différentes ont été utilisées pour étudier la réponse génétique à la contamination métallique : une approche de génétique des populations chez L. terrestris et une approche de génétique quantitative chez A. halleri. Tout d’abord, il s’est agi d’identifier et de valider de nouveaux marqueurs microsatellites chez L. terrestris. Ensuite, ces marqueurs ont été utilisés afin de caractériser la diversité génétique neutre chez des vers collectés sur des sites agricoles et urbanisés. Parallèlement, l'architecture génétique de la tolérance et de l'hyperaccumulation de Zn chez A. halleri a été explorée à l’aide d’un croisement intraspécifique entre une population métallicole et une population non métallicole. Une densité élevée de marqueurs SNP a été utilisée pour procéder à l'étape de cartographie QTLNatural habitats are more and more destructed and fragmented by urban expansion and human activities. The fragmentation of natural and agricultural areas by buildings and new infrastructures affects the size, connectivity and the quality of habitats. The populations of organisms inhabiting these anthropized territories are then more isolated. However, differentiation between populations of the same organism depends on demographic and genetic processes such as genetic drift, gene flow, mutation and natural selection. Only species that have developed special tolerance mechanisms can persist under changed environmental conditions. The introduction of contaminants such as metals in the environment may influence plants and animals evolution by modifying the evolutionary forces and thus generating differences between populations. In this work, attention was focused on the genetic consequences of metallic pollution on two species, the earthworm Lumbricus terrestris and the plant model Arabidopsis halleri. Two different approaches have been used to study the genetic response to metallic contamination: a population genetic approach was performed in L. terrestris and a quantitative genetic approach was carried on in A. halleri. First, it was a question of identifying and validating new microsatellite markers in L. terrestris. These markers were then used to characterize the neutral genetic diversity in worms collected from agricultural and urban sites. Secondly, genetic architecture of Zn tolerance and Zn hyperaccumulation was conducted investigated for the first time using an intraspecific crossing between metallicolous and non-metallicolous individuals of A. halleri. High density of SNP markers was used to proceed to the QTL mapping step
3
Santure, Anna Wensley, and n/a. "Quantitative genetic models for genomic imprinting." University of Otago. Department of Zoology, 2006. http://adt.otago.ac.nz./public/adt-NZDU20060811.134008.
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A gene is imprinted when its expression is dependent on the sex of the parent from which it was inherited. An increasing number of studies are suggesting that imprinted genes have a major influence on medically, agriculturally and evolutionarily important traits, such as disease severity and livestock production traits. While some genes have a large effect on the traits of an individual, quantitative characters such as height are influenced by many genes and by the environment, including maternal effects. The interaction between these genes and the environment produces variation in the characteristics of individuals. Many quantitative characters are likely to be influenced by a small number of imprinted genes, but at present there is no general theoretical model of the quantitative genetics of imprinting incorporating multiple loci, environmental effects and maternal effects. This research develops models for the quantitative genetics of imprinting incorporating these effects, including deriving expressions for genetic variation and resemblances between relatives. Imprinting introduces both parent-of-origin and generation dependent differences in the derivation of standard quantitative genetic models that are generally equivalent under Mendelian expression. Further, factors such as epistasis, maternal effects and interactions between genotype and environment may mask the effect of imprinting in a quantitative trait. Maternal effects may also mimic a number of signatures in variance and covariance components that are expected in a population with genomic imprinting. This research allows a more comprehensive understanding of the processes influencing an individual�s characteristics.
4
Shen, Xia. "Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation." Doctoral thesis, Uppsala universitet, Beräknings- och systembiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-170091.
Abstract:
This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision. Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes. The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).
5
Keightley, Peter D. "Studies of quantitative genetic variation." Thesis, University of Edinburgh, 1988. http://hdl.handle.net/1842/12340.
6
Gunn, Melissa Rose School of Biological Earth & Environmental Science UNSW. "The use of microsatellites as a surrogate for quantitative trait variation in conservation." Awarded by:University of New South Wales. School of Biological, Earth and Environmental Science, 2003. http://handle.unsw.edu.au/1959.4/22457.
Abstract:
Conservation biologists are interested in maintaining genetic variation in small populations, with a view to maintaining fitness and the ability of the species to adapt to changing environmental conditions. The most important type of genetic variation is therefore that which affects fitness and reproduction, and is therefore subject to natural selection. Such fitness traits are often quantitative, i.e. are the result of a suite of loci, and are continuously variable. Microsatellite markers are a popular method of determining the level of variation present in a species??? genome. The assumption is made that microsatellites, which are neutral markers, behave in the same manner as quantitative traits. If this assumption were proved incorrect, then the use of neutral markers in conservation monitoring would have to be re-evaluated. In this study, experiments have been conducted using Drosophila melanogaster to test the assumption that variation in quantitative traits under stabilising selection declines at the same rate as heterozygosity in microsatellite markers, during a population bottleneck. Experimental population bottlenecks were of two effective population sizes (Ne), Ne=2 for one generation and Ne=60 for 35 generations. Based on the effective population size, we expected both types of bottlenecks to lose 25% of neutral genetic variation. Ten replicates of each bottleneck were maintained, along with four large control populations with Ne=320. In each population, heterozygosity (He) for eight microsatellite loci was compared with the heritability and additive genetic variance of two quantitative traits subject to balancing selection: fecundity and sternopleural bristle number. Microsatellite heterozygosity decreased in accordance with neutral predictions, whereas additive genetic variation in quantitative traits altered more than expected in both large and in bottlenecked populations relative to the initial sampling values, indicating that variation in quantitative traits was not being lost at the same rate as predicted by neutral theory. For most traits, the changes in additive genetic variance were congruent in all populations, large or bottlenecked. This congruence suggests that a common process was affecting all populations, such as adaptation. A mite infestation in early generations is a possible source of selective pressure. When bottlenecked populations were compared to the contemporaneous large populations (Ne = 320), the additive genetic variance of most traits was seen to have been lost in accordance with predictions from the loss of microsatellite heterozygosity. Loss of variation in microsatellites can thus be used to predict the loss of variation in quantitative traits due to bottlenecks, but not to predict the potentially much larger changes due to other processes such as adaptation. The effects of concurrent environmental stress and reduced population size were also evaluated. Endangered populations are often subject to environmental stress in addition to reduced population size, but the effect of stress on the additive genetic variance of fitness traits in organisms undergoing population bottlenecks is unknown. If the presence of stress alters the level of additive genetic variance in fitness traits, the viability of such populations could be substantially affected. The loss of microsatellite heterozygosity was not affected by the presence of a stress agent during a bottleneck. I found some significant effects of stress on the additive genetic variance of sternopleural bristles and fecundity; there was also a significant interaction between stress and the response to directional selection in sternopleural bristles. There was also an increase in the coefficient of variation of VA for sternopleural bristles. Stress may therefore affect the manner in which populations respond to selective pressures.
7
Cerqueira, Pedro Henrique Ramos. "Structural equation models applied to quantitative genetics." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11134/tde-05112015-145419/.
