Dissertations / Theses on the topic 'Genetic trait'
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Salmon, Anderson Tricia. "Sickle Cell Trait and Genetic Counseling." ScholarWorks, 2017. https://scholarworks.waldenu.edu/dissertations/4020.
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Sickle cell trait (SCT) is a very prevalent disorder in the United States, especially among African Americans or people of African descent. However, even with the prevalence of the disorder, there are no standardized guidelines for providing patients with information about SCT and the implications of the disorder at physicals and well-check visits. The purpose of this evidence-based project was to increase awareness for African American patients 18-44 years old in the practice setting about SCT and to provide options for testing and genetic counseling. Kotter's contemporary change theory was used as a guide to implement the new practice approach. A quasi-experimental, single-group, pretest-posttest-only design was used to explore the relationship between providing consistent SCT education and the impact on the rate of SCT screening and genetic counseling. A total of 71 patients participated in the program. The analysis showed a significant (p < 0.001) mean difference of 18.16 points from the preintervention SCT and genetics test mean, which indicated that the intervention was successful in raising SCT and genetics knowledge scores among the target population. The results demonstrated that the implementation of SCT education in the practice setting can enhance social implications related to SCT awareness and opportunities for SCT testing and genetic counseling. The implementation of SCT clinical guidelines can help to increase awareness about SCT and improve the overall population health and reduce the financial burden affiliated with care of those with sickle cell disease and SCT complications.
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Finucane, Hilary Kiyo. "Functional and cross-trait genetic architecture of common diseases and complex traits." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/112906.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, 2017Cataloged from PDF version of thesis.
Includes bibliographical references (pages 201-245).
In this thesis, I introduce new methods for learning about diseases and traits from genetic data. First, I introduce a method for partitioning heritability by functional annotation from genome-wide association summary statistics, and I apply it to 17 diseases and traits and many different functional annotations. Next, I show how to apply this method to use gene expression data to identify diseaserelevant tissues and cell types. I next introduce a method for estimating genetic correlation from genome-wide association summary statistics and apply it to estimate genetic correlations between all pairs of 24 diseases and traits. Finally, I consider a model of disease subtypes and I show how to determine a lower bound on the sample size required to distinguish between two disease subtypes as a function of several parameters.
by Hilary Kiyo Finucane.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Mathematics
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Lu, Yue. "Genetic mapping of quantitative trait loci for slow-rusting traits in wheat." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/32179.
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Doctor of PhilosophyDepartment of Agronomy
Guihua Bai
Allan K. Fritz
Wheat leaf rust, caused by Puccinia triticina, is an important fungal disease worldwide. Growing resistant cultivars is an effective practice to reduce the losses caused by the disease, and using slow-rusting resistance genes can improve the durability of rust resistance in the cultivars. CI13227 is a winter wheat line that shows a high level of slow-rusting resistance to leaf rust and has been studied extensively. In this research, two recombinant inbreed line (RIL) populations derived from CI13227 x Suwon (104 RILs) and CI13227 x Everest (184 RILs) and one doubled haploid (DH) population derived from CI13227 x Lakin with 181 lines were used to identify quantitative trait loci (QTLs) for slow leaf rusting resistance. Each population and its parents were evaluated for slow-rusting traits in two greenhouse experiments. A selected set of 384 simple sequence repeat markers (SSRs), single nucleotide polymorphism markers (SNPs) derived from genotyping-by-sequencing (GBS-SNPs) or 90K-SNP chip (90K-SNPs) were analyzed in the three populations. Six QTLs for slow-rusting resistance, QLr.hwwgru-2DS, QLr.hwwgru-7BL, QLr.hwwgru-7AL, QLr.hwwgru-3B_1, QLr.hwwgru-3B_2, and QLr.hwwgru-1D were detected in the three populations with three stable QTLs, QLr.hwwgru-2DS, QLr.hwwgru-7BL and QLr.hwwgru-7AL. These were detected and validated by Kompetitive Allele-Specific PCR (KASP) markers converted from GBS-SNPs and 90K-SNPs in at least two populations. Another three QTLs were detected only in a single population, and either showed a minor effect or came from the susceptible parents. The KASP markers tightly linked to QLr.hwwgru-2DS (IWB34642, IWB8545 and GBS_snpj2228), QLr.hwwgru-7BL (GBS_snp1637 and IWB24039) and QLr.hwwgru-7AL (IWB73053 and IWB42182) are ready to be used in marker-assisted selection (MAS) to transfer these QTLs into wheat varieties to improve slow-rusting resistance in wheat.
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Porter, Heather Frances. "Multi-trait methods for genetic association testing." Thesis, King's College London (University of London), 2018. https://kclpure.kcl.ac.uk/portal/en/theses/multitrait-methods-for-genetic-association-testing(d040066c-8b0f-4f1b-bd0c-7be3f144b7e2).html.
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The early stages of the genome-wide association study (GWAS) era were dominated by studies focusing on single phenotypes, while in recent years there has been growing interest in multi-trait GWAS. A wide variety of multi-trait GWAS methods have been developed, but publications introducing new methods are highly inconsistent in their evaluation of method performance, obscuring their relative merit. Facilitated by burgeoning national biobank resources, multi-trait analyses are set to become more routinely applied, making understanding their relative performance increasingly important. We develop a simulation framework to model the complex networks underlying multivariate genetic epidemiology. We exploit our simulation framework to perform a comprehensive comparison study of the leading multi-trait GWAS methods, providing a web application and open-source software program implementing our simulation framework for further benchmarking of multi-trait GWAS methods. Motivated by our comparison results, we develop novel methodology and present a series of multi-trait analyses. We perform multi-trait genome-wide analyses on publicly available GWAS summary statistics on 19 traits – metabolic, anthropometric and psychiatric. We develop and apply two summary statistic methods: one that has increased power to detect pleiotropic effects on multiple traits, and one that is more powerful for detecting heterogeneous genetic effects. Polygenic risk scores (PRS) are now a commonly used tool for performing phenotype prediction from genetics, assessing the genetic aetiology underlying diseases, and testing for shared genetic aetiology among traits. Using UK Biobank data, we explore the predictive ability of PRS computed across multiple traits for Major Depressive Disorder (MDD). The MDD PRS itself has so far offered modest prediction of MDD case/control status; we explore the use of PRS built on traits correlated with MDD to improve predictive ability. We build main effect and interaction models, using both AIC and BIC stepwise variable selection, and cross-validation, to establish the most predictive models.
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Schaeffer, George Barry. "Genetic evaluation of a linear trait description." Thesis, Virginia Polytechnic Institute and State University, 1985. http://hdl.handle.net/10919/101262.
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Data for this study were 79,997 evaluations for 12 individual body and udder traits of Holstein cows. Type scores were subjectively assigned by trained personnel of Select Sires, Inc., Plain City, OH, through their corrective mating and young sire evaluation programs.
