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1
Macdonald, Stuart J. "Evolutionary and genomic analyses of complex traits in Drosophila." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365832.
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Kirin, Mirna. "Genetic analysis of retinal traits." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9619.
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Retina is a unique site in the human body where the microcirculation can be imaged directly and non-invasively, allowing us to study in vivo the structure and pathology of the human microcirculation. Retinal images can be quantitatively assessed with computerized imaging techniques, enabling us to measure several different quantitative traits derived from the retinal vasculature. Arterial and venular calibres are the most extensively studied traits of the retinal microvasculature and numerous epidemiological studies demonstrated promising associations with systemic and ocular diseases as well as with disease markers. However, there has been a lack of research into pathophysiological processes leading to retinal vascular signs, and how they link retinal microcirculation with coronary and cerebral microvasculature change. Information about genetic determinants underlying retinal vascular structure is therefore important for understanding the processes leading to microvascular pathophysiology. Two genome wide association studies have been published so far revealing four loci associated with retinal venular calibre and one locus with arteriolar calibre. Here the results from the genome-wide association analysis of 10 different retinal vessel traits in two population based cohorts are presented. Retinal images were measured in non-mydriatic fundus images from 808 subjects in the Orkney Complex Disease Study (ORCADES) and 390 subjects from the Croatian island of Korcula, using the semi-automated retinal vasculature measurement programme SIVA and VAMPIRE. Using pairwise estimates of kinship based on genomic sharing, heritability was calculated for each trait. Estimates of tortuosity measure and fractal dimensions present first published reports of heritability estimates for those traits. In addition correlation analysis with systemic risk factor was also completed, confirming already published results as well as revealing some new associations. A genome wide association analysis of retinal arteriolar width revealed a genome wide significant hit (1.8x10-7) in a region of chromosome 2q32 (within TTN gene). Replication was sought in a further independent Scottish population (LBC) and additional 400 retinal images were graded. The result did not replicate, however the direction of the effect was consistent and a larger sample size is required. Analysis of the remaining traits did not yield genome wide significant result,s and will also require larger sample sizes. Genetic analysis of a binary retinal trait was also explored in a case control study of retinal detachment, which is an important cause of vision loss. A two-stage genetic association discovery phase followed by a replication phase in a combined total of 2,833 RRD cases and 7,871 controls was carried out. None of the SNPs tested in the discovery phase reached the threshold for association. Further testing was carried out in independent case-control series from London (846 cases) and Croatia (120 cases). The combined meta-analysis identified one association reaching genome-wide significance for rs267738 (OR=1.29, p=2.11x10-8), a missense coding SNP and eQTL for CERS2 encoding the protein ceramide synthase 2. Additional genetic risk score, pathway analysis and genetic liability analysis were also carried out.
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Hendel, Thomas. "Genetic Tools for the Analysis of Neural Networks in Flies." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-80505.
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Marlow, Angela J. "Genetic analysis of multivariate traits in dyslexia." Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404177.
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Randall, Joshua Charles. "Large-scale genetic analysis of quantitative traits." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:addfb69d-602c-43e3-ab18-6e6d3b269076.
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Recent advances in genotyping technology coupled with an improved understanding of the architecture of linkage disequilibrium across the human genome have resulted in genome-wide association studies (GWAS) becoming a useful and widely applied tool for discovering common genetic variants associated with both quantitative traits and disease risk. After each GWAS was completed, it left behind a set of genotypes and phenotypes, often including anthropometric measures used as covariates. Genetic associations with anthropometric measures are not well characterized, perhaps due to lack of power to detect them in the sample sizes of individual studies. To improve power to detect variants associated with complex phenotypes such as anthropometric traits, data from multiple GWAS can be combined. This thesis describes the methods and results of several such analyses performed as part of the Genome-wide Investigation of ANThropemtric measures (GIANT) consortium, and compares various different methods that can be used to perform combined analyses of GWAS. In particular, the comparisons focus on comparing differences between meta-analysis methods, in which only summary statistics that result from within-study association testing are shared between studies, and mega-analysis methods in which individual-level genotype and phenotype data is analysed together. Finally, a brief discussion of technological means that have the potential to help overcome some of the challenges associated with performing mega-analyses is offered in order to suggest future work that could be undertaken in this area.
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Groves-Kirkby, Nick. "Genetic analysis of variation in complex traits." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:4541c4e4-4538-4348-bb4b-0df6673344d2.
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Variation is a universal property of life, and much of contemporary genetics research is directed towards understanding the causes of variation in traits. Here I present the results of my investigations into the genetic and other causes of trait variation in humans and mice. I address these questions in the context of two distinct research projects, which use pre-existing data to investigate the causes of trait variation, through a range of analytic techniques. I first extract trait data from historic breeding records from the incipient Collaborative Cross (a genetic reference population of recombinant inbred mice) and use them to map genetic factors affecting litter size and other reproductive traits. Mapping reveals significant quantitative trait loci associated with litter size and time between litters, as well as a number of suggestive loci. I characterise the genetic effects at these loci and investigate candidate genes. The most robust finding, a litter size locus on chromosome 5, explains around 3% of observed variation and 24% of the variation attributable to genetics. Using data obtained from the Netherlands Twin Registry - a longitudinal database of Dutch twins - I investigate the prevalence of parent of origin effects on gene expression traits in peripheral blood in humans. I first phase individuals' genotypes by parental origin and use these genotypes to calculate the heritability of over 44,000 gene expression traits partitioned into that attributable to matching and nonmatching parent of origin. I replicate prior genomewide heritability estimates for many traits, but I find little evidence of widespread parent-of-origin effects on human gene expression in blood. On further examination, the small sample size severely limits the power to detect such effects. Nonetheless, I identify approximately 200 genes enriched for immune system processes that show evidence of parent-of-origin-specific effects on heritability.
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Riveros, Mckay Aguilera Fernando. "Genetic studies of cardiometabolic traits." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/289420.
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Diet and lifestyle have changed dramatically in the last few decades, leading to an increase in prevalence of obesity, defined as a body mass index >30Kg/m2, dyslipidaemias (defined as abnormal lipid profiles) and type 2 diabetes (T2D). Together, these cardiometabolic traits and diseases, have contributed to the increased burden of cardiovascular disease, the leading cause of death in Western societies. Complex traits and diseases, such as cardiometabolic traits, arise as a result of the interaction between an individual's predisposing genetic makeup and a permissive environment. Since 2007, genome-wide association studies (GWAS) have been successfully applied to complex traits leading to the discovery of thousands of trait-associated variants. Nonetheless, much is still to be understood regarding the genetic architecture of these traits, as well as their underlying biology. This thesis aims to further explore the genetic architecture of cardiometabolic traits by using complementary approaches with greater genetic and phenotype resolution, ranging from studying clinically ascertained extreme phenotypes, deep molecular profiling, or sequence level data. In chapter 2, I investigated the genetic architecture of healthy human thinness (N=1,471) and contrasted it to that of severe early onset childhood obesity (N=1,456). I demonstrated that healthy human thinness, like severe obesity, is a heritable trait, with a polygenic component. I identified a novel BMI-associated locus at PKHD1, and found evidence of association at several loci that had only been discovered using large cohorts with >40,000 individuals demonstrating the power gains in studying clinical extreme phenotypes. In chapter 3, I coupled high-resolution nuclear magnetic resonance (NMR) measurements in healthy blood donors, with next-generation sequencing to establish the role of rare coding variation in circulating metabolic biomarker biology. In gene-based analysis, I identified ACSL1, MYCN, FBXO36 and B4GALNT3 as novel gene-trait associations (P < 2.5x10-6). I also found a novel link between loss-of-function mutations in the "regulation of the pyruvate dehydrogenase (PDH) complex" pathway and intermediate-density lipoprotein (IDL), low-density lipoprotein (LDL) and circulating cholesterol measurements. In addition, I demonstrated that rare "protective" variation in lipoprotein metabolism genes was present in the lower tails of four measurements which are CVD risk factors in this healthy population, demonstrating a role for rare coding variation and the extremes of healthy phenotypes. In chapter 4, I performed a genome-wide association study of fructosamine, a measurement of total serum protein glycation which is useful to monitor rapid changes in glycaemic levels after treatment, as it reflects average glycaemia over 2-3 weeks. In contrast to HbA1c, which reflects average glucose concentration over the life-span of the erythrocyte (~3 months), fructosamine levels are not predicted to be influenced by factors affecting the erythrocyte. Surprisingly, I found that in this dataset fructosamine had low heritability (2% vs 20% for HbA1c), and was poorly correlated with HbA1c and other glycaemic traits. Despite this, I found two loci previously associated with glycaemic or albumin traits, G6PC2 and FCGRT respectively (P < 5x10-8), associated with fructosamine suggesting shared genetic influence. Altogether my results demonstrate the utility of higher resolution genotype and phenotype data in further elucidating the genetic architecture of a range of cardiometabolic traits, and the power advantages of study designs that focus on individuals at the extremes of phenotype distribution. As large cohorts and national biobanks with sequencing and deep multi-dimensional phenotyping become more prevalent, we will be moving closer to understanding the multiple aetiological mechanisms leading to CVD, and subsequently improve diagnosis and treatment of these conditions.
