Dissertations / Theses on the topic 'Quantitative trait loci'
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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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Turri, Maria Grazia. "Mapping of behavioural quantitative trait loci." Thesis, University of Oxford, 2002. http://ora.ox.ac.uk/objects/uuid:89823fa1-c1d3-49e3-acb9-46da18b12245.
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Anxiety is a common disorder which affects about 25% of the population and whose pathophysiology is still poorly understood. Animal models of disease have been widely used to investigate the molecular basis of human disorders, including psychiatric illnesses. This thesis is about the study of the genetic basis of a mouse model of anxiety. I have carried out a QTL mapping study of behavioural measures thought to model anxiety. I report results from 1,636 mice, assessed for a large number of phenotypes in five ethological tests. Mice belonged to two F2 intercrosses originated by four lines generated in a replicate selection experiment. By comparing mapping results between the two crosses, I have demonstrated that selection operated on the same relatively small number of loci in the four selected lines. Analysis of genetic effect of QTL across phenotypes has allowed me to identify loci with specific roles on different dimensions of anxious behaviour, therefore enhancing our understanding of the anxiety phenotype in mice. For some of these QTL I have also accomplished fine mapping experiments: a locus on chromosome 15 is now contained in an interval of only 3 centimorgans. This work is the basis for further molecular dissection of the genetic loci that underlie anxiety and provides a starting point for the discovery of genes involved in a common psychiatric condition.
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Joehanes, Roby. "Multiple-trait multiple-interval mapping of quantitative-trait loci." Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1605.
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Santana, Morant Dámaris. "Bayesian mapping of multiple quantitative trait loci." [Gainesville, Fla.] : University of Florida, 2005. http://purl.fcla.edu/fcla/etd/UFE0012166.
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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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Martinez, de la Vega Octavio. "Quantitative trait loci estimation in plant populations." Thesis, University of Reading, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.358346.
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Logeswaran, Sayanthan. "Mapping quantitative trait loci in microbial populations." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4881.
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Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual the extreme progeny may be selected by multiple generations of asexual reproduction and selection. In this thesis I will analyse this method of measuring phenotype in asexual cross progeny. The aim is to examine the behaviour of marker allele frequency due to selection over many generations, and also to identify statistically significant changes in frequency in the selected population. I will show that stochasticity in marker frequency in the selected population arises due the finite initial population size. For Mendelian traits, the initial population size should be at least in the low to mid hundreds to avoid spurious changes in marker frequency in the selected population. For quantitative traits the length of time selection is applied for, as well as the initial population size, will affect the stochasticity in marker frequency. The longer selection is applied for, the more chance of spurious changes in marker frequency. Also for quantitative traits, I will show that the presence of epistasis can hinder changes in marker frequency at selected loci, and consequently make identification of selected loci more difficult. I also show that it is possible to detect epistasis from the marker frequency by identifying reversals in the direction of marker frequency change. Finally, I develop a maximum likelihood based statistical model that aims to identify significant changes in marker frequency in the selected population. I will show that the power of this statistical model is high for detecting large changes in marker frequency, but very low for detecting small changes in frequency.
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Yang, Jie. "Nonparametric functional mapping of quantitative trait loci." [Gainesville, Fla.] : University of Florida, 2006. http://purl.fcla.edu/fcla/etd/UFE0014762.
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Greenshields, David. "Isolation of adaptive quantitative trait loci in Antirrhinum." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/14950.
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Understanding the genetic basis of quantitative traits represents a huge goal in modern molecular and evolutionary biology. Here, the natural genetics of the genus Antirrhinum, within which separate species can be successfully interbred, are used to investigate differences in a range of morphological characteristics. The two species used in the study, Antirrhinum majus and Antirrhinum molle, have become adapted to very diverse environments and consequently exhibit large variance in a wide range of traits. A large-scale FI mutant screen, from a cross between a transposon-active A. majus line and A. molle, isolated segregating mutations for flower size, flower colour, trichome density and branching in self-pollinated F2 populations. Amplified Fragment Length Polymorphism analysis of the F2 and the use of molecular maps have shown the mutations generally correspond to known Quantitative Trait Loci, and the roles of genes linked to these regions are discussed. The technique sheds some light on the molecular and evolutionary mechanisms underpinning diversity in Antirrhinum and has implications for the use of transposon-tagging in locating QTL in other plant systems.