After editing data to remove incomplete, erroneous and duplicate records, 56,642 records were used to calculate overall and regional age adjustment factors. Genetic parameters were estimated. Heritabilities ranged from .40 for stature to .14 for fore udder. Standard errors ranged from .039 for stature to .018 for fore udder. Genetic correlations ranged from +.75 between teats and udder support to -.61 between feet and legs. Phenotypic correlations were generally smaller than genetic correlations, ranging from .56 between udder support and teats to -.23 for dairyness and strength. These findings were in general agreement with previous research.
Genetic evaluations for the 12 individual linear traits were made using Herdmate Comparison (HC) and Best Linear Unbiased Prediction (BLUP) methods. Mean evaluations by HC were near zero, and ranged from .026 for stature to -.027 for teats. Mean repeatability also showed very little variation, ranging from .404 for stature to .241 for teats. BLUP evaluations were similar to HC evaluations, with mean evaluation ranging from .121 for feet to -.183 for dairyness. Direct correlations between BLUP and HC evaluations ranged from .90 for stature to .74 for dairyness.
Forty-eight different combinations of minimum daughter numbers and model variables were tested to predict sires' overall evaluations for type from linear trait evaluations using regression analysis. Results indicate that with 5 or more daughters per sire, all predictions tested were similar in accuracy for Predicted Difference for Type.M.S.
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Forsberg, Simon. "Complex Trait Genetics : Beyond Additivity." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-307837.
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The link between the genotype and the phenotype of an organism is immensely complex. Despite this it can, to a great extent, be captured using models that assume that gene variants combine their effects in an additive manner. This thesis explores aspects of genetics that cannot be fully captured using such additive models. Using experimental data from three different model organisms, I study two phenomena that fall outside of the additive paradigm: genetic interactions and genetic variance heterogeneity. Using the model plant Arabidopsis thaliana, we show how important biological insights can be reached by exploring loci that display genetic variance heterogeneity. In the first study, this approach identified alleles in the gene CMT2 associated with the climate at sampling locations, suggesting a role in climate adaption. These alleles affected the genome wide methylation pattern, and a complete knock down of this gene increased the plants heat tolerance. In the second study, we demonstrate how the observed genetic variance heterogeneity was the result of the partial linkage of many functional alleles near the gene MOT1, all contributing to Molybdenum levels in the leaves. Further, we explore genetic interactions using data from dogs and budding yeast (Saccharomyces cerevisiae). In the dog population, two interacting loci were associated with fructosamine levels, a biomarker used to monitor blood glucose. One of the loci displayed the pattern of a selective sweep in some of the studied breeds, suggesting that the interaction is important for the phenotypic breed-differences. In a cross between two strains of yeast, with the advantage of large population size and nearly equal allele frequencies, we identified large epistatic networks. The networks were largely centered on a number of hub-loci and altogether involved hundreds of genetic interactions. Most network hubs had the ability to either suppress or uncover the phenotypic effects of other loci. Many multi-locus allele combinations resulted in phenotypes that deviated significantly from the expectations, had the loci acted in an additive manner. Critically, this thesis demonstrates that non-additive genetic mechanisms often need to be considered in order to fully understand the genetics of complex traits.
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Gunn, Melissa Rose School of Biological Earth & Environmental Science UNSW. "The use of microsatellites as a surrogate for quantitative trait variation in conservation." Awarded by:University of New South Wales. School of Biological, Earth and Environmental Science, 2003. http://handle.unsw.edu.au/1959.4/22457.
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Conservation biologists are interested in maintaining genetic variation in small populations, with a view to maintaining fitness and the ability of the species to adapt to changing environmental conditions. The most important type of genetic variation is therefore that which affects fitness and reproduction, and is therefore subject to natural selection. Such fitness traits are often quantitative, i.e. are the result of a suite of loci, and are continuously variable. Microsatellite markers are a popular method of determining the level of variation present in a species??? genome. The assumption is made that microsatellites, which are neutral markers, behave in the same manner as quantitative traits. If this assumption were proved incorrect, then the use of neutral markers in conservation monitoring would have to be re-evaluated. In this study, experiments have been conducted using Drosophila melanogaster to test the assumption that variation in quantitative traits under stabilising selection declines at the same rate as heterozygosity in microsatellite markers, during a population bottleneck. Experimental population bottlenecks were of two effective population sizes (Ne), Ne=2 for one generation and Ne=60 for 35 generations. Based on the effective population size, we expected both types of bottlenecks to lose 25% of neutral genetic variation. Ten replicates of each bottleneck were maintained, along with four large control populations with Ne=320. In each population, heterozygosity (He) for eight microsatellite loci was compared with the heritability and additive genetic variance of two quantitative traits subject to balancing selection: fecundity and sternopleural bristle number. Microsatellite heterozygosity decreased in accordance with neutral predictions, whereas additive genetic variation in quantitative traits altered more than expected in both large and in bottlenecked populations relative to the initial sampling values, indicating that variation in quantitative traits was not being lost at the same rate as predicted by neutral theory. For most traits, the changes in additive genetic variance were congruent in all populations, large or bottlenecked. This congruence suggests that a common process was affecting all populations, such as adaptation. A mite infestation in early generations is a possible source of selective pressure. When bottlenecked populations were compared to the contemporaneous large populations (Ne = 320), the additive genetic variance of most traits was seen to have been lost in accordance with predictions from the loss of microsatellite heterozygosity. Loss of variation in microsatellites can thus be used to predict the loss of variation in quantitative traits due to bottlenecks, but not to predict the potentially much larger changes due to other processes such as adaptation. The effects of concurrent environmental stress and reduced population size were also evaluated. Endangered populations are often subject to environmental stress in addition to reduced population size, but the effect of stress on the additive genetic variance of fitness traits in organisms undergoing population bottlenecks is unknown. If the presence of stress alters the level of additive genetic variance in fitness traits, the viability of such populations could be substantially affected. The loss of microsatellite heterozygosity was not affected by the presence of a stress agent during a bottleneck. I found some significant effects of stress on the additive genetic variance of sternopleural bristles and fecundity; there was also a significant interaction between stress and the response to directional selection in sternopleural bristles. There was also an increase in the coefficient of variation of VA for sternopleural bristles. Stress may therefore affect the manner in which populations respond to selective pressures.
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Ahmed, Helal Uddin. "Mapping stress tolerance genetic loci in Arabidopsis thaliana." Thesis, University of Newcastle Upon Tyne, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246628.
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Broadley, Simon Andrew. "The genetic analysis of a complex trait : multiple sclerosis." Thesis, University of Cambridge, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620291.
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Huq, Md Nazmul. "The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour." Thesis, Linköpings universitet, Biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-78393.
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Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.
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Tang, Ling-fung Paul, and 鄧凌鋒. "Dissecting the genetics of complex trait in mouse: an attempt using public resources and in-houseknockout." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B43572170.
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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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Sebastian, Rachel Louise. "The genetic mapping and quantitative trait analysis of Brassica oleracea." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396237.
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Harenza, Jo Lynne. "Genetic Dissection of Quantitative Trait Loci for Substances of Abuse." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3190.