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Causal models have been used in different areas of knowledge in order to comprehend the causal associations between variables. Over the past decades, the amount of studies using these models have been growing a lot, especially those related to biological systems where studying and learning causal relationships among traits are essential for predicting the consequences of interventions in such system. Graph analysis (GA) and structural equation modeling (SEM) are tools used to explore such associations. While GA allows searching causal structures that express qualitatively how variables are causally connected, fitting SEM with a known causal structure allows to infer the magnitude of causal effects. Also SEM can be viewed as multiple regression models in which response variables can be explanatory variables for others. In quantitative genetics studies, SEM aimed to study the direct and indirect genetic effects associated to individuals through information related to them, beyond the observed characteristics, such as the kinship relations. In those studies typically the assumptions of linear relationships among traits are made. However, in some scenarios, nonlinear relationships can be observed, which make unsuitable the mentioned assumptions. To overcome this limitation, this paper proposes to use a mixed effects polynomial structural equation model, second or superior degree, to model those nonlinear relationships. Two studies were developed, a simulation and an application to real data. The first study involved simulation of 50 data sets, with a fully recursive causal structure involving three characteristics in which linear and nonlinear causal relations between them were allowed. The second study involved the analysis of traits related to dairy cows of the Holstein breed. Phenotypic relationships between traits were calving difficulty, gestation length and also the proportion of perionatal death. We compare the model of multiple traits and polynomials structural equations models, under different polynomials degrees in order to assess the benefits of the SEM polynomial of second or higher degree. For some situations the inappropriate assumption of linearity results in poor predictions of the direct, indirect and total of the genetic variances and covariance, either overestimating, underestimating, or even assign opposite signs to covariances. Therefore, we conclude that the inclusion of a polynomial degree increases the SEM expressive power.Modelos causais têm sido muitos utilizados em estudos em diferentes áreas de conhecimento, a fim de compreender as associações ou relações causais entre variáveis. Durante as últimas décadas, o uso desses modelos têm crescido muito, especialmente estudos relacionados à sistemas biológicos, uma vez que compreender as relações entre características são essenciais para prever quais são as consequências de intervenções em tais sistemas. Análise do grafo (AG) e os modelos de equações estruturais (MEE) são utilizados como ferramentas para explorar essas relações. Enquanto AG nos permite buscar por estruturas causais, que representam qualitativamente como as variáveis são causalmente conectadas, ajustando o MEE com uma estrutura causal conhecida nos permite inferir a magnitude dos efeitos causais. Os MEE também podem ser vistos como modelos de regressão múltipla em que uma variável resposta pode ser vista como explanatória para uma outra característica. Estudos utilizando MEE em genética quantitativa visam estudar os efeitos genéticos diretos e indiretos associados aos indivíduos por meio de informações realcionadas aos indivíduas, além das característcas observadas, como por exemplo o parentesco entre eles. Neste contexto, é tipicamente adotada a suposição que as características observadas são relacionadas linearmente. No entanto, para alguns cenários, relações não lineares são observadas, o que torna as suposições mencionadas inadequadas. Para superar essa limitação, este trabalho propõe o uso de modelos de equações estruturais de efeitos polinomiais mistos, de segundo grau ou seperior, para modelar relações não lineares. Neste trabalho foram desenvolvidos dois estudos, um de simulação e uma aplicação a dados reais. O primeiro estudo envolveu a simulação de 50 conjuntos de dados, com uma estrutura causal completamente recursiva, envolvendo 3 características, em que foram permitidas relações causais lineares e não lineares entre as mesmas. O segundo estudo envolveu a análise de características relacionadas ao gado leiteiro da raça Holandesa, foram utilizadas relações entre os seguintes fenótipos: dificuldade de parto, duração da gestação e a proporção de morte perionatal. Nós comparamos o modelo misto de múltiplas características com os modelos de equações estruturais polinomiais, com diferentes graus polinomiais, a fim de verificar os benefícios do MEE polinomial de segundo grau ou superior. Para algumas situações a suposição inapropriada de linearidade resulta em previsões pobres das variâncias e covariâncias genéticas diretas, indiretas e totais, seja por superestimar, subestimar, ou mesmo atribuir sinais opostos as covariâncias. Portanto, verificamos que a inclusão de um grau de polinômio aumenta o poder de expressão do MEE.
8
Mayo, Oliver. "Contributions to quantitative and population genetics : a collection of publications with introduction." Title page, contents and introduction only, 1987. http://web4.library.adelaide.edu.au/theses/09SD/09sdm473.pdf.
Abstract:
Title from container. Includes bibliographies and indexes. Contributions to quantitative and population genetics -- The biochemical genetics of man -- The theory of plant breeding -- Natural selection and its constraints.
9
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.
Abstract:
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.
10
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.
Abstract:
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.
11
Ali, Abdirahman. "Quantitative genetics and genomics of production and disease in beef cattle." Thesis, The University of Sydney, 2013. http://hdl.handle.net/2123/12296.
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Cattle grazing in extensive open pasture of tropical areas are subjected to several environmental stressors such as heat and humidity, high incidence of disease, cattle ticks and worm infestations. These stressors have major impacts on productivity and animal welfare. The overall focus of this PhD thesis was to conduct classical genetic and modern quantitative genomics analyses for growth and carcass related traits, and disease and parasite tolerance/resistance traits in beef cattle. The specific objectives were: (1) to estimate genetic parameters for growth, carcass related traits, and tropical environment stressors, e.g., infectious bovine keratoconjunctivitis or “pinkeye”, cattle tick counts, and helminth or worm egg counts in Australian tropical adapted beef cattle; (2) to identify genetic markers or gene(s) linked to growth and ultrasound measures of carcass related traits in tropical Australian cattle, and bovine tuberculosis (BTB) traits in African zebu cattle using a genome-wide scan methodology; and (3) to evaluate the feasibility of genome-wide epistasis association for growth and carcass related traits using a two-step two-locus model for Australian tropical beef cattle. Field test data obtained from different sources were used in this thesis. Genetic parameter estimates were computed using mixed models by fitting an additive polygenic animal term as a random effect, whereas in genome association analyses, the genetic markers were fitted as fixed effect and significance of marker effects on the traits were evaluated for association. The heritabilities of tropical stressors traits ranged from low to moderate, suggesting genetic selection is feasible, though the selection response will be slow in this resource population. There was no evidence of unfavourable genetic correlations between environment stressors and growth traits; hence selection against environmental stressors would not have a detrimental effect on production performance. A genome-wide scan identified seven SNP markers on chromosome 14 associated with serum concentration of insulin-like growth factor-1, subcutaneous fat depth, and body condition score measured in Australian Brahman cattle. The rs29020688 marker located in the intronic region of Bos taurus XK, Kell blood group complex subunit-related family, member 4 (XKR4) gene was strongly associated with increased blood levels of insulin-like growth factor-1 (IGF-1), and rs29010471 marker located in the intronic of Bos taurus protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene was strongly associated with subcutaneous fat deposits. These positional genes could be candidate genes influencing IGF-1 and subcutaneous fat depth, and can potentially be used as biomarkers for these traits. Similarly, this thesis investigated associations between SLC11A1 candidate gene and a panel of microsatellite markers and several diagnostic tests of bovine tuberculosis (BTB) phenotypes. Polymorphisms at SLC11A1 alleles 211, 215 and 217 and alleles in ILSTS006 (Alleles: 286, 288, 290, and 292) and BM2113 (Alleles: 133 and 141) were significantly associated with decreased BTB disease incidence in African zebu cattle; hence these could be considered in a marker assisted selection for screening BTB tolerant animals. This study was able to successfully model epistasis interactions between two-SNP loci using two-step approach. Using experimental field data, it was demonstrated and validated that two-step two-locus epistatic interactions are computationally feasible at a genome-wide scale. If automated recording technology for extensive gazing beef cattle becomes available in the future, this will enable the collection of high dimensional data on animals. In addition large number of animals are expected to be genotyped and imputed up to very high marker densities using imputation techniques. These resources will enable the estimation of genetic parameters more accurately and will allow biomarkers and genes underlying many complex traits in animals in extensive grazing system to be identified.
12
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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Canuto, Daniela Sílvia de Oliveira [UNESP]. "Diversidade genética em populações de Myracrodruon urundeuva (F.F. & M.F. Allemão) utilizando caracteres quantitativos." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/106199.
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canuto_dso_dr_ilha.pdf: 546568 bytes, checksum: 277ddfa04a5cb5726a68fcc227b176bd (MD5)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
A aroeira Myracrodruon urundeuva (F.F. & M.F. Allemão) é conhecida pela extraordinária durabilidade e resistência de sua madeira, possui reconhecido valor econômico e apresenta diversas aplicações, entre elas, a confecção de esteios, postes moirões e dormentes, extração de tanino e bálsamo. Seis populações da espécie estão sendo conservadas ex situ em delineamentos experimentais na Fazenda de Ensino, Pesquisa e Extensão da FEIS/UNESP, em Selvíria-MS, onde se pretende ampliar a base genética, recombinar a variabilidade genética e produzir sementes para reflorestamentos. Das seis populações duas são procedentes de área com pouca perturbação antrópica: Estação Ecológica do Instituto Florestal em Paulo de Faria-SP e Estação Ecológica do Seridó em Serra Negra do Norte-RN. As outras quatro são de área com forte perturbação antrópica: Bauru-SP, Itarumã-GO, Petrolina-PE e Selvíria-MS. Dessa forma, foram avaliados nove testes de progênies de M. urundeuva para caracteres quantitativos empregando-se a metodologia REML/BLUP (máxima verossimilhança restrita / melhor predição linear não viciada), assumindo que as progênies são parentes no grau de meios-irmãos e a metodologia MHPRVG para a análise de adaptabilidade e estabilidade nos testes de progênies provenientes da Estação Ecológica de Paulo de Faria em quatro sistemas de plantio (ambientes) diferentes. Este trabalho permitiu estudar os caracteres de desenvolvimento silvicultura nos testes de progênies, a variabilidade genética, o ganho de seleção a partir do Índice Multiefeito, a propagação sexuada e assexuada, a sobreposição de geração e a estabilidade e adaptabilidade das progênies de M. urundeuva. Verificou-se que as progênies de M. urundeuva em relação aos caracteres silviculturais analisados: altura total, diâmetro médio da copa (DMC), diâmetro à altura do peito (DAP)...