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Ritchey, Brian Michael. "Quantitative Trait Loci Mapping Of Macrophage Atherogenic Phenotypes." Cleveland State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=csu1510080975338565.
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Polineni, Pavana. "Developing a web accessible integrated database and visualization tool for bovine quantitative trait loci." Thesis, Texas A&M University, 2003. http://hdl.handle.net/1969.1/2449.
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A quantitative trait locus (QTL) is the location of a gene that affects a trait that is measured on a quantitative (linear) scale. Many important agricultural traits such as weight gain, milk fat content and intramuscular fat in cattle are quantitative traits. There is a need to integrate genomic sequence data with QTL data and to develop an analytical tool to visualize the data. Without integration, application of this data to agricultural enterprise productivity will be slow and inefficient. My thesis presents a web-accessible tool called the Bovine QTL Viewer developed to solve this problem. It consists of an integrated database of bovine QTL and the QTL viewer to view the QTL and their relative chromosomal position. This tool generates dynamic and interactive images and supports research in the field of genomics. For this tool, the data is modeled and the QTL viewer is developed based on the requirements and feedback of experts in the field of bovine genomics.
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Podisi, Baitsi Kingsley. "Quantitative trait loci mapping of sexual maturity traits applied to chicken breeding." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5561.
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Many phenotypes are controlled by factors which include the genes, the environment, interactions between genes and interaction between the genotypes and the environment. Great strides have been made to understand how these various factors affect traits of agricultural, medical and environmental importance. The chicken is regarded as a model organism whose study would not only assist efforts towards increased agricultural productivity but also provide insight into the genetic determination of traits with potential application in understanding human health and disease. Detection of genomic regions or loci responsible for controlling quantitative traits (QTL) in poultry has focussed mainly on growth and production traits with limited information on reproductive traits. Most of the reported results have used additive-dominance models which are easy to implement because they ignore epistatic gene action despite indications that it may be important for traits with low heritability and high heterosis. The thesis presents results on the detection of loci and genetic mechanisms involved in sexual maturity traits through modelling both additive-dominance gene actions and epistasis. The study was conducted on an F2 broiler x White Leghorn layer cross for QTL detection for age, weight, abdominal fat, ovary weight, oviduct weight, comb weight, number of ovarian yellow follicles, a score for the persistence of the right oviduct and bone density. In addition, body weight QTL at 3, 6, 12, 24, 48 and 72 weeks of age, QTL for growth rate between the successive ages and QTL for the parameters of the growth curve were also detected. Most of the QTL for traits at sexual maturity acted additively. A few of the QTL explained a modest proportion of the phenotypic variation with most of the QTL explaining a small component of the cumulative proportion of the variation explained by the QTL. Body weight QTL were critical in determining the attainment of puberty. The broiler allele had positive effects on weight at first egg and negative effects on age at first egg. Most QTL affecting weight at first egg overlapped with QTL for age at first egg and for early growth rate (6-9 weeks) suggesting that growth rate QTL are intimately related to the onset of puberty. Specific QTL for early and adult growth were detected but most QTL had varying influence on growth throughout life. Chromosome 4 harboured most of QTL for the assessed traits which explained the highest proportion of the phenotypic variation in the traits confirming its critical role in influencing traits of economic importance. There was no evidence for epistasis for almost all the studied traits. Evidence for role of epistasis was significant for ovary weight and suggestive for both growth rate and abdominal fat.
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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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Clevinger, Elizabeth. "Mapping Quantitative Trait Loci for Soybean Quality Traits from Two Different Sources." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/33468.