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It has been reported that an individual’s initial level of response to a drug might be predictive of his or her future risk of becoming dependent, thus basal gene expression profiles underlying those drug responses may be informative for both predicting addiction susceptibility and determining targets for intervention. This dissertation research aims to elucidate genetic risk factors underlying acute alcohol and nicotine dependence phenotypes using mouse genetic models of addiction. Phenotyping, brain region-specific mRNA expression profiling, and genetic mapping of a recombinant inbred panel of over 25 mouse strains were performed in order to identify quantitative trait loci (QTL) harboring candidate genes that may modulate these phenotypes. Previous BXD (B6 x D2) behavioral studies performed in our laboratory identified an ethanol-induced anxiolysis-like QTL (Etanq1) in the light dark box (LDB). We hypothesized that genetic variation within Nin (a gene within the Etanq1 support interval involved in microtubule-anchoring) may modulate anxiolytic-like responses to acute ethanol in the LDB as well as other preclinical models of anxiety, the elevated plus maze (EPM), and marble burying (MB) task. Molecular studies have allowed us to confirm cis regulation of Nin transcript levels in the NAc. To elucidate potential mechanisms mediating Etanq1, the pharmacological tools, diazepam and HZ166 (a benzodiazepine derivative) were utilized to interrogate whether GABAA receptor activation modulates ethanol’s anxiety-like behaviors in the LDB. We show that the LDB phenotype, percent time spent (PTS) in the light following a brief restraint stress, is not being modulated through direct activation of GABAA α2/α3 receptor subunits. To genetically dissect Etanq1 as well as parse the ethanol anxiolytic-like phenotype, we have assayed 8 inbred strains, selected based on genotypes at Nin, in various preclinical models of anxiety. Principal components analysis of these behavioral data suggests that the gene(s) modulating the ethanol anxiolytic-like component in the LDB do not overlap with similar phenotypes in the elevated plus maze (EPM), nor the MB phenotype. Furthermore, site-specific delivery of an sh-Nin lentivirus into the NAc of D2 mice revealed that Nin may modulate one LDB endophenotype, latency to enter the light side of the LDB, which loaded as a part of the “anxiolysis” principal component. These data strongly imply that basal neuronal Nin expression in the NAc is important for acute ethanol anxiolytic-like behavior, perhaps through a novel mechanism involving synaptic remodeling. In separate behavioral QTL mapping studies, we hypothesized that genetic variation regulating expression of Chrna7 modulates the reward-like phenotype, conditioned place preference (CPP), for nicotine. We provide evidence for genetic regulation of Chrna7 across the BXD panel of mice and through pharmacological and genetic behavioral studies, confirm Chrna7 as a quantitative trait gene modulating CPP for nicotine in mice. Microarrays, followed by network analyses, allowed us to identify a genetically co-regulated network within the nucleus accumbens (NAc), differentially expressed in mice null for Chrna7, which was similarly correlated in the BXD panel of mice. Our network and molecular analyses suggest a putative role for Chrna7 in regulating insulin signaling in the NAc, which together, may contribute to the enhanced sensitivity to nicotine observed in strains of mice that lack or have low mRNA levels of Chrna7 in the NAc. Overall, this research has elucidated and confirmed new genetic risk factors underlying alcohol and nicotine dependence phenotypes and has enabled a better understanding of the neurogenomic bases of alcohol and nicotine addiction. Future studies that further investigate the signaling pathways and/or gene interactions involving Nin and Chrna7 may lead the field to new candidates for pharmacotherapies that may be tailored for use in individuals with susceptible genotypes. Supported by NIAAA grants P20AA017828 and R01AA020634 to MFM, NIDA T32DA007027 to WLD, and NIDA R01DA032246 to MFM and MID.
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Zhu, Guohua. "Ascertainment in two-phase sampling designs for segregation and linkage analysis /." Connect to text online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1112844349.
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Thesis (Ph. D.)--Case Western Reserve University, 2005.[School of Medicine] Department of Epidemiology and Biostatistics. Includes bibliographical references. Available online via OhioLINK's ETD Center.
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Thomas, A. "Data structures, methods of approximation and optimal computation for pedigree analysis." Thesis, University of Cambridge, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372922.
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Kim, Sulgi. "Genetic Association Tests for Binary Traits with an Application." Case Western Reserve University School of Graduate Studies / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=case1247020107.
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Nyström, Per-Erik. "Quantitative trait loci in pig production /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1999. http://epsilon.slu.se/avh/1999/91-576-5712-2.pdf.
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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.
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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).
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Carlborg, Örjan. "New methods for mapping quantitative trait loci /." Uppsala : Dept. of Animal Breeding and Genetics, Swedish Univ. of Agricultural Sciences ([Institutionen för husdjurens genetik], Sveriges lantbruksuniv.), 2002. http://projkat.slu.se/SafariDokument/210.htm.
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Basu, Shravani M. "Genetic mapping and trait analysis in bambara groundnut [Vigna subterranea (L.) Verdc.]." Thesis, University of Nottingham, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415496.
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Liu, Ni. "Detection of trait-associated restriction fragment length polymorphisms in chicken." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=55509.
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The gene encoding chicken growth hormone (GH) was isolated from a chicken genomic library. The size of the gene was 4 kb. It was digested with PstI and subcloned into pUC18. Three of the PstI fragments were used for restriction fragment length polymorphisms (RFLPs) analysis at the GH locus in two chicken strains (fat and lean line). Four polymorphic sites were detected using a PstI fragment (PII) as a probe. One polymorphism was located at a SacI restriction site (PS1), and three at MspI sites (PM1, PM2 and PM3). A method based on polymerase chain reaction (PCR) was developed for detecting polymorphisms at PM3 site. A fragment of 823 base pairs which contained the PM3 polymorphic site was amplified. Three genotypes (+/+,$-$/$-$ and +/$-$) were distinguished by examining the MspI digested PCR products in either agarose or polyacrylamide gel.Ten anonymous cDNA clones were also isolated from a chicken liver cDNA library and used for RFLPs analysis. Three of these clones were found to be able to detected RFLPs at MspI sites in chicken strains (strain 7, 8, 9, 8R, S and K) indicating that a high frequency of genes are polymorphic and can be used as markers in mapping experiments. One of the three clones was present on a haploid genetic element. Segregation analysis showed that the inheritance of this haploid gene was determined by the genotype of the female parent.
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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/.
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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.
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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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Gale, Joanne. "Statistical Methods for the Analysis of Quantitative Trait Data in Genetic Association Studies." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504345.
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Armstrong, Jenny. "The genetic architecture of a reproductive life-history trait in a wild passerine." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/11913/.