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Albertsdóttir, Elsa. "Genetic analysis of competition traits in Icelandic horses /." Uppsala : Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/10360486.pdf.
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Keith, Deborah J. "Genetic analysis of quantitative traits in Brassica napus." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296926.
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Edmunds, S. V. "Genetic analysis of tritrophic interactions between entompathogenic nematodes, symbiotic bacteria and blood-sucking flies." Thesis, Liverpool John Moores University, 2018. http://researchonline.ljmu.ac.uk/9708/.
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Mosquitoes are responsible for millions of deaths a year through the viruses and parasites they vector. Many of these vector species have successfully expanded their range into temperate climates due to a combination of climate change and the easy movement of goods and people around the world. The temperate climate of the U.K. is home to 34 native species, several of which bite humans and are capable of vectoring pathogens more commonly associated with warmer climates, therefore the threat of mosquito-borne illness in the U.K. is a very real possibility. Many vector mosquito species have evolved resistance to traditional chemical insecticides and the search for novel control strategies in endemic areas is a priority in vector control. Entomopathogenic nematodes (EPNs) are microscopic roundworms, which are obligate parasites of insects from the family Rhabditae. In particular, soil-dwelling nematodes from the genera Heterorhabditis and Steinernema. Presently EPNs are used in a range of plant-based industries as a chemical-pest control. However, previous laboratory research has shown that EPNs are capable of killing more than 250 species of insect including a selection of vector species and nuisance arthropods. This thesis is concerned with discovering whether commercially available and naturally occurring strains of EPNs from the U.K. could be used as an effective biocontrol agent for mosquito and chironomid species. This study includes a snapshot of the current EPN diversity in the U.K. which found four different Steinernema species, including the first molecular confirmation of Steinernema carpocapsae. EPNs from both field-collected and commercial sources were capable of killing and parasitizing two native and tropical mosquito species and Chironomus plumosus. Commercial strains were more effective at killing both, however, the native field-collected, mosquito species Ochlerotatus detritus was susceptible to field-caught EPNs, unlike the tropical, lab-reared Aedes aegypti. EPNs were found to be capable of tolerating the extremes of habitat that mosquito species can inhabit in laboratory tests. These studies have shown that with further research including viable field trials that EPNs could be very useful to add to a range of vector and nuisance control measures when used appropriately.
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Ball, Nia. "Temperament traits in cattle : measurement and preliminary genetic analysis." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/10716.
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The aims of this project were i) to take measures of behaviour in cattle that could be demonstrated to be reliable indicators of temperament traits, and ii) to look for areas of the genome harbouring genes involved in these traits. Behavioural tests were carried out on a large number of animals from a Charolais x Holstein cross-bred herd. Four different tests were examined for their potential to measure different temperament traits: a Flight-from-Feeder Test (FF), a Social Separation Test (SS), a Novel Object Test (NO) and a Handling Test (HA). The results of the tests were assessed using two criteria: inter-animal variability and intra-animal repeatability. The FF, SS and HA Tests showed high values in these two criteria. Experiments were then carried out to validate these three tests, by examining whether relationships were seen between responses from different test situations that were though to measure the same traits. Full validation of the three tests was not achieved. Experiments were also carried out to investigate how stable the behaviour measurements remained with increasing age. Results of SS and HA Tests carried out at four months of age were compared with those from the same tests repeated on the animals at 12 months of age. A relationship was found between SS measures from the two ages. Results from behavioural tests carried out on heifers at 10 months of age were compared with behaviour scored in the dairy parlour at 30 months. The measurements at the younger age were not predictive of adult behaviour in the diary. In order to localise areas of the genome involved in the behavioural traits, preliminary Quantitative Trait Loci (QTL) analysis was carried out on four chromosomes. Associations between behavioural phenotypes from the FF and SS Tests and the inheritance of DNA markers were examined for a large number of animals. The possible effects of environmental factors on the test results were examined prior to the analysis. Four putative QTL locations were identified.
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Taylor, Dennis Leland. "A genetic analysis of molecular traits in skeletal muscle." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274158.
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Genome Wide Association Studies (GWASs) have identified variants associated with disease that promise to deliver insights into disease aetiology. However, because many GWAS variants lie in non-coding genomic regions, it is difficult to define the genes and pathways underlying a GWAS signal. The possibility of linking GWAS variants to molecular traits, combined with the development of high throughput assays, has motivated the mapping of molecular quantitative trait loci (QTLs), genetic associations with molecular traits such as gene expression (eQTLs) and DNA methylation (mQTLs). The Finland-United States Investigation of NIDDM (FUSION) tissue biopsy study is motivated by the desire to understand the molecular pathogenesis of Type 2 diabetes (T2D), a complex disease where the vast majority of the ~100 independent GWAS loci occur in non-coding regions. To elucidate the molecular mechanisms underlying these signals, we collected skeletal muscle biopsies, a T2D-relevant tissue, from 318 extensively phenotyped individuals who exhibit a range of glucose tolerance levels. From these biopsies, we generated genotype, gene expression, and DNA methylation information, enabling us to directly measure the effects of T2D on molecular traits, and to link non-coding T2D GWAS loci to candidate molecular targets. In this thesis, I present a catalogue of genetic effects on gene expression and DNA methylation. I use this catalogue firstly, to reveal basic biology of the genetic regulators of skeletal muscle molecular traits, and secondly, to identify molecular traits that are relevant to T2D, glycemic, and other complex traits. In regards to basic biology, I characterise the broader genomic context of QTLs by calculating the enrichment of QTLs in chromatin states across a diverse panel of cell/tissue types. I also identify key skeletal muscle transcription factors (TFs) and classify them as activators or repressors by aggregating the effects of QTLs predicted to perturb TF binding sites. In addition, I characterise the properties of methylation sites associated with gene expression and use inference models to dissect these methylation-expression relationships, classifying cases where the genetic effect is mediated by methylation, expression, or is independent. I also integrate molecular trait genetics with complex traits. First, I perform a conditional analysis, mapping GWAS variants for T2D and glycemic traits to molecular traits, prioritising disease relevant skeletal muscle molecular traits. Second, recognising QTLs may also be specific to a disease state or environmental context, I leverage the rich phenotyping of participants to map genotype by environment (GxE) effects on gene expression—eQTLs that exhibit effects specific to an environmental context. Altogether, these analyses form a thorough survey of the genetic regulators of skeletal muscle expression and DNA methylation, and provide an important resource for interpreting complex diseases.