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Soybeans are economically and agriculturally the most important legume in the world, providing protein and oil to the food and animal feed industries and base ingredients for hundreds of chemical products. Their value could be enhanced, however, if the oil and protein content remained high and the oligosaccharide and phytate contents were lowered to make soybeans more acceptable for human and animal consumption.
A soybean population of 55 families segregating for genes controlling quality traits was chosen for this study. Both parental lines have high sucrose and low stachyose. The former contains a high level of phytate while the latter is low phytate. The objective of this experiment was to determine whether or not both parents had the same gene(s) for low stachyose. An additional objective was to determine quantitative trait loci (QTL) controlling quality traits: sucrose, stachyose and phytate. An acetonitrile precipitation method and a modified colorimetric method were used to determine amounts of sugars and phytate, respectively. The phenotypic data for stachyose was analyzed and it was determined that two recessive genes control low stachyose content in this population. A map was constructed using 141 SSR markers and 15 molecular linkage groups (MLGs) were identified. After analyzing trait and marker data in QTL Cartographer, potential QTL were found on MLGs: B1, C2, D1b, F, M and N. Sucrose and stachyose QTL were identified on B1, C2, M and N. Phytate QTL were observed on B1, D1b, F and N. The markers identified for quality traits in this population may be useful in marker-assisted selection and the germplasm should be useful for the development of a cultivar.Master of Science
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Bao, Haikun. "Bayesian hierarchical regression model to detect quantitative trait loci /." Electronic version (PDF), 2006. http://dl.uncw.edu/etd/2006/baoh/haikunbao.pdf.
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Gong, Xiaohua. "Mapping Quantitative Trait Loci in Outbred Half-sib Populations." NCSU, 2009. http://www.lib.ncsu.edu/theses/available/etd-05042009-160015/.
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Quantitative trait loci (QTL) mapping in outbred populations faces some challenges unique to the divergent genetic background and complex pedigree relationships. Motivated by a dairy cattle half-sib data set from a grand daughter design, we present in this dissertation a series of endeavors to address various challenges along the analysis flow of QTL mapping. A first step is to infer the haplotypes in sires based on the observed genotypes in sires and his offspring. Our method was shown to outperform peer methods with greater robustness and accuracy yet with fast speed performance. Then in light of adapting the multiple interval mapping method to within-family QTL analysis, we extended the modeling framework by allowing for heteroscedastic residual variances and upgraded the Windows QTL Cartographer accordingly. The advantageous post-analysis result parsing from Windows QTL Cartographer and more importantly, the improved analysis outputs due to more powerful maximum likelihood-based mixture modeling than the least squares regression manifest our efforts in delivering better methodology via practically user friendly software. We further developed a mixed model approach for the purpose of QTL mapping across multiple families that was aimed at modeling QTL effects as both the fixed effect across families and the random effect within families. Our mixed model was shown to encompass similar or higher statistical testing performance on QTL variation than the widely used variance component modeling approach, yet still allowing permutations for obtaining chromosome-wide or genome-wide significance threshold. What's more, the flexibility of our mixed model in constructing alternative hypotheses testing on either fixed or random QTL effects or both was shown to offer interesting insight into the varying sources of signal that would not be unveiled by least squares regression or variance component methods. In concluding our comprehensive approach to QTL linkage mapping in dairy cattle populations, we continue to explore methods of fine mapping by combining both the linkage disequilibrium and linkage information and prospective method improvements are being sought.
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Marklund, Lena. "Genome analysis of quantitative trait loci in the pig /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1997. http://epsilon.slu.se/avh/1997/91-576-5416-6.gif.
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Ai, Ni, and 艾妮. "A novel framework for expression quantitative trait loci mapping." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B4715214X.
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Arloth, Janine. "Expression quantitative trait loci as possible biomarkers on depression." Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-185767.
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Burns, Malcolm James. "Quantitative trait loci mapping in 'Arabidopsis' : theory and practice." Thesis, University of Birmingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.405862.
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Nash, Nathan Wilkes. "Elucidation of quantitative trait loci for depression and anxiety." Thesis, King's College London (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.417280.