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Understanding the capacity for species to respond to changes in their environment and the rate at which they are able to do so is a key topic in evolutionary biology and of increasing importance in wildlife conservation and management. However the mechanisms involved in mediating these responses are poorly understood. Specifically, while reactive responses may be advantageous in the short term persistent directional changes in environmental conditions may require a more profound response in order for organisms to adapt and persist successfully. Here I use data from two long-term studies of the great tit Parus major and apply a range of statistical techniques to dissect the genetic architecture of laying date, a reproductive life-history trait, to discern the extent to which a genetic component of variation contributes to observed phenotypic variation. A heritable component of variation exists in both populations, but specific regions of the genome contributing to trait variation could not be detected by quantitative trait loci mapping (Chapters 2 & 3), genome-wide association (Chapters 2 & 3) or chromosome partitioning (Chapter 4) analyses. These findings are consistent with a highly polygenic basis for variation in laying date, variation maintained by many genes of small effect. Attempts to increase the statistical power by combining two phenotypic datasets to increase overall sample size (Chapter 3) and increasing marker density (Chapter 5) drew similar conclusions, with an absence of genome-wide significant QTL. Despite evidence of a strong association on chromosome 3 (Chapter 5), an overall lack of consistency between analyses and datasets on regions exhibiting the highest associations suggests that power to detect genomic regions, particularly when variation may be determined by many variants of small effect, is low. I conclude that while genetic variation exists, environmental factors and phenotypic plasticity likely account for much of the variation in laying date.
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Bečanović, Kristina. "Genetic regulation of autoimmune neuroinflammation /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-726-6.
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Dierks, Claudia. "Molecular genetic analysis of quantitative trait loci (QTL) for osteochondrosis in Hanoverian warmblood horses." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980656702.
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Tyler, Jennie. "Defective regulatory T cell function in type 1 diabetes : a trait under genetic control?" Thesis, King's College London (University of London), 2013. https://kclpure.kcl.ac.uk/portal/en/theses/defective-regulatory-t-cell-function-in-type-1-diabetes(e3b3ac01-273b-4014-8a17-af5b6d0e21c6).html.
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Type 1 diabetes (T1D) is an autoimmune disease, resulting from the specific destruction of the insulin‐producing beta‐cells in the islets of the pancreas. Islet‐specific autoreactive T cells are instrumental in this process and although these cells are present in individuals with and without T1D, their exhibition of a memory phenotype in diabetic individuals indicates they may have been previously activated in these patients. This suggests a breakdown in peripheral tolerance, implying regulatory T cells (Tregs) may be involved. Indeed, CD4+ CD25hi FOXP3+ Tregs do not differ in frequency in T1D, but their function is impeded. This defect is present in both recentonset type‐1 diabetics (ROT1D) and long‐standing type 1 diabetics (LST1D) suggesting it is a stable phenotype, possibly under genetic control. Also, it is known that the production and signalling of interleukin‐2 (IL‐2); a cytokine essential for the maintenance of Tregs, is defective in T1D. The aim of this thesis was to ascertain whether defective Treg function in T1D is genetically determined or a consequence of the disease. The first section of this thesis examined the effect of a T1D‐associated IL2RA single nucleotide polymorphism (SNP) on Treg function, by means of a genotype‐immunophenotype study. Non‐diabetic donors homozygous for the susceptible allele at this SNP exhibited diminished Treg fitness and suppressive action, suggesting that defective Treg function is a contributing factor in T1D. The latter section utilised T1D‐discordant monozygotic twins and healthy controls to examine Treg function and the IL‐2‐dependent generation of regulatory type 1 (Tr1) cells. Due to the low number of twins obtained nothing conclusive can be drawn from the study on Treg function. However, the results from the Tr1 generation assay suggest the possible existence of an IL‐2 signalling defect in non‐diabetic twins.
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Brito, Lais Costa. "Censored and multi-trait Bayesian models for genetic evaluation of milk, weight and reproductive traits in Guzerá cattle in tropical conditions." Universidade Federal de Viçosa, 2016. http://www.locus.ufv.br/handle/123456789/22443.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
Objetivou-se com este trabalho estimar parâmetros genéticos para características de produção de leite (produção de leite em até 305 dias – PL305), peso (peso aos 120 – P120, aos 365 – P365 e aos 550 dias – P550) e reprodutiva (idade ao primeiro parto - IPP) em bovinos da raça Guzerá utilizando modelos multicaracterísticos e comparar metodologias que se baseiam na utilização de dados censurados de idade ao primeiro parto. Os dados foram cedidos pela Associação Brasileira dos Criadores de Zebu (ABCZ) e Embrapa Gado de Leite em parceria com o Centro Brasileiro de Melhoramento do Guzerá (CBMG 2 ). O arquivo de pedigree (120.599 animais) incluiu animais com registros fenotípicos e todos os ancestrais conhecidos. Registros censurados foram definidos como dados de IPP que extrapolaram os limites de 740 e 1860 dias. Os registros de IPP (69.157 informações) foram analisados por meio de sete diferentes metodologias: método linear convencional (LM); de simulação (SM); de penalidade (PM); modelos bicaracterística limiar-linear em que se considerou (TLcens) ou não (TLmiss) informações prévias sobre os registros censurados; e a metodologia de análise de sobrevivência por meio do modelo de riscos proporcionais de Weibull segmentado em que se considerou (PWPHcens) ou não (PWPH) os registros censurados. Para as análises de sobrevivência, os valores para o critério de informação da deviance (DIC) sugerem o uso de 0 e 2 nós na função base para os métodos PWPH e PWPHcens, respectivamente. Os componentes de variância genética aditiva estimados para os métodos LM, PM e TLmiss foram similares. As estimativas de herdabilidade para IPP variaram de 0,19 (TLcens) à 0,28 (SM) e 0,40 (PWPH) e 0,46 (PWPHcens). De forma geral, as correlações entre os valores genéticos obtidos por meio das diferentes metodologias e a porcentagem de touros selecionados em comum variaram de -0,28 (SM x PWPH) à 0,99 (TLmiss x LM), indicando reordenamento moderado entre os animais. As comparações baseadas na metodologia de validação cruzada, indicam a metodologia TLmiss como a melhor opção para predição dos valores genéticos dos animais para a característica IPP na população Guzerá. Para estimação dos parâmetros genéticos utilizando modelos multicaracterísticos, foram considerados os efeitos sistemáticos de sexo e idade ao parto. Os efeitos aleatórios genético aditivo e de grupo de contemporâneo (rebanho, ano e estação de parto) foram considerados. Adicionalmente, os efeitos aleatórios genético aditivo materno e de ambiente permanente materno foram considerados para a característica peso à desmama. As estimativas de herdabilidade foram 0,29 (PL305), 0,42 (P120), 0,49 (P365), 0,56 (P550) e 0,25 (IPP). As correlações genéticas entre as características de peso foram maiores que 0,83 e entre PL305 e as demais foram de 0,25 (PL305 x P205), 0,32 (PL305 x P365) e 0,36 (PL305 x P550). A característica IPP foi negativamente correlacionada com as características de leite e de peso. Os resultados sugerem que a seleção para a produção de leite não compromete a seleção para características de peso e reprodutivas, bem como é passível a inclusão de dados censurados de IPP na avaliação genética por meio do uso de um modelo de limiar-linear em bovinos da raça Guzerá.