The aroeira Myracrodruon urundeuva (F.F. & M.F. Allemão) has been known for the extraordinary durability and resistance of its wood, it has recognized economic value and presents several uses, as for, posts, and sleepers, tannin extraction, and balm. Six populations of the species has been conserved by ex situ design in Experimental Station of Education, Research, and Extension of FEIS/UNESP, in Selvíria-MS Brazil, where to intend to enlarge the genetic base, mix up the genetic variability and to produce seeds for reforestations. Two out of six populations are coming from sites with little anthopic disturbance: Ecological Station of the Instituto Forestal in Paulo de Faria-SP, Brazil and Ecological Station of Seridó in Serra Negra- RN, Brazil. The others four are from sites with large anthopic disturbance: Bauru-SP, Itarumã-GO, Petrolina-PE and Selvíria-bad. In that way, were evaluated nine progeny trial of M. urundeuva to study the traits using the methodology of REML/BLUP (máxima verossimilhança restrita/melhor predição linear não viciada), stating that the are half site and the MHPRVG methodology for the adaptability and stability analyses by trials from Ecological Station of Instituto Florestal of Paulo de Faria by four different plantation systems (atmospheres). This research to study the traits of development forestation in the progeny trials, the genetic variability, the selection gain starting by Index Multi-effects´, the propagation sexual and assexual, Superiority of elite trees in relationship of the progenies and the stability and adaptability of the progenies of M. urundeuva. Verified that the progenies of M. urundeuva in relation to the traits analyzed silviculturais: total height, medium diameter of the cup (DMC), diameter to the height of the chest (DAP) they had a satisfactory development, and the progenies originating from of the Ecological Station... (Complete abstract click electronic access below)
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Scoville, Alison G. "Phenotypic Plasticity and the Post-Modern Synthesis: Integrating Evo-Devo and Quantitative Genetics in Theoretical and Empirical Studies." DigitalCommons@USU, 2008. https://digitalcommons.usu.edu/etd/212.
Abstract:
Mainstream evolutionary biology lacks a mature theory of phenotype. Following from the Modern Synthesis, researchers tend to assume an unrealistically simple mapping of genotype to phenotype, or else trust that the complexities of developmental architecture can be adequately captured by measuring trait variances and covariances. In contrast, the growing field of evolutionary developmental biology (evo-devo) explicitly examines the relationship between developmental architecture and evolutionary change, but lacks a rigorous quantitative and predictive framework. In my dissertation, I strive to integrate quantitative genetics and evo-devo, using both theoretical and empirical studies of plasticity. My first paper explores the effect of realistic development on the evolution of phenotypic plasticity when there is migration between two discrete environments. The model I use reveals that nonadditive developmental interactions can constrain the evolution of phenotypic plasticity in the presence of stabilizing selection. In my second paper, I examine the manner in which the genetically controlled responsiveness of traits to each other is shaped by selection and can in turn shape the phenotypic response to selection. Here, results indicate that developmental entanglement through plasticity can facilitate rapid multivariate adaptation in response to a novel selective pressure. In my final paper, I examine patterns of gene expression underlying ancestral plasticity and adaptive loss of melanin in Daphnia melanica. My results indicate that the developmental mechanism underlying ancestral plasticity has been co-opted to facilitate rapid adaptation to an introduced predator.
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Silva, Heyder Diniz. "Aspectos biométricos da detecção de QTL'S ("Quantitative Trait Loci") em espécies cultivadas." Universidade de São Paulo, 2001. http://www.teses.usp.br/teses/disponiveis/11/11134/tde-18102002-162652/.
Abstract:
O mapeamento de QTL's difere dos demais tipos de pesquisas conduzida em genética. Por se tratar basicamente de um procedimento de testes múltiplos, surge, neste contexto, um problema que se refere ao nível de significância conjunto da análise, e consequentemente, seu poder. Deste modo, avaliou-se, via simulação computacional de dados, o poder de detecção de QTL's da análise de marcas simples, realizada por meio de regressão linear múltipla, utilizando o procedimento stepwise" para seleção das marcas e procedimentos baseados em testes individuais, utilizando os critérios FDR e de Bonferroni para determinação nível de significância conjunto. Os resultados mostraram que o procedimento baseado em regressão múltipla, utilizando o procedimento stepwise" foi mais poderoso em identificar as marcas associadas a QTL's e, mesmo nos casos em que este procedimento apresentou poder ligeiramente inferior aos demais, verificou-se que o mesmo tem como grande vantagem selecionar apenas as marcas mais fortemente ligadas aos QTL's. Dentre os critérios FDR e de Bonferroni, o primeiro mostrou-se, em geral, mais poderoso, devendo ser adotado nos procedimentos de mapeamento por intervalo. Outro problema encontrado na análise de QTL's refere-se µa abordagem da interação QTL's x ambientes. Neste contexto, apresentou-se uma partição da variância da interação genótipos x ambientes em efeitos explicados pelos marcadores e desvios, a partir da qual obtiveram-se os estimadores da proporção da variância genética (pm), e da variância da interação genótipos x ambientes (pms), explicadas pelos marcadores moleculares. Estes estimadores independem de desvios das frequências alélicas dos marcadores em relação µ as esperadas (1:2:1 em uma geração F2, 1:1 em um retrocruzamento, etc.), porém, apresentam uma alta probabilidade de obtenção de estimativas fora do intervalo paramétrico, principalmente para valores elevados destas proporções. Contudo, estas probabilidades podem ser reduzidas com o aumento do número de repetições e/ou de ambientes nos quais as progênies são avaliadas. A partir de um conjunto de dados de produtividade de grãos, referentes µ a avaliação de 68 progênies de milho, genotipadas para 77 marcadores moleculares codominantes e avaliadas em quatro ambientes, verificou-se que as metodologias apresentadas permitiram estimar as proporções pm e pms, bem como classificar as marcas associadas a QTL's, conforme seu nível de interação. O procedimento permitiu ainda a identificação de regiões cromossômicas envolvidas no controle genético do caractere sob estudo conforme sua maior ou menor estabilidade ao longo dos ambientes.In general terms, QTL mapping di®ers from other research ac-tivities in genetics. Being basically a multiple test procedure, problems arise which are related to the joint level of signi¯cance of the analysis, and consequently, to its power. Using computational simulation of data, the power of simple marker analysis, carried out through multiple linear regression, using stepwise procedures to select the markers was obtained. Procedures based on single tests, using both the FDR and the Bonferroni criteria to determinate the joint level of signi¯cance were also used. Results showed that the procedure based on multiple regression, using the stepwise technique, was the most powerful in identifying markers associated to QTL's. However, in cases where its power was smaller, its advantage was the ability to detect only markers strongly associates with QTL's. In comparision with the Bonferroni method, the FDR criterion was in general more powerful, and should be adopted in the interval mapping procedures. Additional problems found in the QTL analysis refer to the QTL x environment interaction. We consider this aspect by par-titioning the genotype x environment interaction variance in components explained by the molecular markers and deviations. This alowed estimating the proportion of the genetic variance (pm), and genotype x environment variance (pms), explained by the markers. These estimators are not a®ected by deviations of allelic frequencies of the markers in relation to the expected values (1:2:1 in a F2 generation, 1:1 in a backcross , etc). However, there is a high probability of obtaining estimates out of the parametric range, specially for high values of this proportion. Nevertheless, these probabilities can be reduced by increasing the number of replications and/or environments where the progenies are evaluated. Based on a set of grain yield data, obtained from the evaluation of 68 maize progenies genotyped for 77 codominant molecular markers, and evaluated as top crosses in four environments, the presented methodologies allowed estimating proportions pm and pms as well the classification of markers associated to QTL's, with respect to its level of genotype x environment interaction. The procedure also allowed the identification of chromosomic regions, involved in the genetical control of the considered trait, according to its stability, in relation to the observed environmental variation.
16
Nielsen, Johanna Fonss. "Evolutionary genetics of meerkats (Suricata suricatta)." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7677.