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Li, Jiahan. "Statistical model for mapping quantitative trait loci in autotetraploid." [Gainesville, Fla.] : University of Florida, 2008. http://purl.fcla.edu/fcla/etd/UFE0022877.
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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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Jung, Jeesun. "High resolution linkage and association study of quantitative trait loci." Texas A&M University, 2004. http://hdl.handle.net/1969.1/2681.
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As a large number of single nucleotide polymorphisms (SNPs) and microsatellite
markers are available, high resolution mapping employing multiple markers or
multiple allele markers is an important step to identify quantitative trait locus (QTL)
of complex human disease. For many complex diseases, quantitative phenotype values
contain more information than dichotomous traits do.
Much research has been done on conducting high resolution mapping using information
of linkage and linkage disequilibrium. The most commonly employed approaches
for mapping QTL are pedigree-based linkage analysis and population-based
association analysis. As one of the methods dealing with multiple alleles markers,
mixed models are developed to work out family-based association study with the information
of transmitted allele and nontransmitted allele from one parent to offspring.
For multiple markers, variance component models are proposed to perform association
study and linkage analysis simultaneously. Linkage analysis provides suggestive
linkage based on a broad chromosome region and is robust to population admixtures.
One the other hand, allelic association due to linkage disequilibrium (LD) usually
operates over very short genetic distance, but is affected by population stratification.
Combining both approaches plays a synergistic role in overcoming their limitations
and in increasing the efficiency and effectiveness of gene mapping.
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Pearson, Caroline. "Analysis of a hierarchial Bayesian method for quantitative trait loci /." Electronic version (PDF), 2007. http://dl.uncw.edu/etd/2007-2/pearsonc/carolinepearson.pdf.
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Purcell, Shaun. "Sample selection and complex effects in quantitative trait loci analysis." Thesis, King's College London (University of London), 2003. https://kclpure.kcl.ac.uk/portal/en/theses/sample-selection-and-complex-effects-in-quantitative-trait-loci-analysis(730a92fb-113b-42c1-8f38-8a085bb37112).html.
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Zhou, Hua, Jin Zhou, Eric Sobel, and Kenneth Lange. "Fast genome-wide pedigree quantitative trait loci analysis using MENDEL." BioMed Central, 2014. http://hdl.handle.net/10150/610091.
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The linkage era left a rich legacy of pedigree samples that can be used for modern genome-wide association sequencing (GWAS) or next-generation sequencing (NGS) studies. Family designs are naturally equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Unfortunately, pedigree likelihoods are notoriously hard to compute, and current software for association mapping in pedigrees is prohibitively slow in processing dense marker maps. In a recent release of the comprehensive genetic analysis software MENDEL, we implemented an ultra-fast score test for association mapping with pedigree-based GWAS or NGS study data. Our implementation (a) works for random sample data, pedigree data, or a mix of both(b) allows for covariate adjustment, including correction for population stratification
(c) accommodates both univariate and multivariate quantitative traits
and (d) allows missing values in multivariate traits. In this paper, we assess the capabilities of MENDEL on the Genetic Analysis Workshop 18 sequencing data. For instance, when jointly testing the 4 longitudinally measured diastolic blood pressure traits, it takes MENDEL less than 51 minutes on a standard laptop computer to read, quality check, and analyze a data set with 959 individuals and 8.3 million single-nucleotide polymorphisms (SNPs). Our analysis reveals association of one SNP in the q32.2 region of chromosome 1. MENDEL is freely available on http://www.genetics.ucla.edu/software webcite.
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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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Kadarmideen, Haja Najeemudin. "Statistical methods to map quantitative trait loci for binary traits in half-sib populations." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ33306.pdf.
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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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Zhao, Honghua. "Use of linkage disequilibrium for quantitative trait loci mapping in livestock." [Ames, Iowa : Iowa State University], 2006.
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Silver, Nicholas. "Mapping and characterisation of quantitative trait loci controlling fetal haemoglobin expression." Thesis, King's College London (University of London), 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443959.