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Morrill, Benson H. "Quantitative Genetic Analysis of Reproduction Traits in Ball Pythons." DigitalCommons@USU, 2011. https://digitalcommons.usu.edu/etd/1005.
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Although the captive reproduction of non-avian reptiles has increased steadily since the 1970’s, a dearth of information exists on successful management practices for large captive populations of these species. The data reported here come from a captive population of ball pythons (Python regius) maintained by a commercial breeding company, The Snake Keeper, Inc. (Spanish Fork, UT). Reproductive data are available for 6,480 eggs from 937 ball python clutches. The data presented suggest that proper management practices should include the use of palpation and/or ultrasound to ensure breeding occurs during the proper time of the female reproductive cycle, and that maintenance of proper humidity during the incubation of eggs is vitally important.
Ball python reproduction traits (clutch size, clutch mass, relative clutch mass, egg mass, hatch rate, egg length, egg width, hatchling mass, healthy offspring per clutch, week laid, and days of incubation) were recorded for the clutches laid during this study. For the 937 clutches, the identity of the dam and sire were known for 862 (92%) and 777 (83%) of the clutches, respectively. A multivariate model that included nine of the 11 traits listed above was compiled. Heritability and genetic and phenotypic correlations were calculated from the multivariate analysis. The trait that showed the most promise for use in artificial selection to increase reproduction rates was clutch size due to considerable genetic variation, high heritability, and favorable genetic correlations with other reproduction traits.
Although large datasets have been published for twinning in avian species, relatively few are available for non-avian reptiles. Reported here are 14 sets of twins produced from 6,480 eggs from 937 ball python clutches. The survival rate for twins during the first 3 months of life in our study was 97%. Interestingly, 11 of the sets of twins were identical in sex and phenotype, and additional genetic data suggested the rate of monozygotic twinning within this captive population of ball pythons was higher than that of dizygotic twinning. Further, using microsatellite analysis we were able to generate data that shows three sets of python twins were genetically identical.
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Nagy, Réka. "Genetic analysis using family-based populations." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/28978.
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Most human traits are influenced by a combination of genetic and environmental effects. Heritability expresses the proportion of trait variance that can be explained by genetic factors, and the 1980s heralded the beginning of studies that aimed to pinpoint genetic loci that contribute to trait variation, also known as quantitative trait loci (QTLs). Subsequently, the availability of cheap, high-resolution genotyping chips ushered in the era of genome-wide association studies (GWAS). These genetic studies have discovered many associations between single-nucleotide polymorphisms (SNPs) and complex traits, but these associations do not explain the genetic component of these traits entirely. This is known as the ‘missing heritability’ problem. Within this thesis, 40 medically-relevant human complex traits are studied in order to identify new QTLs. These traits include eye biometric traits, blood biochemical traits and anthropometric traits measured in approximately 28,000 individuals belonging to family-based samples from the general Scottish population (the Generation Scotland study) or from population isolates from Croatian (Korčula, Vis) or Scottish (Shetland, Orkney) islands. These individuals had been genotyped using commercially-available arrays, and unobserved genotypes were imputed using the Haplotype Reference Consortium (HRC) dataset. In parallel to standard GWAS, these traits are analysed using two other statistical genetics approaches: variance component linkage analysis and regional heritability (RH) mapping. Each study is analysed separately, in order to detect study-specific genetic effects that may not generalise across populations. At the same time, because most traits are available in several studies, this also enables meta-analysis, which boosts the power of discovery and can reveal cross-study genetic effects. These methods are a priori complementary to each other, exploiting different aspects of human genetic variation, such as the segregation of variants within families (identity by descent, IBD), or the presence of the same variant throughout the general population (identity by state, IBS). The strengths and weaknesses of these methods are systematically assessed by applying them to real and simulated datasets.
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Jayawardena, Mahen. "An e-Science Approach to Genetic Analysis of Quantitative Traits." Doctoral thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-111597.
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Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.eSSENCE
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Drew, Robert Edward. "Genetic analysis of traits associated with domestication in rainbow trout." Online access for everyone, 2006. http://www.dissertations.wsu.edu/Dissertations/Spring2006/r%5Fdrew%5F122205.pdf.
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Verma, Vinesh. "Genetic analysis of agronomic traits in wheat (Triticum aestivum L.)." Thesis, University of Reading, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270848.
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Goddard, Katrina Blouke. "Study design issues in the analysis of complex genetic traits /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/9565.
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Jayawardena, Mahen. "Parallel algorithms and implementations for genetic analysis of quantitative traits." Licentiate thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-85815.
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Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be regulated by multiple genetic loci. Standard computational tools for analysis of quantitative traits use linear regression models for relating the observed phenotypes to the genetic composition of individuals in a population. However, using these tools to simultaneously search for multiple genetic loci is very computationally demanding. The main reason for this is the complex nature of the optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms and implementation techniques for such optimization problems. The new computational tools will eventually enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the algorithm used for global optimization in the standard, serial software is parallelized and implemented on a grid system. Then, we also describe a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be deployed on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithms such as DIRECT. Finally, a pilot implementation of a grid portal providing a graphical front-end for our code is implemented. After some further development, this portal can be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.
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Mahjani, Behrang. "Methods from Statistical Computing for Genetic Analysis of Complex Traits." Doctoral thesis, Uppsala universitet, Avdelningen för beräkningsvetenskap, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-284378.
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The goal of this thesis is to explore, improve and implement some advanced modern computational methods in statistics, focusing on applications in genetics. The thesis has three major directions. First, we study likelihoods for genetics analysis of experimental populations. Here, the maximum likelihood can be viewed as a computational global optimization problem. We introduce a faster optimization algorithm called PruneDIRECT, and explain how it can be parallelized for permutation testing using the Map-Reduce framework. We have implemented PruneDIRECT as an open source R package, and also Software as a Service for cloud infrastructures (QTLaaS). The second part of the thesis focusses on using sparse matrix methods for solving linear mixed models with large correlation matrices. For populations with known pedigrees, we show that the inverse of covariance matrix is sparse. We describe how to use this sparsity to develop a new method to maximize the likelihood and calculate the variance components. In the final part of the thesis we study computational challenges of psychiatric genetics, using only pedigree information. The aim is to investigate existence of maternal effects in obsessive compulsive behavior. We add the maternal effects to the linear mixed model, used in the second part of this thesis, and we describe the computational challenges of working with binary traits.eSSENCE
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Dhliwayo, Thanda. "Genetic mapping and analysis of traits related to improvement of popcorn." [Ames, Iowa : Iowa State University], 2008.
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Pirzada, Rashid Hussain. "Genetic analysis of production, fertility and health traits of dairy cows." Thesis, Bangor University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364588.
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Linney, Yvonne. "A quantitative genetic analysis of schizotypal personality traits and neuropsychological functioning." Thesis, King's College London (University of London), 2001. http://kclpure.kcl.ac.uk/portal/en/theses/a-quantitative-genetic-analysis-of-schizotypal-personality-traits-and-neuropsychological-functioning(cdce6371-4dd0-401e-873d-75fc5571afc1).html.