Abstract:
Cooperative species have long been the focus of much research due to the ‘special difficulty’ cooperation poses to the theory of evolution via natural selection. Despite this long history of scientific interest we actually know relatively little about the evolutionary genetics of cooperative mammalian species, especially in the wild. In this study I use long-term data from the Kalahari Meerkat Project to investigate some aspects of the evolutionary genetics of meerkats (Suricata suricatta). First, I reconstructed a genetically-validated pedigree of the Kalahari meerkat population. 1,494 meerkats (83% of the total known population) were genotyped at a panel of 18 highly variable microsatellite markers. This genetic data, in combination with phenotypic information and two different programs, COLONY2 and MASTERBAYES, was used to infer familial relationships. The resulting pedigree spanned seven generations and included 1,614 individuals of which 1,076 had both parents known. I conclude by discussing the particular merits of using COLONY2 to infer familial relationships for social animals such as meerkats. Second, I investigated the extent of inbreeding and inbreeding depression in early life traits in the Kalahari meerkat population. In the pedigree, 44% of individuals have non-zero (F>0) inbreeding coefficients. Although I found more inbreeding in meerkats than initially expected, there were few cases of inbreeding between very close relatives. Nonetheless, even low to moderate inbreeding appeared to result in inbreeding depression for pup mass at emergence, hind-foot length, growth until independence, and juvenile survival. I also found some tentative evidence for a positive effect of the social environment in ameliorating the effects of inbreeding depression. Third, I conducted a quantitative genetic analysis on mass, skull length, skull width, forearm length, and hind-foot length in up to five key meerkat life stage periods, while accounting for a number of fixed effects, including inbreeding coefficient. By attempting to apportion variance in these traits to a variety of sources I found that birth litter identity often explained much of the variance in morphological traits, although the magnitude of this effect appeared to decline with age. Furthermore, when birth litter was removed from models, the amount of variance explained by additive genetic effects tended to increase. Finally, I conducted a quantitative genetic analysis on two measures of cooperative care and on adult mass. Fixed effects, including inbreeding and relatedness coefficients, were also examined, which revealed that inbred individuals contribute more to pup-feeding, and that helper-recipient relatedness was negatively associated with baby-sitting. I found low heritable variation for baby-sitting (h2 = 0.10) and pup-feeding (h2 = 0.08), and higher heritable variation for adult body mass (h2 = 0.19). I also estimated the magnitude of non-genetic sources of variation in these traits and provide evidence for positive genetic correlations between baby-sitting and pup-feeding, and baby-sitting and adult mass.
17
Whiteley, Rachel. "Quantitative and molecular genetic variation in Ulmus laevis Pall. /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish Univ. of Agricultural Sciences, 2004. http://epsilon.slu.se/s313.pdf.
18
Kölling, Nils. "Quantitative genetics of gene expression during fruit fly development." Thesis, University of Cambridge, 2016. https://www.repository.cam.ac.uk/handle/1810/256090.
Abstract:
Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also been applied to highthroughput RNA sequencing (RNA-seq) data in order to find loci associated with different levels of gene expression, called expression quantitative trait loci (eQTL). Because of the large amount of data that is required for such high-resolution eQTL studies, most of them have so far been carried out in humans, where the cost of data collection could be justified by a possible future impact in human health. However, due to the rapidly falling price of high-throughput sequencing it is now also becoming feasible to perform high-resolution eQTL studies in higher model organisms. This enables the study of gene regulation in biological contexts that have so far been beyond our reach for practical or ethical reasons, such as early embryonic development. Taking advantage of these new possibilities, we performed a high-resolution eQTL study on 80 inbred fruit fly lines from the Drosophila Genetic Reference Panel, which represent naturally occurring genetic variation in a wild population of Drosophila melanogaster. Using a 3′ Tag RNA-sequencing protocol we were able to estimate the level of expression both of genes as well as of different 3′ isoforms of the same gene. We estimated these expression levels for each line at three different stages of embryonic development, allowing us to not only improve our understanding of D. melanogaster gene regulation in general, but also investigate how gene regulation changes during development. In this thesis, I describe the processing of 3′ Tag-Seq data into both 3′ isoform expression levels and overall gene expression levels. Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene categories enriched or depleted in eQTLs. Finally, I extend the proximal eQTL calling approach to distal variants to find gene regulatory mechanisms acting in trans. Taken together, this thesis describes the design, challenges and results of performing a multivariate eQTL study in a higher model organism and provides new insights into gene regulation in D. melanogaster during embryonic development.
19
Webb, Karen Lynn. "The quantitative genetics of sound production in Gryllus firmus /." Thesis, McGill University, 1991. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59905.
Abstract:
The species-specific calling songs of male crickets are used by females for species recognition and mate choice. Heritabilities of variation of morphological structures involved in song production, components of the calling song, and body size were estimated for G.firmus. All morphological structures were shown to possess significant additive genetic variation (h$ sp2 sb{ rm S+D} > 0.42)$. One of the five song components examined, pulse rate, was shown to have a significant heritability (h$ sp2 sb{ rm S+D}$ = 0.35). Due to the low correlation between body size and song components, it is unlikely that female G.firmus could use the calling song to assess male body size or wing morph (micropterous or macropterous).
20
Cardno, Alastair George. "The quantitative genetics of clinical variation in psychotic illnesses." Thesis, Cardiff University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394591.
21
Howell, Philip Martin. "Marker-assisted selection and quantitative genetics in oilseed rape." Thesis, University of East Anglia, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267464.
22
Marks, Christopher. "Quantitative Genetics of Zebrafish Ontogeny Under Changing Environmental Conditions." University of Akron / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=akron1334778150.
23
Boddhireddy, Prashanth. "Development of highly recombinant inbred populations for quantitative-trait locus mapping." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1671.
24
Liu, Fuhua. "Quantitative genetics of male-haploid organisms used for biological control." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ35227.pdf.
25
Yu, Haipeng. "Designing and modeling high-throughput phenotyping data in quantitative genetics." Diss., Virginia Tech, 2020. http://hdl.handle.net/10919/97579.
Abstract:
Quantitative genetics aims to bridge the genome to phenome gap. The advent of high-throughput genotyping technologies has accelerated the progress of genome to phenome mapping, but a challenge remains in phenotyping. Various high-throughput phenotyping (HTP) platforms have been developed recently to obtain economically important phenotypes in an automated fashion with less human labor and reduced costs. However, the effective way of designing HTP has not been investigated thoroughly. In addition, high-dimensional HTP data bring up a big challenge for statistical analysis by increasing computational demands. A new strategy for modeling high-dimensional HTP data and elucidating the interrelationships among these phenotypes are needed. Previous studies used pedigree-based connectetdness statistics to study the design of phenotyping. The availability of genetic markers provides a new opportunity to evaluate connectedness based on genomic data, which can serve as a means to design HTP. This dissertation first discusses the utility of connectedness spanning in three studies. In the first study, I introduced genomic connectedness and compared it with traditional pedigree-based connectedness. The relationship between genomic connectedness and prediction accuracy based on cross-validation was investigated in the second study. The third study introduced a user-friendly connectedness R package, which provides a suite of functions to evaluate the extent of connectedness. In the last study, I proposed a new statistical approach to model high-dimensional HTP data by leveraging the combination of confirmatory factor analysis and Bayesian network. Collectively, the results from the first three studies suggested the potential usefulness of applying genomic connectedness to design HTP. The statistical approach I introduced in the last study provides a new avenue to model high-dimensional HTP data holistically to further help us understand the interrelationships among phenotypes derived from HTP.Doctor of Philosophy
Quantitative genetics aims to bridge the genome to phenome gap. With the advent of genotyping technologies, the genomic information of individuals can be included in a quantitative genetic model. A new challenge is to obtain sufficient and accurate phenotypes in an automated fashion with less human labor and reduced costs. The high-throughput phenotyping (HTP) technologies have emerged recently, opening a new opportunity to address this challenge. However, there is a paucity of research in phenotyping design and modeling high-dimensional HTP data. The main themes of this dissertation are 1) genomic connectedness that could potentially be used as a means to design a phenotyping experiment and 2) a novel statistical approach that aims to handle high-dimensional HTP data. In the first three studies, I first compared genomic connectedness with pedigree-based connectedness. This was followed by investigating the relationship between genomic connectedness and prediction accuracy derived from cross-validation. Additionally, I developed a connectedness R package that implements a variety of connectedness measures. The fourth study investigated a novel statistical approach by leveraging the combination of dimension reduction and graphical models to understand the interrelationships among high-dimensional HTP data.
26
Canuto, Daniela Silvia de Oliveira. "Diversidade genética em populações de Myracrodruon urundeuva (F.F. & M.F. Allemão) utilizando caracteres quantitativos /." Ilha Solteira : [s.n.], 2009. http://hdl.handle.net/11449/106199.