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Somorjai, Ildikó M. L. "Quantitative trait loci for fitness traits in Arctic charr, conservation in rainbow trout and correlations among traits." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/MQ61949.pdf.
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Lisec, Jan. "Identification and characterization of metabolic Quantitative Trait Loci (QTL) in Arabidopsis thaliana." Phd thesis, Universität Potsdam, 2008. http://opus.kobv.de/ubp/volltexte/2008/2590/.
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Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach.
This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL).
Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis.
The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.
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Brown, Andrew Anand. "Multivariate methods for the discovery of quantitative trait loci and gene networks." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501705.
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WANG, TAO. "MODELING AND INFERRING QUANTITATIVE TRAIT LOCI USING LINKAGE DISEQUILIBRIUM IN NATURAL POPULATIONS." NCSU, 2001. http://www.lib.ncsu.edu/theses/available/etd-20011012-133341.
Full textAbstract:
Quantitative trait loci (QTL) are those chromosome regions that contribute to variation of quantitative traits. Analysis of QTL is helpful for further study of molecular basis of the quantitative genetic variation. The discovery of highly abundant and dense polymorphic markers (e.g., single nucleotide polynorphisms, or SNPs) covering a whole genome provides an opportunity to localize QTL in a variety of populations. While classical linkage studies have a relatively limited resolution in QTL localization, the association mapping or linkage disequilibrium (LD) mapping approach can offer an alternative way for fine mapping of genes. Currently there are few LD methods available for QTL mapping in natural populations. Development of more efficient methods is still a challenging problem. In this thesis, we first review the LD approach for fine mapping of QTL in Chapter 1. Some basic issues in LD analysis and recent developments in LD methodology are discussed. Particular attention is paid to limitations and potential problems of these methods. This provides the motivation for the research in this thesis.Next, we explore Cockerham's genetic model (Cockerham, 1954) for quantitative traits in Chapter 2. A revised form of the Cockerham model is presented using some coding variables. The relationship between Cockerham model and some specific genetic models for designed experimental populations, such as backcross or F2, is then established. We study extensively the properties of QTL effects and partitions of various genetic variance components for these reduced models under both linkage equilibrium and linkage disequilibrium situations. A general multi-locus-two-allele model is also proposed that may serve as a basis for mapping QTL in natural populations. The main research of the thesis is on development of an exact multipoint likelihood approach to infer QTL in natural populations. In Chapter 3, we first generalize the formulation of the likelihood analysis for a polymorphic marker locus and a trait locus in a general natural population. From this generalization, we derive a closed form solutionof an efficient EM algorithm for the likelihood analysis. This is a major achievement of the research. The importance of this generalization is that it can be readily and systematically extended to multiple markers and multiple QTL.Based on this formulation, a multipoint likelihood analysis with the EM algorithm is developed that can take into account higher-order linkage disequilibria between QTL and markers without making approximation to the likelihood function. This analysis can offer a simultaneous estimation of the linkage disequilibrium structure between a QTL and multiple markers. From this estimation, we find that the linkage disequilibrium between one or a subset of markers and a QTL conditional on other markers can offer as a more accurate measure for fine mapping of QTL. In Chapter 4, we further extend the analysis to multiple QTL and propose a general framework for likelihood analysis of multiple QTL and markers. With this approach, the joint gametic frequencies of QTL and markers (thus various measures of linkage disequilibria between QTL and markers) as well as various genetic effects of QTL (including epistasis) can be estimated simultaneously. This general approach has a lot of potential for a complete analysis of genetic architecture of quantitative traits in natural populations. Although the foundation of this general framework has been laid down, more studies are still needed on a number of issues, such as efficiency and reliability of the optimization algorithm, statistical tests for QTL identification, model selection of complex QTL, and more efficient approaches to analyze large data sets. In the last chapter (Chapter 5), we draw some general conclusions from the research. We discuss the advantages as well as limitations of the approach developed in this thesis and problems for further research.