We aimed to estimate genetic parameters for 305-d milk yield (MY305), growth (weaning – WW, yearling – YW and long yearling weights - LYW) and reproductive (age at first calving - AFC) traits in Guzerá cattle by using Bayesian multi-trait models and compare methodologies for handling censored data of age at first calving by Bayesian models. Data were provided by Brazilian Association of Zebu Cattle (ABCZ) and Embrapa Dairy Cattle Research Unit in partnership with the Brazilian Center of Guzerá Genetic Improvement (CBMG 2 ). The pedigree file (120,599 animals) included animals with phenotypic records and their known ancestors. Censored records were defined as AFC records out of range of 740 and 1860 days. Data including 69,157 AFC records were analyzed using seven different methods: conventional linear method (LM), simulation method (SM), penalty method (PM), a bitrait threshold-linear model considering (TLcens) or not (TLmiss) any prior information about censored records; and piecewise Weibull proportional hazards methodology considering (PWPHcens) or not (PWPH) censored records. For survival analyses, deviance information criterion (DIC) values suggested 0 and 2 piecewise change points in the baseline function of PWPH and PWPHcens methods, respectively. The additive genetic variance components estimated from LM, PM and TLmiss were similar. Heritability estimates for AFC ranged from 0.19 (TLcens) to 0.28 (SM) in non-survival approaches, and 0.40 and 0.46 to PWPH and PWPHcens methods, respectively. In general, genetic breeding values correlations from different methods and the percentage of selected bulss in common indicated moderate reranking, ranging from -0.28 (SM x PWPH) to 0.99 (TLmiss and LM). Comparisons based on cross-validation analyses, indicated TLmiss as a suitable alternative for predicting breeding values for AFC in this Guzerá population. In second chapter, systematic effects included sex and age at calving. The additive genetic and contemporary group (herd, year and season of birth) were included as random effects. Additionally, maternal genetic and permanent effects were included as random effects for weaning weight trait. Heritability estimates were 0.29 (MY305), 0.42 (WW), 0.49 (YW), 0.56 (LYW) and 0.25 (AFC). Genetic correlations between weight measures were higher than 0.83 and 0.25 (MY305 x WW), 0.32 (MY305 x YW) and 0.36 (MY305 x LYW) for other traits. AFC trait was negatively genetically correlated with milk and weight measures. These results suggest that selection for milk yield do not jeopardize selection for beef and reproductive efficiency and AFC censored data could be included in genetic evaluation considering a threshold-linear model in Guzerá cattle.
Tese enviada por e-mail em 31/10/2018 pela secretaria do curso. Versão impressa não foi enviada.(Não foi encontrada no departamento)
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Deviona. "Genetic analysis of root growth direction in soybean." Kyoto University, 2018. http://hdl.handle.net/2433/235097.
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Cabrera, Cárdenas Claudia Paola. "Bioinformatics tools for the genetic dissection of complex traits in chickens." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3864.
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This thesis explores the genetic characterization of the mechanisms underlying complex traits in chicken through the use and development of bioinformatics tools. The characterization of quantitative trait loci controlling complex traits has proven to be very challenging. This thesis comprises the study of experimental designs, annotation procedures and functional analyses. These represent some of the main ‘bottlenecks’ involved in the integration of QTLs with the biological interpretation of high-throughput technologies. The thesis begins with an investigation of the bioinformatics tools and procedures available for genome research, briefly reviewing microarray technology and commonly applied experimental designs. A targeted experimental design based on the concept of genetical genomics is then presented and applied in order to study a known functional QTL responsible for chicken body weight. This approach contrasts the gene expression levels of two alternative QTL genotypes, hence narrowing the QTL-phenotype gap, and, giving a direct quantification of the link between the genotypes and the genetic responses. Potential candidate genes responsible for the chicken body weight QTL are identified by using the location of the genes, their expression and biological significance. In order to deal with the multiple sources of information and exploit the data effectively, a systematic approach and a relational database were developed to improve the annotation of the probes of the ARK-Genomics G. gallus 13K v4.0 cDNA array utilized on the experiment. To follow up the investigation of the targeted genetical genomics study, a detailed functional analysis is performed on the dataset. The aim is to identify the downstream effects through the identification of functional variation found in pathways, and secondly to achieve a further characterization of potential candidate genes by using comparative genomics and sequence analyses. Finally the investigation of the body weight QTL syntenic regions and their reported QTLs are presented.
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Cook, David E. "Assessing Genetic and Environmental Influence on Traits Associated with Natto Quality." Thesis, Virginia Tech, 2008. http://hdl.handle.net/10919/33034.
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Food grade soybean production is a high value alternative to conventional soybean use. The production of natto, a fermented soyfood, requires soybean cultivars that consistently express specific quality traits over a range of growing environments. Therefore, it is necessary to evaluate genetic and environmental influence for natto quality traits to ensure consistent performance. A multi location experiment was conducted in 2006 and 2007 to address the influence of soybean cropping system (double crop vs. full season) and environmental factors on traits associated with natto quality. Two statistical models were used to analyze the effects of planting system and environment on agronomic traits such as yield, maturity, and seed size and natto quality traits such as water absorption, water loss after steaming, seed coat deficiency, and rate of water absorption. Genotype variation was significant for all traits, but genetic differences for water loss after steaming were minimal. Planting system significantly influenced all natto quality traits. Seed coat deficiency and rate of water absorption displayed the most differential response and double crop plantings produced superior characteristics. Genotype à environment interactions were significant for all traits, but they did not confound selecting superior natto cultivars. Significant environment and year effects indicate environmental sensitivity, but genotype rankings rarely changed. The results indicate that genotype was the most important factor controlling the natto quality traits tested. These results suggest breeding for superior natto cultivars is possible but environmental influence must be accounted for and multi environment testing is necessary for genotype natto quality evaluation.Master of Science
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Crawford, Paul Joseph. "The genetic basis of variation in thermal plasticity in Drosophila melanogaster." Thesis, Kansas State University, 2013. http://hdl.handle.net/2097/16117.
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Master of ScienceDepartment of Biology
Theodore J. Morgan
The organismal response to temperature represents one of the most ubiquitous processes that occur in the natural world, and this response is critical for survival in most habitats. Increased attention should be focused on how organisms cope with temperature extremes, either through adaptation, plasticity, or a combination of both, as climate models predict increased variations in temperature accompanied by novel thermal extremes. Drosophila melanogaster is an excellent resource for answering questions pertaining to how organisms persist in environmental extremes because they originated in central tropical Africa and have since colonized nearly the entire globe, exposing them to many novel thermal stressors. In this work I elucidated regions of the genome contributing to phenotypic variation in cold tolerance and thermal plasticity. A quantitative trait locus (QTL) approach was used, which involved phenotyping roughly 400 recombinant inbred lines (RILs) of D. melanogaster from the Drosophila Synthetic Population Resource (DSPR). The DSPR captures genetic variation from around the globe, allowing for precision mapping of cold tolerance and thermal plasticity QTL, while simultaneously determining the frequency of the QTL alleles. Upon development at both 18°C and 25°C, RILS were measured for a common cold tolerance metric, chill-coma recovery time (CCR), and a plasticity value was derived as the change in CCR between environments. Analysis of variance revealed significant effects of sex, line (RIL), treatment (temperature), and line by treatment interaction (GxE). Mapped QTL for chill-coma recovery time at 18°C and 25°C spanned the same regions as several studies previously reported, validating the automated phenotyping method used and the mapping power of the DSPR. QTL between CCR at 18°C and 25°C overlapped significantly, and QTL for thermal plasticity shared the similar regions as QTL for CCR, but also exhibited two non-overlapping QTL on the left arm of the third chromosome. This study demonstrated the tremendous amount of variation present in cold tolerance phenotypes and identified candidate regions of the genome that contribute to thermal plasticity and require further investigation.