Abstract:
Orientador: Mário Luiz Teixeira de MoraesBanca: Marco Eustáquio de Sá
Banca: Miguel Luiz Menezes Freitas
Banca: Edson Seizo Mori
Banca: Ananda Virgínia de Aguiar
Resumo: A aroeira Myracrodruon urundeuva (F.F. & M.F. Allemão) é conhecida pela extraordinária durabilidade e resistência de sua madeira, possui reconhecido valor econômico e apresenta diversas aplicações, entre elas, a confecção de esteios, postes moirões e dormentes, extração de tanino e bálsamo. Seis populações da espécie estão sendo conservadas ex situ em delineamentos experimentais na Fazenda de Ensino, Pesquisa e Extensão da FEIS/UNESP, em Selvíria-MS, onde se pretende ampliar a base genética, recombinar a variabilidade genética e produzir sementes para reflorestamentos. Das seis populações duas são procedentes de área com pouca perturbação antrópica: Estação Ecológica do Instituto Florestal em Paulo de Faria-SP e Estação Ecológica do Seridó em Serra Negra do Norte-RN. As outras quatro são de área com forte perturbação antrópica: Bauru-SP, Itarumã-GO, Petrolina-PE e Selvíria-MS. Dessa forma, foram avaliados nove testes de progênies de M. urundeuva para caracteres quantitativos empregando-se a metodologia REML/BLUP (máxima verossimilhança restrita / melhor predição linear não viciada), assumindo que as progênies são parentes no grau de meios-irmãos e a metodologia MHPRVG para a análise de adaptabilidade e estabilidade nos testes de progênies provenientes da Estação Ecológica de Paulo de Faria em quatro sistemas de plantio (ambientes) diferentes. Este trabalho permitiu estudar os caracteres de desenvolvimento silvicultura nos testes de progênies, a variabilidade genética, o ganho de seleção a partir do Índice Multiefeito, a propagação sexuada e assexuada, a sobreposição de geração e a estabilidade e adaptabilidade das progênies de M. urundeuva. Verificou-se que as progênies de M. urundeuva em relação aos caracteres silviculturais analisados: altura total, diâmetro médio da copa (DMC), diâmetro à altura do peito (DAP)... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The aroeira Myracrodruon urundeuva (F.F. & M.F. Allemão) has been known for the extraordinary durability and resistance of its wood, it has recognized economic value and presents several uses, as for, posts, and sleepers, tannin extraction, and balm. Six populations of the species has been conserved by ex situ design in Experimental Station of Education, Research, and Extension of FEIS/UNESP, in Selvíria-MS Brazil, where to intend to enlarge the genetic base, mix up the genetic variability and to produce seeds for reforestations. Two out of six populations are coming from sites with little anthopic disturbance: Ecological Station of the Instituto Forestal in Paulo de Faria-SP, Brazil and Ecological Station of Seridó in Serra Negra- RN, Brazil. The others four are from sites with large anthopic disturbance: Bauru-SP, Itarumã-GO, Petrolina-PE and Selvíria-bad. In that way, were evaluated nine progeny trial of M. urundeuva to study the traits using the methodology of REML/BLUP (máxima verossimilhança restrita/melhor predição linear não viciada), stating that the are half site and the MHPRVG methodology for the adaptability and stability analyses by trials from Ecological Station of Instituto Florestal of Paulo de Faria by four different plantation systems (atmospheres). This research to study the traits of development forestation in the progeny trials, the genetic variability, the selection gain starting by Index Multi-effects', the propagation sexual and assexual, Superiority of elite trees in relationship of the progenies and the stability and adaptability of the progenies of M. urundeuva. Verified that the progenies of M. urundeuva in relation to the traits analyzed silviculturais: total height, medium diameter of the cup (DMC), diameter to the height of the chest (DAP) they had a satisfactory development, and the progenies originating from of the Ecological Station... (Complete abstract click electronic access below)
Doutor
27
Hunter, S. Jayne. "The quantitative analysis of green fluorescent protein in plants." Thesis, University of Sheffield, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340248.
28
Bégin, Michelle Anne. "Identifying quantitative trait loci involved in radiation-induced lung disease in mice." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=99321.
Abstract:
The goal of this thesis was to identify genetic loci involved in radiation-induced lung disease in mice. Phenotypic analysis was completed for alveolitis, pulmonary fibrosis, survival time, mast cells/mm2 and cell counts in bronchoalveolar lavage (BAL) to assess lung damage. Genome scans and linkage analysis were completed for two backcross cohorts (75%C3H/HeJ-25%C57Bl/6J or 25%C3H/HeJ-75%C57BU6J) using each of the phenotypes measured. Putative susceptibility loci were identified for alveolitis on chromosomes 12 (LOD=3.35), 14 (LOD=2.22) and 19 (LOD=1.7) in the mostly C3H/HeJ backcross cohort and on chromosome 14 (LOD=2.7) in the mostly C57BI/6J backcross cohort. Linkage using the pulmonary fibrosis scores provided supportive evidence for a quantitative trait loci (QTL) on chromosome 17 (LOD=2) in the mostly C57BI/6J background, and two unique putative linkage regions were localized on chromosome 2 (LOD=2.2) in the mostly C3H/HeJ cohort and 14 (LOD=2) in the mostly C57BI/6J cohort. Supporting evidence for linkage on chromosomes 12 and 14 in the mostly C3H/HeJ background and chromosome 14 in the mostly C57BI/6J background was obtained using cellular markers. Additionally, survival time mapped to the linkage regions isolated for alveolitis and pulmonary fibrosis, suggesting that the development of radiation-induced lung disease influences the survival time of the mice. Within each cohort there were sex dependent linkage intervals, indicating that male and female mice may possess different factors involved in the development of alveolitis and/or pulmonary fibrosis. These results suggest that there are multiple genetic loci involved in the development of radiation-induced lung disease in mice.
29
Lee, Vivian S. "Optical studies of human blood cells : the quantitative determination of platelet viability." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.291299.
30
Vaez, Torshizi Rasoul. "Quantitative genetic analyses of production and reproduction traits in Australian merino sheep." Thesis, The University of Sydney, 1996. https://hdl.handle.net/2123/27593.
Abstract:
Restricted Maximum Likelihood (REML) procedures based on a derivative-free algorithm using the Simplex method and fitting an animal model were used to estimate variance and covariance components for several performances of productive traits, namely, body weight measured at birth, weaning, 10 month, 16 month and 22 months of age, greasy fleece average daily gain to 4, 10, 16 and 22 months of age, clean fleece average daily gain to 10, 16, 22 months of age and mean fibre diameter measured at 10, 16 and 22 months of age. For these traits, the importance of maternal effects, either additive genetic or environmental, were investigated. The interrelationship among the performances of each trait were studied, and then were used to determine the efficiencies of indirect selection at early ages compared with later ages for improvement of an animal's lifetime production.
31
Baldoni, Pedro Luiz 1989. "Modelos lineares generalizados mistos multivariados para caracterização genética de doenças." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/307180.
Abstract:
Orientador: Hildete Prisco PinheiroDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação
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Resumo: Os Modelos Lineares Generalizados Mistos (MLGM) são uma generalização natural dos Modelos Lineares Mistos (MLM) e dos Modelos Lineares Generalizados (MLG). A classe dos MLGM estende a suposição de normalidade dos dados permitindo o uso de várias outras distribuições bem como acomoda a superdispersão frequentemente observada e também a correlação existente entre observações em estudos longitudiais ou com medidas repetidas. Entretanto, a teoria de verossimilhança para MLGM não é imediata uma vez que a função de verossimilhança marginal não possui forma fechada e envolve integrais de alta dimensão. Para solucionar este problema, diversas metodologias foram propostas na literatura, desde técnicas clássicas como quadraturas numéricas, por exemplo, até métodos sofisticados envolvendo algoritmo EM, métodos MCMC e quase-verossimilhança penalizada. Tais metodologias possuem vantagens e desvantagens que devem ser avaliadas em cada tipo de problema. Neste trabalho, o método de quase-verossimilhança penalizada (\cite{breslow1993approximate}) foi utilizado para modelar dados de ocorrência de doença em uma população de vacas leiteiras pois demonstrou ser robusto aos problemas encontrados na teoria de verossimilhança deste conjunto de dados. Além disto, os demais métodos não se mostram calculáveis frente à complexidade dos problemas existentes em genética quantitativa. Adicionalmente, estudos de simulação são apresentados para verificar a robustez de tal metodologia. A estabilidade dos estimadores e a teoria de robustez para este problema não estão completamente desenvolvidos na literatura
Abstract: Generalized Linear Mixed Models (GLMM) are a generalization of Linear Mixed Models (LMM) and of Generalized Linear Models (GLM). The class of models GLMM extends the normality assumption of the data and allows the use of several other probability distributions, for example, accommodating the over dispersion often observed and also the correlation among observations in longitudinal or repeated measures studies. However, the likelihood theory of the GLMM class is not straightforward since its likelihood function has not closed form and involves a high order dimensional integral. In order to solve this problem, several methodologies were proposed in the literature, from classical techniques as numerical quadrature¿s, for example, up to sophisticated methods involving EM algorithm, MCMC methods and penalized quasi-likelihood. These methods have advantages and disadvantages that must be evaluated in each problem. In this work, the penalized quasi-likelihood method (\cite{breslow1993approximate}) was used to model infection data in a population of dairy cattle because demonstrated to be robust in the problems faced in the likelihood theory of this data. Moreover, the other methods do not show to be treatable faced to the complexity existing in quantitative genetics. Additionally, simulation studies are presented in order to verify the robustness of this methodology. The stability of these estimators and the robust theory of this problem are not completely studied in the literature
Mestrado
Estatistica
Mestre em Estatística
32
Santos, Wanderley dos. "Interação genótipo x ambiente em progênies de Cordia trichotoma (Vell.) Arráb. ex Steud. e Dalbergia nigra (Vell.) Allemão ex Benth em sistema de plantio misto /." Ilha Solteira, 2018. http://hdl.handle.net/11449/180487.