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Rao, Shaoqi. "Genetic Analysis of Sheep Discrete Reproductive Traits Using Simulation and Field Data." Diss., Virginia Tech, 1997. http://hdl.handle.net/10919/30490.
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The applicability of restricted maximum likelihood (REML) in genetic analyses of categorical data was evaluated using simulation and field data. Four genetic models were used to simulate underlying phenotypic variates, which were derived as the sum of additive genetic and environmental effects (Model 1A and 1B) or additive genetic and permanent and temporary environmental effects (Model 2A and 2B). Fifty-eight replicates were simulated, each of which contained 5000 ewes by 500 sires and 5000 dams and with up to five records per ewe. The usual transformation of heritability estimated on the categorical scale to the normal scale for fertility and litter size performed better for a simple animal model than for a repeatability model. Genetic correlation estimates between the two categorical traits for Model 1B and 2B were .49 ± .01 and .48 ± .04, respectively, and were close to the expected value of .50. However, permanent and temporary environmental correlations whose input values were each .50 were underestimated with estimates of .41 ± .05 and .26 ± .03, respectively for Model 2B, and .33 ± .02 for the temporary environmental correlation for Model 1B.
Bivariate genetic analyses of litter size with growth and fleece traits were carried out by REML for the data of Suffolk, Targhee and Polypay. Direct heritabilities for most growth traits in all the breeds were low (<.20). Maternal genetic and maternal permanent environmental effects were important for all body weights except for the weaning weight at 120 d for Polypay sheep. Estimates of heritability and permanent environmental effects for litter size for these breeds ranged from .09 to .12 and .00 to .05, respectively. Heritabilities for grease fleece weight and fiber diameter were high for Targhee and Polypay sheep. Direct genetic correlations between growth and litter size were favorable for Suffolk and Targhee but weak for Polypay sheep. Genetic correlations between maternal effects for growth and direct effects for litter size for the breeds were generally small. Within-trait maternal-direct genetic correlations for growth in the breeds were variable and generally negative. Direct genetic correlations of litter size with grease fleece weight and fiber diameter were variable across the breeds.Ph. D.
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Do, Ron. "Global Analysis of genetic variants associated with cardiovascular disease and related metabolic traits." Thesis, McGill University, 2010. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=95134.
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Coronary heart disease (CHD) is the leading cause of morbidity and mortality in the western world. CHD is common throughout the world and is multifactorial, caused by the accumulation or interaction of quantitative changes in various intermediate traits (risk factors or metabolic phenotypes). Intermediate traits that are commonly studied include plasma levels of cholesterol (ie. low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) and total cholesterol), body mass index (BMI) and blood pressure, which are all believed to be influenced by a combination of genetic and environmental factors (such as diet, alcohol, and exercise). In this thesis, the identification of novel genetic variants in candidate genes (a non-synonymous variant in farnesyl-diphosphate farnesyltransferase 1 (FDFT1) and a non-coding variant in insulin-induced gene 2 protein (INSIG2)) that are associated with total cholesterol and low density lipoprotein cholesterol is described. In addition, detailed investigation of common genetic variants in known genes identified from genome-wide association studies in the context of other genetic, phenotypic and environmental factors are reported. In particular, INSIG2 variants were observed to act in concert with a trans-acting variant in the sorbin and SH3 domain containing 1 gene (SORBS1) to influence LDL-C and apoB levels in Quebec, European and South Asian population samples. In addtition, fat mass and obesity associated gene (FTO) variants were observed to influence adiposity-related traits, resting metabolic rate and plasma leptin levels. I also report the role of dietary intake in modifying the effect of 9p21 variants on myocardial infarction and cardiovascular disease in the multi-ethnic INTERHEART study and in a Finnish sample, FINRISK. Finally, the utility of exome sequencing in identifying the genetic cause of a mendelian lipid disorder is demonstrated in a study that identifies compound heterozygoLa maladie coronarienne athéroscléreuse est l'une des causes principales de morbidité et de mortalité dans le monde occidental. Elle est commune à travers le monde et est multifactorielle, causée par une accumulation ou une interaction de changements quantitatifs de divers traits intermédiaires (facteurs de risque ou phénotypes métaboliques). Les traits intermédiaires souvent étudiés comprennent les taux plasmatiques de cholestérol (e.g. le cholestérol des lipoprotéines de faible densité (C-LDL), le cholestérol lié aux lipoprotéines de haute densité (C-HDL) et le cholestérol total), l'indice de masse corporelle (IMC) et la pression artérielle, qui sont tous présumés être influencés par une combinaison de facteurs génétiques et environnementaux (tels que l'alimentation, l'alcool, et l'exercice). Dans cette thèse, l'identification de nouveaux variants génétiques (un variant non-synonyme du gène farnesyl-diphosphate farnesyltransferase 1 (FDFT1) et un variant non-codant du gène insulin-induced gene 2 protein (INSIG2)) de gènes candidats associés au cholestérol total et au C-LDL est décrite. De plus, une investigation détaillée des variants génétiques communs dans des gènes connus identifiés à partir d'études d'associations pangénomiques dans le contexte d'autres facteurs génétiques, phénotypiques et environnementaux sont aussi présentés dans cette thèse. En particulier, il a été démontré que les variants du gène INSIG2 agissent de concert avec un variant 'trans-acting' du gène sorbin and SH3 domain containing 1 (SORBS1) pour influencer les niveaux de C-LDL et les niveaux d'apoB dans des populations du Québec, d'Europe et d'Asie du Sud. De même, les variants du gène de fat mass and obesity associated (FTO) ont été observés à influencer des traits liées à l'adiposité, au taux métabolique au repos et au niveaux de leptine plasmatique. Dans ma thèse, je décris également le rôle de l'apport aliment
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Dahlgren, Andreas. "Analysis of Complex Genetic Traits in Population Cohorts using High-throughput Genotyping Technology." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8291.
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Johnson, Michelle D. "Genetic analysis of hypertension and expression quantitative traits in the spontaneously hypertensive rat." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508322.
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Marques, Daniele Botelho Diniz. "Genetic parameters and genomic analysis of semen quality and fertility traits in pigs." Universidade Federal de Viçosa, 2017. http://www.locus.ufv.br/handle/123456789/18797.