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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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Papachristou, Charalampos. "Constructing confidence regions for the locations of putative trait loci using data from affected sib-pair designs." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1124226056.
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Thesis (Ph. D.)--Ohio State University, 2005.Title from first page of PDF file. Document formatted into pages; contains xv, 122 p.; also includes graphics. Includes bibliographical references (p. 117-122). Available online via OhioLINK's ETD Center
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Tinker, Nicholas Andrew. "Studies on the analysis of genetic markers and quantitative trait loci in plant breeding populations." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=41774.
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Laboratory experiments, genetic simulation, and theoretical analyses were performed to address several objectives related to the use of genetic markers in plant breeding programs. Two software packages were developed: GREGOR provides flexible and efficient computer algorithms for performing genetic simulation experiments, and KIN provides improved methods for estimating coancestry from known pedigrees. Random amplified polymorphic DNA (RAPD) markers were investigated in elite barley lines, and estimates of genetic distance based on RAPD markers were compared to estimates based on coancestry. Both types of estimate can provide information that is useful to breeders and geneticists. Genetic simulation was used to investigate the power, accuracy and precision of several methods that are available for analyzing quantitative trait loci (QTL). In most cases, simplified methods of QTL analysis based on linear regression were similar or superior to more complex methods based on mixture models. Methods for genetic analysis using selective genotyping and pooled DNA were also investigated. These methods may allow precise estimates of the positions of markers and QTL to be made.
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Banerjee, Samprit. "Bayesian genome-wide QTL mapping for multiple traits." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2009r/banerjee.pdf.
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Galagedara, Nelomie Nayanathara. "Identification of Quantitative Trait Loci for Resistance to Tan Spot in Durum Wheat." Thesis, North Dakota State University, 2018. https://hdl.handle.net/10365/28765.
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Tan spot, caused by Pyrenophora tritici-repentis (Ptr), is a major foliar disease on wheat. The pathosystem involves three pairs of necrotrophic effector (NE) and host sensitivity (S) gene interactions, namely Ptr ToxA-Tsn1, Ptr ToxB-Tsc2 and Ptr ToxC-Tsc1. Additionally, genetic factors conferring race-nonspecific resistance have been identified. The objectives of this study were to map tan spot resistance QTL and investigate the role of NE-S interactions in disease in durum using association and bi-parental mapping. Evaluation of a worldwide collection of durum accessions allowed identifying highly resistant nineteen lines to multiple Ptr races. Association mapping revealed genomic regions on chromosomes 1A, 2B and 3B significantly associated with resistance to tan spot, which likely correspond to Tsc1, Tsc2 and racenonspecific resistance. Using a bi-parental population derived from Ben and PI 41025, we found that ToxA-Tsn1 interaction plays no significant role in disease, instead a major race-nonspecific QTL on chromosome 5A was identified.
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Emebiri, Livinus Chinenye, and -. "Detection and Genetic Mapping of Quantitative Trait Loci Influencing Stem Growth Efficiency in Radiata Pine." The Australian National University. Department of Forestry, 1997. http://thesis.anu.edu.au./public/adt-ANU20010822.164445.
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Needle-to-stem unit rate (NESTUR) is a stem growth index of conifer seedling trees that measures the efficiency of stemwood production per unit of needle growth. Five experiments were carried out in this thesis using progenies of two unrelated full-sib radiata pine crosses. The initial experiment (experiment 1) applied the bulked segregant analysis technique to determine whether RAPD analysis could be successfully extended to the development of molecular markers for NESTUR in radiata pine. The NESTUR values of 174 progenies of the full-sib family 12038 x 10946 were determined. Based on the genotypic analysis of the individuals, two quantitative trait loci (QTL) controlling NESTUR were identified at ANOVA P-levels of 0.01-0.001. An absence of RAPD fragment markers generated by primers OPE-06 and OPA-10 was associated with low NESTUR values, while primer UBC-333 generated a 550 bp band that was associated with high NESTUR values. Linkage to components of NESTUR (increments in stem diameter and stem volume) was demonstrated for one of the QTL, while the other was unique to NESTUR, and not shared with the components. There was a significant interaction between the two QTLs. Presence of OPA-101200 locus appeared to inhibit expression of the QTL linked to UBC-333 [subscript 550].
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To further analyse the quantitative trait loci (QTLs) controlling NESTUR, a linkage map was constructed from RAPD markers segregating in 93 haploid progeny of another full sib cross (30040 x 80121) (experiment 2). Two hundred and sixty-two (262) markers were mapped to 14 linkage groups of at least 7 markers, ranging in size from 39 to 183 cM. The 14 linkage groups covered approximately 1511 cM of genetic map distance.
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In experiment 3, the linkage map was used to map QTLs controlling NESTUR, as well as increments in seedling stem diameter, volume, and height and needle volume. Altogether, five putative QTLs were detected for NESTUR, with explained variation ranging from 9 to 22%. Of the five QTLs detected, 3 were coincidental with those for stem growth in height, diameter and volume. The two QTL positions that were unique to NESTUR were flanked by QTLs for the component traits. Together, effects of the five QTLs explained 48% of the total phenotypic variation for NESTUR.
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Ability of identified markers to predict the phenotype and seedlings with growth potential was assessed in the cross 30040 x 80121, using six RAPD markers associated with NESTUR at ANOVA P-levels of 0.01-0.001 (experiment 4). The correlation between observed NESTUR and predicted values was 0.70. Differences in observed vs. predicted values were not large and did not indicate serious misclassifications, such as classification of an upper ranking individual into the lower group, or vice versa.
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Over a two-year growth period, the ability of NESTUR to predict stem growth was strongly affected by seedling age. In contrast, markers linked to NESTUR showed a consistent ability to predict stem growth, irrespective of seedling age. Compared with the top 1% of the original population, seedlings selected for their genotypic values showed a higher stem volume growth of 103% in the first year, and 76% in the second year.
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The expression of QTLs for stem volume, stem diameter, height, number of branches, number of whorls, and branches/whorl were compared at 5, 12, and 24 months of age. Two QTLs detected for height showed contrasting expression over two years, one was gradually reduced from LOD of 2.70 to 0.43 and the other increased from 1.12 to 2.45. Compared with the pattern observed for height, LOD scan profiles for diameter and volume showed less temporal change of peaks, suggesting that the genetic control for height growth is probably more unstable than that of diameter. QTLs controlling the phenotype at the time of measurement (ie the final phenotype) showed similar magnitude of effects on that trait's respective increments (or growth rate).
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Coan, Jr James A. "The heritability of trait frontal EEG asymmetry and negative emotionality: Sex differences and genetic nonadditivity." Diss., The University of Arizona, 2003. http://hdl.handle.net/10150/280273.