Abstract:
Orientador: Ananda Virginia de AguiarResumo: As espécies nativas podem ser utilizadas para diversos usos em sistemas de produção, bem como para recuperação ambiental. Porém, poucas dessas espécies são exploradas economicamente devida à falta de oferta de sementes com qualidade genética no mercado. De maneira geral, a caracterização genética de populações e a seleção de indivíduos mais produtivos a partir de testes de progênies é a primeira etapa do processo para obtenção de indivíduos mais produtivos para sistemas de produção. Assim, os objetivos desse trabalho foram estimar a variação e a divergência genética, as relações genéticas e fenotípicas entre os caracteres quantitativos, bem como a interação genótipo x ambiente de testes de progênies de polinização aberta de Cordia trichotoma e Dalbergia nigra. As avaliações foram realizadas durante os quatro primeiros anos após o plantio. Os caracteres avaliados foram: diâmetro do coleto a 30 cm do solo, diâmetro a altura do peito 1,30 m do solo, altura total das plantas, altura do primeiro verticilo e sobrevivência. Para a estimativa dos componentes de variância e das análises multivariadas utilizou-se o método REML/BLUP (Melhor predição linear não viciada/máxima verossimilhança restrita). As análises foram realizadas entre as progênies da mesma espécie. Dois testes de progênies de C. trichotoma e D. nigra, em sistema de consórcio, foram instalados em 2012 na empresa Vale Rio Doce, em Linhares-ESpirito Santo, em duas áreas, em duas textura de solos. O delineamento experiment... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Native species can be used for various purposes in production systems, as well as for environmental recovery. However, few of these species are economically exploited due to the lack of genetic quality of seeds in the marketplace. In general, the genetic characterization of populations and the selection of more productive individuals from progeny tests are the first stage of the process to obtain more productive individuals for production systems. The objectives of this work were to estimate the variation and genetic divergence, identify the genetic and phenotypic relationships among the quantitative traits, as well as analyze the genotype x environment interaction of open pollinated progenies of Cordia trichotoma and Dalbergia nigra. The assessments were conducted during the first four years after planting. The evaluation traits were: collection diameter at 30 cm from the soil, diameter at 1.30 m from the soil, total height of the plants, height of first whorl and survival. To estimate the components of variance and multivariate analyzes, the REML/BLUP method (Restricted Maximum Likelihood/Best Linear Unbiased Prediction) was used. The analyses were carried out among the progenies of the same species. The two progenies of Cordia trichotoma and Dalbergia nigra, in a consortium system, were installed in 2012 at Vale Rio Doce, in the municipality of Linhares, Espirito Santo, in two areas, using two distinct soils. The experimental Randomized Complete Block design (RCB) were div... (Complete abstract click electronic access below)
Doutor
33
Rünneburger, Estelle. "Évolution de la canalisation génétique dans un modèle quantitatif de réseau de régulation." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS547/document.
Abstract:
La canalisation génétique est définie comme la capacité d’un organisme à avoir un développement constant en dépit des mutations qui l’affectent. A l’heure actuelle, trois hypothèses majoritaires cherchent à expliquer l’apparition de ce processus : évolutive, congruente et intrinsèque. Pour tester ces hypothèses, j’ai choisi d’étudier les réseaux de régulation. Pour cela, j’ai réutilisé un modèle théorique pour simuler in silico l’évolution des architectures génétiques, et les analyser par les outils de la génétique quantitative. J’ai d’abord étudié les comportements évolutifs de notre modèle et sa capacité de réponse à la sélection stabilisante. Outre l’analyse de l’impact des paramètres du modèle, j’ai mis en évidence l’absence d’équilibre mutation – sélection – dérive après des milliers de générations du fait de l’augmentation progressive de la canalisation. J’ai ensuite montré que les réseaux soumis à des mutations fréquentes et fortes, sélectionnés vers des optimums phénotypiques extrêmes, et dans lesquels certains gènes sont laissés libres d’évoluer sont plus aptes à faire évoluer de la canalisation génétique. Ces résultats nous ont amenés à proposer un double mécanisme impliqué dans l’évolution de la canalisation dans les réseaux de régulation : la réduction de la cible mutationnelle et la redondance de la régulation génique. Je termine ce manuscrit en présentant quelques pistes d’études complémentaires, portant notamment sur l’étude de la canalisation contre les perturbations environnementales et l’utilisation de modèles alternatifsGenetic canalization is defined as the capacity of an organism to undergo a normal development even when the genome is altered by mutations. Currently, three main hypotheses are prone to explain the apparition of such a process: evolutionary, congruent and intrinsic. To test these hypotheses, I chose to study gene regulatory networks. To this end, I used a theoretical model, ran in silico simulations, and analyzed the genetic architecture by using quantitative genetics tools. I first studied the evolutionary behavior of the model, and its capacity to respond to stabilizing selection. In addition to the sensitivity analysis to model parameters, I evidenced the absence of mutation-selection-drift equilibrium after several thousand generations, which reveals the evolution of canalization. I also showed that networks submitted to frequent and large mutations, and/or selected toward extreme phenotypic optima are more prone to evolve genetic canalization. This result leads us to propose a two-fold mechanism able to explain the evolution of canalization in gene regulatory networks: shrinkage of mutational targets and redundancy in genetic regulation. At the end of this manuscript, I propose some possible future studies, such as the study of canalization towards environmental perturbations, and use of alternative models
34
Wang, Xiaoxue. "Quantitative genetics of growth, carcass-quality traits, and disease resistance in hybrid striped bass (Morone chrysops [female] x Morone saxatilis [male])." [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1123.
35
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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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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Sheng, Xiaoming. "Variance components estimation with uncertainty and its application to quantitative genetics." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24986.pdf.
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Taylor, Robert James. "Systems biology of cellular signaling : quantitative experimentation and systems genetics approaches." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7101.
Abstract:
Cellular regulation is governed by dense biomolecular networks consisting of proteins, nucleotides, lipids, and metabolites that dynamically coordinate cellular decision making in the face of complex and time-varying environmental stimuli. Obtaining predictive models of these complex networks is a central goal of systems biology and requires sophisticated technologies for the acquisition and integration of many disparate data types. Recent genomic, proteomic and cellular imaging developments have greatly enabled systems-level studies, but further technological advances are needed. For instance, current high-throughput biochemical and cellular measurement techniques are generally limited to the analysis of cell populations, and the development of single-cell technologies are needed to advance predictive models of cellular networks. Large-scale genetic analyses are highly informative of the complex architecture of cellular networks but further computational methods are required to manage data complexity. In this thesis I present the development of two technologies, a microfluidic single-cell experimental platform and a genetic-network computational analysis platform, to address these issues and apply them to the study of prototypical eukaryotic signaling systems in Saccharomyces cerevisiae.