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O uso generalizado da inseminação artificial (IA) contribuiu grandemente para o sucesso da indústria de suínos, por meio do auxílio e disseminação do progresso genético. Atualmente, reprodutores suínos jovens são selecionados para IA com base em seus valores genéticos para características de produção e, a seleção de reprodutores para características de sêmen, como volume, concentração, motilidade e morfologia, bem como para menor variação intra- reprodutor na sua produção e qualidade, ainda não é uma prática comum. Esta seleção é importante para melhorar o desempenho dos reprodutores nas estações de IA, cujo objetivo é maximizar o número de doses inseminantes produzidas por cada ejaculado. A estimação de parâmetros genéticos e quantificação da variação genética para características de sêmen e para variação intra-reprodutor permitem analisar se essas características devem ser incluídas nos objetivos do melhoramento. Além da estimação de parâmetros genéticos para fins de seleção, o interesse em estudar os processos moleculares e os mecanismos genéticos que afetam as características de sêmen está aumentando nos últimos anos. Os estudos de associação genômica ampla (GWAS) são comumente usados para identificar polimorfismos de base única (SNPs) associados a loci de características quantitativas (QTL) com maiores efeitos. O GWAS em passo único ponderado (WssGWAS) é um método que permite a estimação de efeitos de SNP utilizando informações de todos os animais genotipados, fenotipados e com pedigree na população. Expandindo as fronteiras dos estudos de reprodução em suínos, outro campo importante a ser explorado em programas de melhoramento é a fertilidade dos reprodutores. As características reprodutivas, como a duração da gestação (GL), o número total de leitões nascidos (TNB) e nascidos mortos (SB) são algumas características-chave para a produção eficiente de suínos. Devido às baixas ou moderadas herdabilidades para essas características, é importante identificar todos os fatores que as influenciam e incluir esses fatores nos modelos de avaliação genética. Os efeitos do reprodutor cujo ejaculado foi utilizado para inseminar a matriz e do ejaculado são dois desses fatores importantes que têm o potencial de melhorar os modelos tradicionais utilizados nas avaliações genéticas das características reprodutivas. Dentre os elementos que controlam o tamanho da leitegada, as taxas de fertilização e de sobrevivência pré-natal podem ser influenciadas pelo reprodutor, devido às diferenças genéticas na capacidade de fertilização relacionadas à qualidade do sêmen e/ou à contribuição genética do reprodutor para a viabilidade do embrião. Nesse contexto, os objetivos gerais com este estudo foram 1) estimar os parâmetros genéticos para qualidade e quantidade de sêmen, bem como para a variação intra-reprodutor para essas características; 2) identificar regiões de QTL e genes candidatos associados a características de sêmen por meio do WssGWAS e, subsequentemente, realizar análises de redes gênicas para investigar os processos biológicos compartilhados por genes identificados em diferentes linhas de suínos e 3) estimar parâmetros genéticos para o efeito do reprodutor na GL, TNB e SB e avaliar a inclusão dos efeitos do reprodutor e do ejaculado nos modelos de avaliação genética dessas características. Os resultados desta tese mostraram estimativas moderadas de herdabilidade e correlações genéticas favoráveis entre características de sêmen, indicando que a seleção de reprodutores para essas características pode resultar em razoável progresso genético. Além disso, variação genética relevante foi encontrada para a variabilidade intra-reprodutor para essas características, revelando a possibilidade de seleção de reprodutores para uma menor variação na qualidade e produção de sêmen. Os resultados do WssGWAS apontaram regiões relevantes de QTL que explicaram grandes proporções da variância genética (até 10,8%) para as características de sêmen em vários cromossomos suínos, confirmando a suposição de complexidade genética dessas características. Esta identificação foi possível com o baixo número de animais com fenótipos e genótipos, devido à escolha apropriada do método. Os genes candidatos SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG, LOC102167830, NME5, AZIN2, SPATA7, METTL3 e HPGDS foram identificados associados às características de sêmen nas regiões de QTL identificadas para as linhas de suínos avaliadas. A análise de redes gênicas mostrou genes candidatos encontrados para diferentes linhas de suínos compartilhando caminhos biológicos que ocorrem nos testículos de mamíferos. No que diz respeito à fertilidade do reprodutor, os resultados mostraram que há variação genética devido ao efeito do reprodutor em GL, TNB e SB; e o modelo com inclusão de efeitos de ambiente permanente e genéticos do reprodutor, além do efeito do ejaculado, mostrou o melhor ajuste para os dados. Esta tese resultou em informações científicas importantes e inovadoras na área de reprodução em machos, o que contribuirá para aumentar o conhecimento ainda escasso sobre a seleção genética e a arquitetura genômica de características de qualidade de sêmen e de fertilidade em reprodutores suínos.
The widespread use of artificial insemination (AI) has greatly contributed to the success of the pig industry by assisting and disseminating the genetic progress. Currently, young boars are selected for AI based on their breeding values for production traits and selecting boars for semen traits, such as volume, concentration, motility and morphology, and for low variation in semen quality and production is still not a common practice. This selection is important for better performance of boars at AI stations, whose objective is to maximize the number of insemination doses produced by each ejaculate. The estimation of genetic parameters and the quantification of genetic variation for semen traits and within-boar variation allow an analysis of whether these traits should be included in the breeding goal. Besides the estimation of genetic parameters for selection purposes, the interest in studying the molecular processes and genetic mechanisms affecting semen traits is increasing in recent years. Genome-wide association studies (GWAS) are commonly used to identify single nucleotide polymorphisms (SNPs) associated with quantitative trait loci (QTL) with major effect. The weighted single-step GWAS (WssGWAS) is a method that allows estimation of SNP effects using information from all genotyped, phenotyped and pedigree animals. Expanding the frontiers of reproduction studies in pigs, another important field to be explored in breeding programs is the boar fertility. Reproductive traits, such as gestation length (GL), total number of piglets born (TNB) and stillborn (SB) are some of the bottleneck traits for efficient pig production. Because of the low to moderate heritabilities for these traits, it is important to identify all factors influencing them and to include these factors in the genetic evaluation models. The service sire (boar which ejaculate dose was used to inseminate the sow) and ejaculate effects are two of those important factors that have the potential to improve the traditional models used in the genetic evaluations of reproductive traits. Among the elements controlling the litter size, the fertilization rate and prenatal survival rate might be influenced by the service sire due to genetic differences in the capacity of fertilization, which is related to sperm quality and/or the boar genetic contribution to viability of the embryo. In this context, my overall aims were 1) to estimate genetic parameters for semen quality and quantity traits, as well as for within-boar variation of these traits; 2) to identify QTL regions and candidate genes associated with semen traits through a WssGWAS and, subsequently, to perform gene network analyses to investigate the biological processes shared by genes identified in different pig lines and 3) to estimate genetic parameters for service sire on reproductive traits GL, TNB and SB and to evaluate the inclusion of service sire and ejaculate effects in the genetic evaluation models of these traits. The results of this thesis showed moderate estimates of heritability and favorable genetic correlations between semen traits, indicating that boar selection for these traits could make reasonable genetic progress. In addition, relevant genetic variation was found for within-boar variability of these traits, revealing the possibility of selection of boars for reduced variation in semen quality and production. Results from WssGWAS pinpointed relevant QTL regions explaining high proportions of genetic variance (up to 10.8%) for semen traits in several pig chromosomes, confirming the assumption of genetic complexity of these traits. This identification was possible with low number of animals having both phenotypes and genotypes due to the appropriate choice of the method. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG, LOC102167830, NME5, AZIN2, SPATA7, METTL3 and HPGDS were identified associated with semen traits in the QTL regions identified for the pig lines evaluated. The gene network analysis showed candidate genes found for different pig lines sharing biological pathways that occur in mammalian testes. Regarding boar fertility, the results showed that there is genetic variation due to service sire effect on GL, TNB and SB; and the model with inclusion of permanent environmental and genetic effects due to service sire, in addition to ejaculate effect, showed the best fit to the data. This thesis resulted in important and innovative scientific information on male reproduction field in pigs, which will contribute to increase the still scarce knowledge about genetic selection and genomic architecture of boar semen quality and fertility traits.
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Larkin, Emma Katherine. "A Genetic Analysis of Correlated Traits: The Apnea Hypopnea Index and Body Mass Index." Connect to text online, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1175825365.
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Thesis (Ph. D.)--Case Western Reserve University, 2007.[School of Medicine] Department of Epidemiology and Biostatistics. Includes bibliographical references. Available online via OhioLINK's ETD Center.
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Salah-ud-Din. "The genetic analysis of production and reproduction traits in Nili-Ravi buffalo in Pakistan /." The Ohio State University, 1989. http://rave.ohiolink.edu/etdc/view?acc_num=osu148767224590405.
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Meehan, Anna, and Henrik Evertsson. "Genetic and Environmental Influences on Psychopathic Personality Traits : A Meta-Analytic Review." Thesis, Örebro universitet, Institutionen för juridik, psykologi och socialt arbete, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:oru:diva-27685.