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The heritability of personality was addressed using a psychophysiological measure, midfrontal EEG asymmetry, and a paper and pencil measure, the Multidimensional Personality Questionnaire (MPQ). The degree to which midfrontal EEG asymmetry was correlated with the scales of the MPQ was assessed. Relatively greater right midfrontal EEG asymmetry was associated with higher Absorption and Negative Emotionality scores in both the Cz and linked mastoid reference schemes in females, but not in males. Relatively greater right midfrontal EEG asymmetry was also associated with higher Traditionalism and Positive Emotionality scores in the Cz reference scheme in females but not in males. Midfrontal EEG asymmetry was found to be modestly heritable in females, but not in males. Further, each of the scales of the MPQ correlated with midfrontal EEG asymmetry demonstrated moderate to high heritability. A bivariate Cholesky model was used to estimate the heritability of the phenotypic correlations between midfrontal EEG asymmetry and each of the scales with which it was related. Only the midfrontal EEG Asymmetry/Negative Emotionality Cholesky model demonstrated sufficient fit the observed data. According to this model, common genetic effects accounted for approximately 40% of the observed phenotypic correlation between midfrontal EEG asymmetry and Negative Emotionality.
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Makino, Seiko. "Investigation of expression quantitative trait loci and regulatory genetic variants in primary human immune cells." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:67d0c1e8-c6f1-4ca7-a311-52f20b79128b.
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The post human genome sequence era has begun to explore various aspects of the functional genome in relation to disease including gene expression, genetic variation and epigenetics. The genetic determinants of common and complex phenotypes are difficult to resolve even though their heritability is recognised. Recent genome-wide association studies (GWAS) for common diseases has identified many new disease susceptibility associated loci. These loci often lie in non-coding regions of the genome and disease associated genetic variants are proposed to act by modulating gene expression. This thesis investigated genetic variation as determinants of gene expression in the context of the immune system especially focused on the innate immune and inflammatory responses. Different primary human immune cell types were collected from healthy volunteers of European ancestry to achieve this. In order to identify genetic variants associating with gene expression, expression quantitative trait loci (eQTL) mapping was conducted in a cell type specific manner. The primary dataset (n=288) consists of CD19+ B-cells from the adaptive immune system and CD14+ monocytes from the innate immune system. 78% of the total cis eQTL were found to be cell type specific and include genes relating to their roles in the immune response. Trans eQTL showed greater cell type specificity and include master regulatory eQTL on the LYZ locus at chromosome 12q15 in monocytes and the KLF4 (9p31) in B-cells. The identified eQTL are implicated in association with autoimmune disease susceptibility including inflammatory bowel disease, diabetes and rheumatoid arthritis. The second analysed dataset (n=64) consists of CD14+ monocytes and macrophages differentiated ex vivo. Macrophages are involved in many inflammatory diseases as well as in the innate immune response. The differential gene expression and eQTL mapping analyses were conducted to investigate macrophages specific gene expression signatures and associations to genetic variants. Macrophage eQTL are involved in signal transduction for the inflammatory response (IL1RN and STAT4) and lipid metabolism (PPARG) with implication for metabolic disease association. The eQTL analyses using primary immune cell types provide insights into genetic variation in association to gene expression which is involved in autoimmunity and disease susceptibility.
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Poon, Fong-Yee. "Genetic architecture of neurogenesis in the adult mouse forebrain : insights from quantitative trait locus analyses." Thesis, University of British Columbia, 2014. http://hdl.handle.net/2429/50395.
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Neural stem cells and their precursors, collectively referred to as neural progenitor cells (NPCs), are present in discrete regions of the mature brain, namely the subgranular zone (SGZ) of the dentate gyrus, the subventricular zone (SVZ), and rostral migratory stream (RMS). These NPCs divide and give rise to new neurons in a process called adult neurogenesis. Genetic influence is a major determinant of adult neurogenesis. However, the genetic architecture underlying NPC proliferation and differentiation is poorly understood. My thesis aims to gain insights into the genes regulating NPC proliferation using a phenotypic-driven, genome-wide approach. I first examined nine inbred mouse strains housed in the same condition and across different ages from 60 days (P60) to 2 years. Wide inter-strain differences and negative impact of age on the number of NPCs were observed in the RMS. Genetic background had a significant effect on NPC proliferation and it also differentially influenced the effect of age on this process. The most dramatic inter-strain difference was detected at P60. Heritability estimated ~50% of the differences in NPC numbers were attributed to the genetic variation among the strains. I used quantitative trait locus (QTL) mapping to survey the entire genome for chromosomal segments referred to as QTLs that contribute to the phenotypic differences. Two panels of recombinant inbred strains, AXB/BXAs and BXDs, were employed for QTL mapping. Genetic variation in QTLs on chromosome (Chr) 6 and 11 were significantly associated with the differences in NPC numbers in the RMS. Additional analyses revealed potential interaction of Chr 6 QTL with other loci. These QTLs are hypothesized to harbor genes important for NPC proliferation and downstream experimentation is required to validate the function of these genes. As proof of concept, a candidate gene called Galanin receptor 2 (Galr2) in the Chr 11 QTL was demonstrated to be a pro-proliferative regulator of NPCs using in vitro techniques manipulating Galr2 expression and Galr2 knockout mice. In summary, I identified novel QTLs underlying NPC proliferation and these loci serve as starting points to identify genes (e.g. Galr2) critical to this process.Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Rance, Kellie Anne. "Genetic mapping of quantitative trait loci for body weight on the X-chromosome in mice." Thesis, University of Edinburgh, 1996. http://hdl.handle.net/1842/12832.
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Evidence of a large sex linked additive effect accounting for 25% (approximately 5g) of the divergence in weight between mouse lines selected for body weight has been described previously. A study was undertaken to map putative X-linked quantitative trait loci (OTL), with the objective of isolating the position(s) and number of QTL, and thereby provide information regarding the genetic mechanisms controlling growth and body weight. A preliminary experiment was carried out to map the QTL on the X-chromosome. An F2 generation was genotyped at 7 microstatellite loci found to be polymorphic in the selection lines. The results of single marker analysis showed significant linkage between X-linked markers and body weight, but DNA was not available for all individuals in the pedigree, so fully informative loci in the F2 generation could not be determined. To enable analysis of fully informative marker loci, the F2 experiments was repeated retaining DNA samples from all individuals within the pedigree. The F2 population was generated from a reciprocal F1 population between an inbred low line (derived from the low selection line) and the high selection line. To enable statistical analysis of an F2 population genotyped at markers on the X-chromosome, an analytical technique was developed based on the multiple regression method of Haley and Knott. The validity of the analysis was tested using simulated data, and the method was developed further to enable analysis of non-inbred data. Using parental genotypes to determine fully informative marker loci in the F2 generation, the phenotypic and genotypic data were analysed using the X-linked multiple regression method for non-inbred data. The analysis of data on 10 week weight indicated a single QTL of large effect (± s.e.) situated at about 23 ± 2 cM from the proximal end of the chromosome, the likelihood curve showing a single well defined peak.