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Ljungberg, Kajsa. "Numerical Algorithms for Mapping of Multiple Quantitative Trait Loci in Experimental Populations." Doctoral thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6248.
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Most traits of medical or economic importance are quantitative, i.e. they can be measured on a continuous scale. Strong biological evidence indicates that quantitative traits are governed by a complex interplay between the environment and multiple quantitative trait loci, QTL, in the genome. Nonlinear interactions make it necessary to search for several QTL simultaneously. This thesis concerns numerical methods for QTL search in experimental populations. The core computational problem of a statistical analysis of such a population is a multidimensional global optimization problem with many local optima. Simultaneous search for d QTL involves solving a d-dimensional problem, where each evaluation of the objective function involves solving one or several least squares problems with special structure. Using standard software, already a two-dimensional search is costly, and searches in higher dimensions are prohibitively slow. Three efficient algorithms for evaluation of the most common forms of the objective function are presented. The computing time for the linear regression method is reduced by up to one order of magnitude for real data examples by using a new scheme based on updated QR factorizations. Secondly, the objective function for the interval mapping method is evaluated using an updating technique and an efficient iterative method, which results in a 50 percent reduction in computing time. Finally, a third algorithm, applicable to the imputation and weighted linear mixture model methods, is presented. It reduces the computing time by between one and two orders of magnitude. The global search problem is also investigated. Standard software techniques for finding the global optimum of the objective function are compared with a new approach based on the DIRECT algorithm. The new method is more accurate than the previously fastest scheme and locates the optimum in 1-2 orders of magnitude less time. The method is further developed by coupling DIRECT to a local optimization algorithm for accelerated convergence, leading to additional time savings of up to eight times. A parallel grid computing implementation of exhaustive search is also presented, and is suitable e.g for verifying global optima when developing efficient optimization algorithms tailored for the QTL mapping problem. Using the algorithms presented in this thesis, simultaneous search for at least six QTL can be performed routinely. The decrease in overall computing time is several orders of magnitude. The results imply that computations which were earlier considered impossible are no longer difficult, and that genetic researchers thus are free to focus on model selection and other central genetical issues.
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Bégin, Michelle Anne. "Identifying quantitative trait loci involved in radiation-induced lung disease in mice." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=99321.
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The goal of this thesis was to identify genetic loci involved in radiation-induced lung disease in mice. Phenotypic analysis was completed for alveolitis, pulmonary fibrosis, survival time, mast cells/mm2 and cell counts in bronchoalveolar lavage (BAL) to assess lung damage. Genome scans and linkage analysis were completed for two backcross cohorts (75%C3H/HeJ-25%C57Bl/6J or 25%C3H/HeJ-75%C57BU6J) using each of the phenotypes measured. Putative susceptibility loci were identified for alveolitis on chromosomes 12 (LOD=3.35), 14 (LOD=2.22) and 19 (LOD=1.7) in the mostly C3H/HeJ backcross cohort and on chromosome 14 (LOD=2.7) in the mostly C57BI/6J backcross cohort. Linkage using the pulmonary fibrosis scores provided supportive evidence for a quantitative trait loci (QTL) on chromosome 17 (LOD=2) in the mostly C57BI/6J background, and two unique putative linkage regions were localized on chromosome 2 (LOD=2.2) in the mostly C3H/HeJ cohort and 14 (LOD=2) in the mostly C57BI/6J cohort. Supporting evidence for linkage on chromosomes 12 and 14 in the mostly C3H/HeJ background and chromosome 14 in the mostly C57BI/6J background was obtained using cellular markers. Additionally, survival time mapped to the linkage regions isolated for alveolitis and pulmonary fibrosis, suggesting that the development of radiation-induced lung disease influences the survival time of the mice. Within each cohort there were sex dependent linkage intervals, indicating that male and female mice may possess different factors involved in the development of alveolitis and/or pulmonary fibrosis. These results suggest that there are multiple genetic loci involved in the development of radiation-induced lung disease in mice.