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To understand the etiology of psychopathic personality traits and thus in the long run to be able to develop successful prevention, a first step is to find out what role genetic and environmental effects play. A meta-review of 15 twin studies (N=26, 981), was conducted to estimate the magnitude of genetic and environmental influences on psychopathic personality traits. The results show that additive genetic (heritable) factors and non-shared environmental factors each explain 50% of the variance in psychopathic personality traits, while shared environmental factors were of no importance. Measure, informant, age, and sex were investigated as potential moderators showing that informant had an impact on the findings. This meta-analysis provides a structured synthesis of the relative genetic and environmental contributions in psychopathic personality traits through various stages of development and across sex.För att förstå etiologin av psykopatiska personlighetsdrag och därmed i det långa loppet kunna utveckla framgångsrik prevention, är ett första steg att klargöra vilken roll genetiska och miljömässiga effekter spelar. En meta-översikt på 15 tvillingstudier (N=26,981), genomfördes för att uppskatta i vilken grad genetiska och miljömässiga faktorer påverkar psykopatiska personlighetsdrag. Resultaten visade att additiva genetiska (ärftliga) och unika miljömässiga faktorer förklarar 50% var av variansen i psykopatiska personlighetsdrag, medan delade miljömässiga faktorer inte var av betydelse. Mått, informant, ålder och kön undersöktes som potentiella moderatorer och visade att informant påverkade resultaten. Denna meta-analys ger en strukturerad syntes av de relativa genetiska och miljömässiga bidrag som påverkar psykopatiska personlighetsdrag genom olika utvecklingsstadier och mellan könen.
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Park, Hee-Bok. "Genetic Analysis of Quantitative Traits Using Domestic Animals : A Candidate Gene and Genome Scanning Approach." Doctoral thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4582.
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Domestication has led to genetic changes that affect quantitative traits in farm animals. Both candidate gene analysis using association tests and genome scans based on linkage analysis have been performed to understand the molecular basis underlying quantitative genetic variation in horses, pigs and chickens. To test a possible association of polymorphisms in the PRKAG3 gene, previously found to be associated with excess glycogen content in pig skeletal muscle, with quantitative traits in the horse, the major coding part of the equine PRKAG3 sequence was identified. Bioinformatic characterization of the equine PRKAG3 gene was conducted. A single nucleotide polymorphism (SNP) causing a missense mutation (Pro258Leu) was found. Screening this SNP showed that the Leu258 allele was more frequent in breeds with heavy muscularity. To assess previously reported associations between polymorphisms in the MC4R gene and obesity-related traits further, we conducted linkage analysis between the MC4R locus and fatness-related traits using a Wild BoarxLarge White intercross. No significant association between segregation at the MC4R locus and fatness was detected in this pedigree. A genome scan of quantitative trait loci (QTLs) has been performed in an intercross between chicken lines divergently selected for growth. Divergent parental lines have been established by selecting for high and low 56-day body weight for over 40 generations. The selection has led to approximately a 9-fold difference in 56-day body weight between lines and resulted in correlated responses for a number of traits including appetite, immune response, body composition and metabolic traits. Phenotypic data on growth and other correlated traits were collected from more than 800 F2 individuals. Genome scans using 145 markers on 26 linkage groups have identified QTLs affecting growth and correlated responses to selection for 56-day body weight. No major QTL explaining a large portion of phenotypic variation in growth was revealed in this study.
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Kranis, Andreas. "Longitudinal aspects of the genetic analysis of reproduction traits in a modern heavy turkey line." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/11012.
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The objective of this thesis was to investigate the longitudinal aspect of the genetics of egg laying in two heavy female turkeys and explore whether considering time features of laying may improve selection efficiency. The dataset consisted of records from two commercial lines, although only one had longitudinal data. The genetic correlation between body weight and total egg number was estimated to be -0.7±0.1 and -0.5±0.1 in the two lines studied. Both estimates were highly negative and larger in magnitude than in traditional and lighter lines, suggesting that the continuous selection for growth hinders genetic progress for egg production. Heritability estimates for body weight were high (around 0.4), while being lower for total egg number (around 0.2 for egg records on which Box-Cox transformation has been applied to reduce their deviation from normality). Since heavier birds tended to lay fewer eggs within a specific period, this implied reduced rates of lay. In order to explore this consequence of the selection for antagonistic traits, a time-to-event trait was formulated that corresponded to the days required for a hen to lay 82 eggs (the average egg production in the dataset). It was shown that the Weibull distribution could satisfactorily serves the baseline function under a survival analysis context. So, a frailty model was constructed to perform a genetic analysis of the time trait and it was found that its heritability estimate was between that for the transformed and untransformed total egg number. Random regression (RR) models were also considered for the longitudinal analysis of egg production. The detailed covariance structure obtained on a longitudinal basis can be used to target more effectively the selection pressure on the most informative stages of laying and thus, to maximise the output of breeding programmes.
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Wittern, Lukas Maximilian. "Genetic analysis of the effect of circadian clock genes on yield component traits in wheat." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/279080.
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Garrido, Martín Diego 1992. "A Multivariate approach to study the genetic determinants of phenotypic traits." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668497.
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We have developed an efficient and reproducible pipeline for the identification of genetic variants affecting splicing (splicing quantitative trait loci or sQTLs), based on an approach that captures the intrinsically multivariate nature of this phenomenon. We employed it to study the multi-tissue transcriptome GTEx dataset, generating a comprehensive catalogue of sQTLs in the human genome. Downstream analyses of this catalogue provide novel insights into the mechanisms underlying alternative splicing regulation and its contribution to human complex traits and diseases. To facilitate the visualization of splicing events in GTEx and other large-scale RNA-seq studies, we developed a software to generate sashimi plots, which supports the aggregated representation of hundreds of samples. Given the growing interest in efficient methods to identify genetic effects on multiple traits, we extended the statistical framework employed for sQTL mapping (Anderson test) to accommodate any quantitative multivariate phenotype and experimental design. We derived the limiting distribution of the test statistic, allowing to compute asymptotic p values. We further demonstrated the advantages and applicability of our approach to GWAS and QTL mapping analyses using simulated and real datasets.Hemos desarrollado un método computacional eficiente y reproducible, que permite la identificación de variantes genéticas que afectan al splicing (splicing quantitative trait loci o sQTLs), y que es capaz de capturar la naturaleza multivariante de este fenómeno. Lo hemos empleado para estudiar el conjunto de datos GTEx, que contiene información sobre el transcriptoma en múltiples tejidos, generando un catálogo completo de sQTLs en el genoma humano. El análisis de dicho catálogo proporciona nuevos conocimientos sobre los mecanismos que subyacen a la regulación del splicing alternativo, así como sobre su contribución a los rasgos complejos y enfermedades humanas. Con el objetivo de facilitar la visualización de eventos de splicing en GTEx y otros estudios de secuenciación de ARN a gran escala, hemos desarrollado un software para generar gráficos de tipo sashimi, que permite la representación agregada de cientos de muestras. En vista del creciente interés por métodos capaces de analizar efectos genéticos en múltiples rasgos de manera eficiente, hemos extendido el marco estadístico empleado para la identificación de sQTLs (test de Anderson) para acomodar cualquier fenotipo multivariante cuantitativo y diseño experimental. Hemos derivado la distribución límite del estadístico, lo que nos permite calcular p valores asintóticos. Además, demostramos las ventajas y la aplicabilidad de nuestro método en GWAS y análisis de QTLs, empleando conjuntos de datos tanto simulados como reales.