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Tang, Ling-fung Paul. "Dissecting the genetics of complex trait in mouse an attempt using public resources and in-house knockout /." Click to view the E-thesis via HKUTO, 2010. http://sunzi.lib.hku.hk/hkuto/record/B43572170.
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Sampson, Joshua Neil. "Clustering genes in genetical genomics /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9549.
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Takeshita, Shigeru. "Genetic and physiological studies to discover novel anti-diabetic agents." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215223.
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Donaldson, Claire Louise. "Spine characteristics in sheep : metrology, relationship to meat yield and their genetic parameters." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/20381.
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The overall accuracy, efficiency and profitability of livestock improvement strategies can be greatly increased by incorporating quantitative genetics into livestock selection and breeding. Since the introduction of quantitative genetics, a range of traits describing the animal e.g. in terms of health, growth, fecundity, production, have been extensively evaluated in terms of genetics and are now commonly manipulated through breeding to achieve specific selection goals. An industry led enquiry as to the possibility of including spine traits in genetic selection to increase back length in sheep was the basis of the present thesis. Collecting information on spine traits (spine length, vertebrae length and vertebrae number) is of particular interest and use to the sheep breeding industry as there may be the potential to increase meat yield from the highly valuable longissimus thoracis et lumborum (LTL or loin), located parallel to the spine, with little associated change in production costs. The thesis focusses on the use of X-ray computed tomography (CT) scanning as a technique which would allow spine traits to be measured in vivo, hence being useful for genetic selection. The topogram scans produced from the CT scanning procedure were analysed to derive spine trait information for the thesis. The scans were from Scottish Blackface (maternal breed stock), Texel (terminal sire breed), Texel cross Mule and Poll Dorset cross Mule (three-way cross slaughter lambs) so as to represent the divergent genotypes found across the different levels of the United Kingdom’s (UK) three-tier crossbreeding structure of sheep. The present study explored as a first step intra- and inter-operator repeatability of assessment of spine traits from CT derived topograms, as a means to investigate the suitability of the approach for widespread uptake within industry where operators will vary. The results showed that there was high repeatability for intra- and inter-operator assessment of spine trait measurements verifying that the CT method could be accepted as a reliable alternative (to slaughter for example) to quantify spine traits. To determine whether spine traits are similar across the range of breeds representing the key genotypes and crosses in the UK sheep industry, numerous CT topograms were analysed. The results showed marked variation in spine traits within and between Scottish Blackface, Texel, Texel cross Mule and Poll Dorset cross Mule breeds and crosses. For example, the Texel breed was found to have the largest within-breed range for thoracolumbar vertebrae number (17 – 21; the majority possessing 19), but the spine length of these animals was, on average, significantly shorter than the other breed/cross groups. The present study concluded that the significant differences between the breeds and breed types for the particular spine traits were possibly indicative of a genetic control for these traits. Furthermore, investigation into the phenotypic correlations between spine and production traits revealed some directional associations which may prove beneficial for meat production. For example, Scottish Blackface lambs which had a longer length of a specific spine region had an associated decrease in the volume of carcass fat. Texel lambs which had a longer length of a specific spine region had a slightly larger loin muscle area, at a given weight. The present study also examined animals from a population of Texel lambs already heavily selected for increased muscling. The Texel muscling quantitative trait locus (TM-QTL), segregating in these animals and generally in the UK’s Texel sheep population, is expressed through a polar overdominance pattern of inheritance and its effect on the loin (localised muscle hypertrophy) is commonly utilised in the selection and breeding of Texel sheep to improve meat production. Examination of topograms from lambs bearing the whole range of TM-QTL genotypes showed little evidence to suggest that the change in loin shape/increased loin muscling, as a result of the TM-QTL and its inheritance, has led to any associated change in the underlying spine characteristics. This suggests that selection for increased muscling associated with the TM-QTL may be achieved independently of changes in the spine traits studied. The potential to breed for certain spine traits to increase vertebrae number and hence chops or loin yield can be enhanced by establishing the genetic parameters for the traits. The present study employed a collection of performance trait records from Texel lambs to provide the basis for genetic analysis. The results showed different levels of heritability for the different spine traits but also high standard errors. For example, heritability of vertebrae number was dependent on vertebra location: for thoracic vertebrae heritability was high (ℎ2 = 0.99; SE = 0.42), for lumbar vertebrae heritability was low (ℎ2 = 0.08; SE = 0.12), whereas in contrast, thoracolumbar vertebrae heritability was moderate (ℎ2 = 0.44; SE = 0.27). Phenotypic and genetic correlations between all combinations of traits were also obtained. Accurate predictions of the size and direction of response to selection can be achieved through such genetic analysis of traits. The more that is known of the genetic characteristics of traits and their genetic correlations with other economically important traits, the more efficiently it can be built into breeding programmes improving the overall performance of stock. The results of this study showed that providing spine measurements can contribute to the diversity of trait information available to breeders. The present study also suggests that there may be opportunities to select for increased spine length/vertebrae number which would benefit the sheep industry in terms of increased chop number/loin yield. Although more data are needed prior to implementation. Practical uptake of selection for spine traits would be enhanced due to the straightforward nature of the measurements and the high operator repeatability.
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Hallsson, Lára R. "Quantitative Trait Evolution in a Changing Environment in a Seed Beetle." Doctoral thesis, Uppsala universitet, Zooekologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-159284.
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During the last decades the climate has been changing more rapidly than in the preceding periods. This is for instance characterized by an increase in temperature. Interestingly, such changes in the environment are not necessarily constant over time as they often show high levels of fluctuation. Organisms are exposed to these changes and respond to them and a recent theoretical model predicts that fluctuations in the environment are important for populations’ response to climate change. The aim of this thesis is to investigate how populations respond to a changing environment, including fluctuations. My thesis is based on the previously mentioned theoretical model and I used a suite of laboratory experiments on the seed beetle Callsosobruchus maculatus, to test the model predictions in a quantitative genetic framework. First, I assessed the genetic architecture of several life history and morphological traits in order to verify that there is sufficient additive genetic variation for the population to respond to changes in the environment. Second, I tested the detailed model predictions explicitly, by investigating whether different types of environmental fluctuations matter for a population’s response. Third, I investigated changes in quantitative genetic variation after i) a rapid shift in temperature and ii) long term selection under increasing temperature including fluctuations. Fourth, I concentrated on sex differences in response to temperature, and finally, I assessed the relative importance of genetic and nongenetic inheritance for traits that differ in their plastic response to a change in the environment. I found that environmental fluctuations are highly important for a population’s response to environmental change. I could detect changes in a set of quantitative genetic parameters, suggesting that a population’s potential to respond to selection, environmental sensitivity and the evolution of phenotypic plasticity are affected by the selective past. I also found that sexes differ in additive genetic variation and plasticity and that parental effects may play an important role in the evolutionary process. Therefore, future studies would benefit greatly from considering details of the selective past and especially environmental fluctuations during attempts to predict how populations respond to a changing environment, particularly with regards to climate change.
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Snedeker, John. "A Genetic Approach to the Role of Primary Cilia in Forebrain Development." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1535458396250938.
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