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Jones, Elizabeth. "Mapping quantitative trait loci for resistance to downy mildew in pearl millet." Thesis, Bangor University, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387360.
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Tomaszewski, Celine. "Fine mapping of biomass yield quantitative trait loci in Lolium perenne L." Thesis, University of Leicester, 2012. http://hdl.handle.net/2381/10827.
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Biomass yield is a complex quantitative trait controlled by many environmental and genetic factors. Therefore its study relies on QTL mapping. In a precursor study, a genetic map of L. perenne was constructed on an inbred-derived F2 population and three major biomass QTL have been found on linkage groups (LGs) 2, 3 and 7. In this study, a fine map of the QTL positions was developed by mapping additional ryegrass specific SSR, rice Sequence Tagged Site and Diversity Array Technology markers. A total of 153 markers were added to the existing map leading to a map density of 3.5 cM. The QTL positions were recalculated for dry weight, fresh weight, dry matter and leaf width and in accordance to the preliminary analysis biomass QTL were localized on LGs 2, 3 and 7 but despite the fine map the QTL intervals were not reduced. In order to analyze the QTL regions, the screening of a L. perenne BAC library was performed using the markers flanking the QTL and several clones were isolated. After analysis using the AFLP fingerprinting method, five clones were send for full sequencing to perform a gene prediction and annotation using the Ab initio approach. The annotation revealed for one of the gene structures predicted homology to the lg1- like gene and four other showed homology to regions flanking genes of interest suggesting the possible presence of the genes within the biomass QTL region. The four genes were: L. perenne heading date (Hd1) gene, Avena strigosa beta-amyrin synthase (Sad1) and cytochrome P450 CYP51H10 (Sad2) genes and Lolium multiflorum gene for cold responsive protein.
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Walling, Grant Anderson. "Detection and mapping of quantitative trait loci in domestic farm livestock species." Thesis, University of Edinburgh, 1998. http://hdl.handle.net/1842/13181.
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The aims of the thesis were to investigate, by simulation, various aspects of the QTL mapping methods and apply the methods to scan the porcine genome for QTLs. The mapping of the porcine genome was achieved using a Meishan x Large White F2 population. These breeds were chosen because they differed significantly for several traits of economic interest. Markers covered approximately 85% of the porcine genome and animals were measured for growth and fatness traits. Chromosomes 4, 7 and 14 had a genome wide significant effect on at least one trait. In all cases the single gene model was significantly better than the polygenic model. The effects on chromosome 4 for growth were in agreement with previous studies notably a similar study using wild boar from Sweden. Chromosome 7 had a large effect on fatness (over 6mm between breeds) and is of considerable interest because the Large White carries the alleles for high fat depth. Chromosome 14 was shown to have a significant effect on growth rate on test. Confidence intervals were produced by the non-parametric bootstrap and were found to be relatively large (in excess of 30cM) for the location on chromosomes 4 and 14. In contrast the confidence intervals on chromosome 7 were smaller and corresponded to the major histocompatilibity complex, a very gene rich region of the genome.
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Masri, Amer. "Use of quantitative trait loci (QTL) affecting muscling in sheep for breeding." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/9526.