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Liang, Wei <1982>. "Molecular strategies for genetic diversity analysis and development of markers linked to resistance traits in apple." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amsdottorato.unibo.it/5910/.
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The goal of many plant scientists’ research is to explain natural phenotypic variation in term of simple changes in DNA sequence. DNA-based molecular markers are extensively used for the construction of genome-wide molecular maps and to perform genetic analysis for simple and complex traits. The PhD thesis was divided into two main research lines according to the different approaches adopted. The first research line is to analyze the genetic diversity in an Italian apple germplasm collection for the identification of markers tightly linked to targeted genes by an association genetic method. This made it possible to identify synomym and homonym accessions and triploids. The fruit red skin color trait has been used to test the reliability of the genetic approaches in this species. The second line is related to the development of molecular markers closely linked to the Rvi13 and Rvi5 scab resistance genes, previously mapped on apple’s chromosome 10 and 17 respectively by using the traditional linkage mapping method. Both region have been fine-mapped with various type of markers that could be used for marker-assisted selection in future breeding programs and to isolate the two resistance genes.
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Paternoster, Lavinia. "Genetic risk factors for stroke-related quantitative traits and their associated ischaemic stroke subtypes." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/4337.
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Stroke is the 2nd leading cause of death in the UK and worldwide. 150,000 people have a stroke each year in the UK (ischaemic stroke being the most common) and a significant proportion of NHS resources go towards the treatment of these individuals (~£2.8 billion). Twin and family history studies have shown that having affected relatives makes you between 30 and 76% more likely to suffer a stroke, suggesting that there is a genetic component to the disease. So far, no genes have been convincingly associated with stroke. Intermediate traits may be useful tools for identifying genetic factors in complex disease. For stroke, two commonly used intermediate traits are carotid intima-media thickness (CIMT) and white matter hyperintensities (WMHs), which both show high heritabilities. These traits have both been studied widely for associations with many candidate gene polymorphisms. In this thesis I systematically reviewed the literature for all genetic association studies of these two traits. Where particular associations have been studied in large numbers I meta-analysed the available data, developing novel methods for meta-analysis of genetic association data. I found there was substantial heterogeneity and small study bias in the literature and most polymorphisms have still been studied in too small numbers to make accurate conclusions. Apolipoprotein E (APOE) ε is the only polymorphism which shows a consistent association with CIMT, even when only the largest studies are analysed (MD 8μm (95% CI 6 to 11) between E4 and E3, and E3 and E2). No polymorphism has shown a convincing association with WMHs and interestingly APOE appears unlikely to be associated with this trait. This is consistent with previous work that shows that APOE is associated with large artery but not small artery stroke. Taking this hypothesis I attempted to investigate the association of APOE comparing patients who have had a large artery stroke with those who have had a small artery stroke in the Edinburgh Stroke Study cohort. However, genotyping of this polymorphism failed and I present investigatory analyses of problems from the genotyping laboratory.
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Huang, Mao. "Genetic Analysis of Quality Traits for Food-Grade Soybean (Glycine max L. Merr.) in a Breeding Population." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354715116.
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Ramalingam, Sathya [Verfasser]. "Genetic and Molecular analysis of yield and physiological traits in three line hybrids in rice (Oryza sativa L.) under aerobic condition : Genetic studies on physiological and morphological traits of three line hybrids / Sathya Ramalingam." München : GRIN Verlag, 2012. http://d-nb.info/1183291213/34.
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Kronhamn, Jesper. "Genetic analysis of genes found on the 4th chromosome of Drosophila - emphasizing the developmental context of Pax6." Doctoral thesis, Umeå universitet, Molekylärbiologi (Teknat- och Medfak), 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-287.
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The small size and the lack of recombination set the fourth chromosome of Drosophila melanogaster apart from the other chromosomes. I have shown that the Minute gene on chromosome 4, earlier named Minute-4, encodes the ribosomal protein RpS3A. Two Pax6 genes, eyeless (ey) and twin of eyeless (toy) are also located on chromosome 4. Pax6 genes are important in head and eye development in both mammals and Drosophila. I have focused much of the study on ey and toy. The first mutant of toy that was characterized showed a headless phenotype. This indicates that Toy is important for the development of both the eye and antennal discs. The phenotype of the null mutation in toy is temperature sensitive due to that transcription of ey is temperature dependent in the eye-antennal primordium in absence of Toy. This temperature dependence was used to find out that the phenocritical period for ey in the adult head development is during embryonic stage 12-16 when ey first is expressed in the eye-antennal primordium. I also conclude that ey is activated by Toy in the eye-antennal primordium. The strong eyD mutation was molecularly characterized and it was finally settled that it is an allele in the ey locus. I also show that eyD homozygotes have a headless phenotype, much stronger than the earlier ey mutations.
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Kiran, Aysha [Verfasser]. "Genetic and phenotypic analysis of complex seed and root traits in oilseed rape (Brassica napus L.) / Aysha Kiran." Gießen : Universitätsbibliothek, 2015. http://d-nb.info/1068874821/34.
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Laenoi, Watchara [Verfasser]. "Genetic analysis and expression study of candidate genes affecting leg weakness-related traits in pigs / Watchara Laenoi. Landwirtschaftliche Fakultät." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1019528095/34.
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Alshugeairy, Zaniab. "Genetic, phenomic and molecular analysis of drought avoidance and recovery traits in rice for the improvement of plant breeding." Thesis, University of Aberdeen, 2013. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=203868.
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Rice (Oryza sativa L.) is one of the main staple foods of the world. With the increase of population and the deficit of irrigated water, the increase in rice production that is predicted will be dependent on areas prone to drought. Root depth is important for plant growth and survival during drought because of its role in facilitating water uptake from deep soil layers. By advances in genomics, the plant root systems can be linked to quantitative trait locus (QTL) information to achieve a most beneficial design of root system architecture. There is a demand to develop and validate techniques that permit estimation of the root system. Therefore, two techniques (root penetration ability to non-woven fabric and a buried herbicide method at depth 30 cm) were used in this study to assess root traits in a total of 36 rice cultivars. The results from these screens were assessed with root traits measured on the same cultivars in the rhizotrons and hydroponic experiment. Correlations between these methods showed that herbicide score at day 35 was most strongly related to traits of the rhizotron experiment, especially number of roots passed 50 cm at 35 days, root angle at day 21, root thickness, water use and % root mass. Using all of these traits obtained in the rhizotron in a best subset regression suggests that up to 71% of the variation in herbicide score can be explained. These data strongly imply that symptoms are related to root development and transpiration demand and are therefore ideal for assessing water extraction by roots at depth. The herbicide method has been applied to screen root depth in 138 recombinant inbred lines derived from crossing between two subspecies Indica Bala and Japonica Azucena. Analysis of mapping population revealed two putative QTLs on chromosome 6 near marker RZ682 and one on chromosome 7 near marker RG351 and two significant QTLs near marker G1010b and G1073 for root depth on chromosome 8. The same method has been used to evaluate root depth in 325 rice diversity panel allowing high resolution genetic mapping. Using efficient mixed model (statistical analyses for genome wide association), four associations were detected, two on chromosome 1 and one on each of chromosome 4 and 6. In addition, the same rice diversity panel has been evaluated for drought avoidance by assessing leaf rolling (as one plant mechanism against drought stress) and drought recovery. A total of three significant associations, on chromosomes 4, 6 and 7 were identified for leaf rolling while only one significant association on chromosome 2 for drought recovery was found. Positional candidate genes underneath QTLs were examined bioinformatically and through the literature revealing several interesting genes which may offer potential for developing drought resistant rice cultivars. Therefore, developing a cost effective high-throughput system that can measure traits related to drought avoidance and drought recovery on a large number of plants would aid genetic studies in breeding and gene identification.