First I describe microfluidic technology for the high-throughput analysis of single-cells subject to complex environmental conditions. Using this platform, I studied cellular response of the mating pathway in Saccharomyces cerevisiae under a series of genetic and time-varying environmental perturbations. This analysis revealed dynamic phenotypes that are not observable under static conditions and allowed for the stratification of system components into distinct functional roles. In addition, I describe advances to this technology that allow for the tracking of individual cells over long experimental time frames. These developments enabled the investigation of sources of cell-to-cell variability not detectable otherwise. Second I describe a computational platform for analyzing complex genetic interaction networks. These networks describe functional relationships between gene systems and can be used to delineate information flows through complex cellular circuits. Genetic interactions networks are dense and information rich, and require sophisticated computational methods for their analysis. In this work, I developed network algorithms to identify biologically informative patterns within a multi-mode genetic interaction network to reveal functional sub-networks and information-hubs of the filamentation pathway in Saccharomyces cerevisiae.
39
Hague, Rachel Elise. "Genetics of quantitative resistance to powdery mildew in Fenman winter wheat." Thesis, University of East Anglia, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267461.
40
Tsang, Chi-ho, and 曾志豪. "A multi-probe quantitative PCR assay for genotyping of influenza B virus." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49828599.
Abstract:
Influenza B virus contributes to a significant portion of influenza disease burden in men. It is structurally similar and replicates in the same manner as the influenza A virus, leading to a comparable clinical presentation between the two viral species. Since 1977, influenza B has caused seasonal epidemics around the world together with A/H1N1 and A/H3N2 subtypes, and has a strong affinity to affect children of school age and young adults.
In the 1980s, two antigenically distinct lineages of influenza B virus emerged, one being the B/Yamagata lineage and the other known as B/Victoria lineage. The most significant antigenic difference between the two is located in the HA1 domain of the viral hemagglutinin. Host immunity is not shared between the two viral lineages. Therefore, the global prevalence of the two influenza B lineages is closely monitored by the World Health Organization in order to decide which viral lineage to include in the annual trivalent influenza vaccines.
Surprisingly, the current methods used in influenza B viral surveillance and lineage discrimination have not seen much technical advancement in nearly 25 years since the emergence of two viral lineages. The current study presents a novel, asymmetric real-time PCR assay which is able to determine the viral lineage in addition to detecting the presence of influenza B virus in clinical specimens.
Asymmetric PCR is performed by deliberately limiting the amount of primers in one side of a PCR reaction. This significantly affects the replication efficiency and sensitivity of the PCR reaction, but at the same time facilitates target sequence detection by hybridization probes, due to an increased number of single stranded products in the reaction. Nevertheless, the use of asymmetric PCR has been avoided in the past. The recent introduction of linear-after-the-exponential (LATE) PCR refines the method by adjusting melting temperature of PCR primers so that TmLimiting – TmExcess ≥ 0°C. The modification is shown to raise the efficiency of asymmetric PCR to those of symmetric PCR, as well as allowing more relaxed criteria for PCR primer and probe design.
In the current asymmetric assay, pan-influenza B primers and probes targeting Victoria and Yamagata linage specific regions of the influenza B HA were evaluated against a similar symmetric influenza B assay published by the World Health Organization. HA plasmid standards and 155 clinical specimens were tested by both assays, in which the two had intra-assay CV% of less than 5%. Albeit the efficiency and sensitivity of WHO published assay was slightly higher, LATE-PCR based assay performed influenza B detection and genotyping simultaneously with the use of hydrolysis probes. The overall sensitivity/ specificity of the genotyping assay are 96.81%/100% while the WHO recommended assay is at 98.94%/100% for influenza B detection. The LATE-PCR based genotyping assay also successfully genotyped 89 out of 94 clinical specimens.
In conclusion, the influenza B genotyping assay evaluated in this study performed favorably and could serve as an alternative to cumbersome viral culture methods to aid in high-throughput global influenza surveillance.published_or_final_version
Microbiology
Master
Master of Medical Sciences
41
Garcia, Guilherme Rodrigues Gomes. "Análise comparativa dos padrões de covariação genética e fenotípica no crânio e mandíbula de Calomys expulsus (Rodentia: Muroidea)." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-14092011-094754/.
Abstract:
Os padrões de covariância genética entre caracteres, expressos pela matriz de covariância aditiva G, desempenham um papel importante na evolução de morfologias complexas, visto que esta matriz influencia a direção e magnitude da resposta à seleção em uma população. Assumindo-se a estabilidade da matriz G ao longo do tempo, pode-se testar explicitamente hipóteses acerca da influência de processos evolutivos sobre a diversificação. Espera-se que esta matriz influencie os padrões expressos por sua equivalente fenotípica P, devido a contingências funcionais e ontogenéticas na relação entre genótipo e fenótipo, que levam à estruturação de modularidade nesta relação, de modo a otimizar a evolvabilidade. No presente trabalho, investiguei a estrutura da covariância genética no crânio e mandíbula de uma população do roedor sigmodontíneo Calomys expulsus, com o objetivo de estimar a similaridade entre covariâncias fenotípicas e genéticas; também avaliei a influência de padrões de modularidade sobre ambos os níveis de organização da variação morfológica. As matrizes P e G que obtive para o crânio e para a mandíbula se mostraram bastante similares no que diz respeito à sua estrutura de covariação e se relacionam parcialmente às hipótese de modularidade estabelecidas. Os resultados que obtive aqui são bastante similares àqueles obtidos para os mamíferos como um todo, portanto suportando a hipótese de estabilidade no padrão de covariâncias genéticas e fenotípicas na evolução do grupo.Patterns of genetic covariance between characters (represented by the additive covariance matrix G) play an important role in the evolution of morphological complexes, since they influence the direction and norm of the response to selection in a population. Therefore, the assumption that G-matrices are stable through evolutionary timescales allows evolutionary biologists to infer the influence of evolutionary processes that operate over biological diversification. These matrices are also expected to influence the patterns expressed in their phenotypic counterparts (P-matrix), because of the imposition of multiple developmental and functional contingencies over the genotype/phenotype map, that leads to its modular organization in order to increase evolvability. Here, I have investigated patterns of genetic covariance structure in the skull and mandible of a population of the vesper mouse Calomys expulsus in order to estimate the level of similarity between additive and phenotypic covariances; I have also evaluated the influence of expected patterns of modularity over both levels of morphological variation. For either skull and mandible, I have obtained P- and G-matrices that are strongly similar in their structure; these matrices also support the modularity hypotheses for developmental and functional constrains, akin to the overall results obtained for mammals, thus supporting the hypothesis of stability in genetic and phenotypic covariance structure in mammalian evolution.
42
Hubbe, Alex. "Análise morfológica craniana de Xenartha atuais e extintos: inferências evolutivas e funcionais." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-26072013-161553/.