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Andersson, Bea Angelica. "Analysis of Selection and Genetic Drift in a Dioecious Plant : Spatial Genetic Structure and Selection in Phenotypic Traits in a Young Island Population of Silene dioica." Thesis, Umeå universitet, Institutionen för ekologi, miljö och geovetenskap, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-96275.
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Selection and genetic drift are often competing forces in shaping genetic structure in populations. Genetic drift will often effectively cancel out the effect of selection when population sizes are small, such as in colonizing island populations. On a small island in the Skeppsvik Archipelago in northern Sweden, a newly founded population of Silene dioica has been monitored since it first established around 1993. Though inhabiting an area of merely 173 m2, the population has been shown to exhibit a genetically differentiated patch structure where closely related individuals are tightly grouped, distanced from other family groups. In this study, the effect of selection was evaluated as compared to that of genetic drift. Variation in phenotypic traits in flowers, leaves and stalks were compared to that of neutral markers, in the form of PST and FST measures, to assess a measure of what proportion of differentiation among patches in phenotypic traits could not be attributed to genetic drift. Males and females were analysed separately to obtain measures of sex specific selection. Signs of divergent and stabilizing selection were found in several traits in both males and females despite the small spatial scale and short time since colonization. Further analysis is needed to assess explanations for trait divergence among patches and direction of selection.
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Hoffstetter, Amber L. "Assessing genome wide breeding strategies for economic traits in soft winter wheat and their impact on genetic architecture." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1448825514.
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Natanzon, Yanina. "METABOLIC SYNDROME IN AN IMMUNOSUPPRESSED POPULATION: GENETIC CONTRIBUTION TO METABOLIC SYNDROME TRAITS IN THE WOMEN'S INTERAGENCY HIV STUDY." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1449252475.
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Schiller, Katja [Verfasser], and Jörn [Akademischer Betreuer] Bennewitz. "Phenotypic and genetic analysis of meat production traits in German Merinoland purebred and crossbred lambs / Katja Schiller ; Betreuer: Jörn Bennewitz." Hohenheim : Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim, 2017. http://d-nb.info/1124051740/34.
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Konigorski, Stefan. "Development and application of new statistical methods for the analysis of multiple phenotypes to investigate genetic associations with cardiometabolic traits." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/19132.
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Die biotechnologischen Entwicklungen der letzten Jahre ermöglichen eine immer detailliertere Untersuchung von genetischen und molekularen Markern mit multiplen komplexen Traits. Allerdings liefern vorhandene statistische Methoden für diese komplexen Analysen oft keine valide Inferenz.
Das erste Ziel der vorliegenden Arbeit ist, zwei neue statistische Methoden für Assoziationsstudien von genetischen Markern mit multiplen Phänotypen zu entwickeln, effizient und robust zu implementieren, und im Vergleich zu existierenden statistischen Methoden zu evaluieren. Der erste Ansatz, C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes), ermöglicht die Assoziation von genetischen Varianten mit multiplen Traits in einem gemeinsamen Copula Modell zu untersuchen. Der zweite Ansatz, CIEE (Causal Inference using Estimating Equations), ermöglicht direkte genetische Effekte zu schätzen und testen.
C-JAMP wird in dieser Arbeit für Assoziationsstudien von seltenen genetischen Varianten mit quantitativen Traits evaluiert, und CIEE für Assoziationsstudien von häufigen genetischen Varianten mit quantitativen Traits und Ereigniszeiten. Die Ergebnisse von umfangreichen Simulationsstudien zeigen, dass beide Methoden unverzerrte und effiziente Parameterschätzer liefern und die statistische Power von Assoziationstests im Vergleich zu existierenden Methoden erhöhen können - welche ihrerseits oft keine valide Inferenz liefern.
Für das zweite Ziel dieser Arbeit, neue genetische und transkriptomische Marker für kardiometabolische Traits zu identifizieren, werden zwei Studien mit genom- und transkriptomweiten Daten mit C-JAMP und CIEE analysiert. In den Analysen werden mehrere neue Kandidatenmarker und -gene für Blutdruck und Adipositas identifiziert. Dies unterstreicht den Wert, neue statistische Methoden zu entwickeln, evaluieren, und implementieren. Für beide entwickelten Methoden sind R Pakete verfügbar, die ihre Anwendung in zukünftigen Studien ermöglichen.In recent years, the biotechnological advancements have allowed to investigate associations of genetic and molecular markers with multiple complex phenotypes in much greater depth. However, for the analysis of such complex datasets, available statistical methods often don’t yield valid inference. The first aim of this thesis is to develop two novel statistical methods for association analyses of genetic markers with multiple phenotypes, to implement them in a computationally efficient and robust manner so that they can be used for large-scale analyses, and evaluate them in comparison to existing statistical approaches under realistic scenarios. The first approach, called the copula-based joint analysis of multiple phenotypes (C-JAMP) method, allows investigating genetic associations with multiple traits in a joint copula model and is evaluated for genetic association analyses of rare genetic variants with quantitative traits. The second approach, called the causal inference using estimating equations (CIEE) method, allows estimating and testing direct genetic effects in directed acyclic graphs, and is evaluated for association analyses of common genetic variants with quantitative and time-to-event traits. The results of extensive simulation studies show that both approaches yield unbiased and efficient parameter estimators and can improve the power of association tests in comparison to existing approaches, which yield invalid inference in many scenarios. For the second goal of this thesis, to identify novel genetic and transcriptomic markers associated with cardiometabolic traits, C-JAMP and CIEE are applied in two large-scale studies including genome- and transcriptome-wide data. In the analyses, several novel candidate markers and genes are identified, which highlights the merit of developing, evaluating, and implementing novel statistical approaches. R packages are available for both methods and enable their application in future studies.
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Blomquist, Thomas M. "Development of Bimodal Gene Expression Analysis and Allele-Specific Competitive PCR for Investigation of Complex Genetic Traits, Lung Cancer Risk." University of Toledo Health Science Campus / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=mco1277151230.
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Galal, Ushma. "The statistical theory underlying human genetic linkage analysis based on quantitative data from extended families." Thesis, University of the Western Cape, 2010. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_2684_1361989724.
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Traditionally in human genetic linkage analysis, extended families were only used in the analysis of dichotomous traits, such as Disease/No Disease. For quantitative traits, analyses initially focused on data from family trios (for example, mother, father, and child) or sib-pairs. Recently however, there have been two very important developments in genetics: It became clear that if the disease status of several generations of a family is known and their genetic information is obtained, researchers can pinpoint which pieces of genetic material are linked to the disease or trait. It also became evident that if a trait is quantitative (numerical), as blood pressure or viral loads are, rather than dichotomous, one has much more power for the same sample size. This led to the
development of statistical mixed models which could incorporate all the features of the data, including the degree of relationship between each pair of family members. This is necessary because a parent-child pair definitely shares half their genetic material, whereas a pair of cousins share, on average, only an eighth. The statistical methods involved here have however been developed by geneticists, for their specific studies, so there does not seem to be a unified and general description of the theory underlying the methods. The aim of this dissertation is to explain in a unified and statistically comprehensive manner, the theory involved in the analysis of quantitative trait genetic data from extended families. The focus is on linkage analysis: what it is and what it aims to do.
There is a step-by-step build up to it, starting with an introduction to genetic epidemiology. This includes an explanation of the relevant genetic terminology. There is also an application section where an appropriate human genetic family dataset is analysed, illustrating the methods explained in the theory sections.