Abstract:
Os Xenarthra representam um clado de mamíferos eutérios. Pouco se sabe sobre a evolução morfológica craniana do grupo. Esta tese iniciou os estudos relativos a esta questão com base na genética quantitativa, na morfometria e na sistemática, e teve por objetivos específicos: 1) avaliar empiricamente se as matrizes de variância e covariância fenotípica (matriz-P) dos diversos gêneros de Xenarthra estudados podem ser utilizadas como substitutas das respectivas matrizes de variância e covariância genética aditiva (matriz-G), uma vez que não existem matrizes-G estimadas para os Xenarthra, e também se elas podem ser utilizadas em estudos macroevolutivos; 2) testar se a diversificação morfológica craniana no grupo ocorreu somente através de deriva genética; e 3) compreender como a relação entre os caracteres morfológicos (módulos) e a magnitude geral de integração podem influir na evolução morfológica craniana. Além destes objetivos focados na evolução do grupo, também foi escopo desta tese inferir o hábito alimentar de taxa fósseis do final do Pleistoceno/início do Holoceno para melhorar o conhecimento sobre a ecologia de alguns grupos fósseis. O banco de dados utilizado foi composto por medidas lineares de aproximadamente 1150 espécimes adultos, representando 12 dos 14 gêneros atuais e sete dos diversos gêneros extintos de Xenarthra. Com base nesses dados, matrizes-P de variância e covariância e de correlação foram estimadas para cada gênero. Essas matrizes foram posteriormente comparadas par a par para avaliar a semelhança na estrutura das diferentes matrizes. Também a partir dessas matrizes, foram obtidas as variâncias entre e intra populações para testar se a diversificação morfológica ocorreu de acordo com a expectativa teórica de diversificação sob a ação exclusiva de deriva genética. As mesmas matrizes-P foram comparadas a diferentes matrizes teóricas de hipóteses de modularidade craniana. As matrizes teóricas expressaram a relação entre os caracteres com base no desenvolvimento e/ou desempenho de função compartilhado pelas partes do crânio. Para cada matriz-P de correlação calculou-se a magnitude geral de integração. Além disto, a dieta dos grupos extintos foi inferida através de análises de funções discriminantes a partir da relação entre forma e função dos animais atuais. Os resultados obtidos indicam que as matrizes-P dos diversos gêneros são similares entre si, o que sugere que matrizes-P podem ser utilizadas tanto como substitutas das matrizes-G quanto no contexto macroevolutivo. Os resultados obtidos refutaram a hipótese nula da diversificação morfológica craniana ocorrendo somente por deriva genética, ao menos nos níveis mais inclusivos da filogenia dos Xenarthra. Consequentemente, a seleção natural provavelmente atuou neste processo de diversificação. Os resultados também sugeriram que o crânio desse grupo está organizado em módulos, sendo os módulos mais conspícuos os relacionados à face. Além disso, foi detectada grande variação na magnitude geral de integração entre gêneros. A variação no padrão modular, mas principalmente na magnitude geral de integração, faz com que os gêneros apresentem diferenças nas possíveis capacidades de responder de forma alinhada às pressões seletivas. Por último, as análises morfofuncionais indicaram elevada diversidade de hábitos alimentares entre os Xenarthra extintosXenarthra are an eutherian mammal clade and little is known about their cranial morphological evolution. This thesis has initiated studies related to this topic and, based on quantitative genetics, morphometrics and systematics, aimed to: 1) empirically assess if the phenotypic variance and covariance matrices (P-matrix) of several genera can be used as surrogates for their respective additive genetic variance and covariance matrices (G-matrix), since G-matrices for Xenarthra are not available, and also if P-matrices can be used in macroevolutionary studies; 2) test whether the skull morphological diversification within the group occurred only through genetic drift; and 3) understand how the relationship between the traits (modules) and overall magnitude of integration may influence cranial morphological evolution. Besides these objectives focused on the evolution of the group, it was also within the scope of this thesis to infer the feeding habits of late Pleistocene/early Holocene fossil taxa to better understand the ecology of some fossil groups. The database used consist of linear measurements of approximately 1150 adult specimens, representing 12 of the 14 extant genera and seven of the several extinct genera of Xenarthra. The data gathered were used to estimate variance/covariance and correlation P-matrices for every genus. These matrices were compared between pairs of genera to evaluate the matrices\' structural similarities. Based on these matrices, within and between population variances were obtained and it was tested whether morphological diversification was in accordance to the theoretical expectation of diversification under genetic drift alone. The same matrices were compared to theoretical matrices expressing modularity hypotheses. These theoretical matrices represent the relationship among traits in reference to the shared development and/or function of different skull\'s anatomical regions (modules). For every correlation P-matrix the overall magnitude of integration was calculated. Moreover, the extinct groups\' diet was inferred through discriminant function analysis relying on the relationship between form and function of extant animals. Results indicate that P-matrices from several genera were structurally similar. This suggests that P-matrices can be used as surrogates of their G-matrices and in the macroevolutionary context. Results refuted the null hypothesis of cranial morphological diversification occurring only due to genetic drift, at least in more inclusive levels of Xenarthran phylogeny. Consequently, natural selection probably acted on this diversification process. The results also suggested that the Xenarthran skull is organized in modules, and the most conspicuous modules are in the face region. A large variation in the overall magnitude of integration among genera was detected. The variation in the modular pattern, but especially in the overall magnitude of integration, allows genera to differ in their potential capacity to respond aligned with selective pressures. Finally, morphofunctional analyses indicate a high diversity of feeding habits among extinct Xenarthra
43
Lindsay, Robert C. "QUANTITATIVE AND MOLECULAR ANALYSIS OF HABITUATION AT THE MAIZE r1 LOCUS." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5655.
Abstract:
Epigenetics is the study of heritable changes in phenotypes that are not the result of changes in DNA sequence. Examples of epigenetic affecters include methylation changes, chromatin modifications, transcription factors, and RNA-based changes. The molecular mechanisms behind epigenetic changes are not fully understood. Canalization is the buffering of gene expression against environmental changes over time, while habituation is semi-stable expression change over time due to selection. This work characterized the molecular changes associated with the kernel color changes of the R-sc:86-17pale allele at the maize red color1 (r1) locus to determine if the changes are epigenetic in nature. The research; 1) quantified the color differences between the progenitor and habituated sublines; 2) Determined that there are not sequence differences between the progenitor and habituated sublines at the 3` end of the Sc||nc1 gene that could account for changes in seed color; 3) and examined the cytosine methylation patterns at the 3` end of the Sc||nc1 gene of the habituated sublines and the progenitor to determine whether there are methylation differences that correspond with the kernel color changes. Quantification of the kernel colors of the R-sc:86-17pale selection sublines showed that there was a statistically significant difference in kernel color. The identical sequence of the R-sc:86 line and the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines at the 3` end of the Sc||nc1 gene is evidence that the kernel color change is not driven by differences in sequence within the r1 gene. The methylation data suggests that some methylation differences in the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines are present, and suggests that the molecular basis of the kernel color is epigenetic in nature.
44
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.
Abstract:
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.
45
Ai, Ni, and 艾妮. "A novel framework for expression quantitative trait loci mapping." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B4715214X.
46
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.
47
Bonnardeaux, Yumiko Graciela. "Seed dormancy in barley (Hordeum vulgare L.) : comparative genomics, quantitative trait loci analysis and molecular genetics." University of Western Australia. Faculty of Natural and Agricultural Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2009.0019.
Abstract:
[Truncated abstract] Under prolonged wet and damp conditions, barley grain with low dormancy can germinate precociously, a condition known as preharvest sprouting that causes a number of detrimental effects in grain quality. In particular, preharvest sprouting renders the grain unsuitable for malting. The aim of this study was to take a genomics approach to identify and characterise candidate genes that could be linked to the control of seed dormancy in barley. This thesis developed a bioinformatic strategy that exploited the availability of gene sequences with functional evidence in the model species of Arabidopsis and rice. The bioinformatic strategy integrated phenotypic data (QTL data) and comparative genomics for a targeted approach in identifying candidate genes with a high probability of having a conserved function in cereals. This bioinformatic study identified two candidate genes ERA1 and ABI2 with strong evidence for a role in seed dormancy based on their function in Arabidopsis in abscisic acid (ABA) signal transduction and their co-location to seed dormancy QTLs in Arabidopsis, rice and wheat. In order to establish whether the candidate genes mapped to seed dormancy QTLs in barley, QTL analyses were performed on a double haploid population, not previously studied, developed from a cross between Stirling, a major Australian malting cultivar, and Harrington, a major Canadian malting cultivar. This cross was specifically chosen for this study, as elucidation of chromosomal regions associated with seed dormancy in the background of a malting cultivar would make a significant contribution for the malting industry. '...' Identification of a seed dormancy QTL on the long arm of 3H, in a region syntenic to the wheat chromosome locations of ESTS aligning to the ERA1 and ABI2 genes, laid the foundation for physical and genetic mapping of the candidate genes to investigate whether the genes co-located to the QTL on 3H. Physical mapping of the genes in wheat barley addition lines confirmed their positions on the long arm of 3H. Genetic mapping of the ERA1 gene was performed using a CAPS marker developed in this thesis. The genetic mapping of the ERA1 gene did not place the gene within either of the minor QTLs on 3HL, although segregation distortion may have influenced the map position of this gene. Further investigation is required to resolve the positioning of the ERA1 and ABI2 genes in relation to the 3H seed dormancy QTL. The main outcomes of this study have been 1) identification of candidate genes for further study; 2) identification of QTLs on the long arm of 3H that were previously unknown; 3) demonstration of the potential differences in dormancy that can be achieved through the use of specific gene combinations, highlighting the importance of minor genes and the epistatic interactions that occur between them and; 4) the development of a CAPS marker for the ERA1 gene, which can be used to track the gene in barley breeding programs to observe its association with important agronomic traits. This thesis also pioneered the implementation of several new technologies including multiplex-ready PCR (Hayden et al. 2008) for fluorescencebased SSR genotyping and QTLNetwork (Yang et al. 2008) for statistical analysis of QTLs. Seed dormancy is a complex trait and is likely to involve the interplay of a number of genes that have a role in other developmental and regulatory processes.
48
Lonergan, Paul Francis. "Genetic characterisation and QTL mapping of zinc nutrition in barley (Hordeum vulgare)." Title page, contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phl847.pdf.
49
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.
Abstract:
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.
50
Campeol, Nadia. "Detection of markers in a low-density region of the barley (Hordeum vulgare L.) genome and their effects on the mapping of quantitative traits." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0002/MQ44137.pdf.