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Breeding programmes that use elite sires with the best estimated breeding values for muscling traits have achieved significant improvement in lamb production in the UK. Further acceleration of the rate of genetic gain for the desirable production traits could be achieved using DNA marker-assisted selection (MAS) breeding strategies. The underlying causal genetic variants associated with improved muscling may be unknown and lying between a cluster of genes known as quantitative trait loci (QTL) or could be single nucleotide polymorphisms (SNP). LoinMAXTM, Texel muscling QTL (TM-QTL) and c.*1232G > A myostatin mutation were genetic variants that reported to be associated with improved muscling characteristics and hence subjected to further analysis in this project. It is essential before incorporating segregating genetic variants in any breeding scheme to comprehensively evaluate their effects on carcass traits. In-vivo scanning (ultrasound scanning (US) and computed tomography scanning (CT)), and carcass video image analyses (VIA) were used in the current studies. Objective VIAprediction weights of the carcass primal cuts could be the backbone of a value-based marketing system that is suggested to replace the current Meat and Livestock Commission (MLC) carcass grades for conformation scores (MLC-C) and fat class (MLC-F). The effect of a single copy of LoinMAXTM QTL (LM-QTL) compared to noncarriers was evaluated in UK crossbred lambs out of Scottish Mule ewes. M. longissimus lumborum (MLL) width, depth and area, as measured by CT scanning, were significantly greater in lambs heterozygous for LM-QTL compared to noncarriers. VIA detected a significant effect of the LM-QTL on the predicted weight of saleable meat yield in the loin primal cut (+2.2%; P < 0.05). The effects of the ovine c.*1232G > A myostatin mutation (MM), found on sheep chromosome 2, on carcass traits in heterozygous crossbred lambs sired by Texel and Poll Dorset rams were studied. Texel crossbred lambs carrying MM had increased loin depth and area. In both crossbred lambs, MM-carriers had significantly higher CT-estimated lean weight and proportion (2 to 4%) and muscle to bone ratios (by ~3%). Poll Dorset heterozygous crossbred animals had higher muscle to fat ratio (28%) and significantly lower fat-related measurements. The c.*1232G > A (MM) mutation as well as TM-QTL effects were evaluated in a different genetic background of Texel x Welsh Mountain crossbreed lambs. Carrying two copies of MM was associated with a significant positive effect on 8 week weight, a negative effect on ultrasound fat depth, a substantial decrease in MLC-fat score, positive impact on VIA-estimated weight of the hind leg, chump and loin primal cuts, as well as the muscularity of the hind leg and loin regions with greater loin muscle width, depth and area. Two copies of MM altered lambs‟ morphological traits with significantly wider carcasses across the shoulders, breast and hind legs and greater areas of the back view of the carcass when measured by VIA. TM-QTL significantly increased US-muscle depth and TM-QTL carriers had significantly greater loin muscle width and area measurements. Comparing TM-QTL genetic groups (homozygote allele carriers (TM/TM), heterozygote carriers of paternal and maternal origin of allele (TM/+ and +/TM, respectively) and homozygote non-carriers (+/+)) and TM-QTL mode of action were then studied. TM/TM carcasses were significantly heavier than non-carriers by 1.6 kg and scored higher conformation values when compared to heterozygote groups only. TM/+ lambs had significantly higher VIA-predicted weight and muscularity in the hind leg and loin, and higher loin dimensions relative to some other genotypic groups. The effect of TM-QTL on some carcass shape measurements was significant. TM-QTL mode of action results on the loin muscling traits supports the earlier reports of polar over dominance. In the light of growing calls to replace the current subjective carcass payment system with the objective VIA system that values the carcass according to the superiority of its cuts, I investigated the ability of US and CT measurements to predict the VIAestimated weights of the carcass primal cuts. Several prediction equations were examined but the best could be achieved when ultrasound measurement, CT linear measurements and live weight were fitted in the model. Since CT scanning information of elite sires is now being used for genetic selection for carcass merit, genetic parameters and genetic relationships between CT scanning measurements and post mortem traits (VIA and MLC-FC) were estimated. However, results were not sufficiently accurate to be of practical use due to lack of data.
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Grignola, Fernando E. "Mapping quantitative trait loci using multiple linked markers via Residual Maximum Likelihood." Diss., Virginia Tech, 1996. http://hdl.handle.net/10919/40323.
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Mapping quantitative trait loci in outbred populations is important since development of inbred lines in livestock species is usually not feasible. Traditional genetic mapping methods, such as Least Squares and Maximum Likelihood, cannot fully accommodate complex pedigree structures, and more sophisticated methods such as Bayesian analysis are very demanding computationally. In this thesis, an alternative approach based on a Residual Maximum Likelihood method for estimation of position and variance of one or two linked QTLs and of additive polygenic and residual variances is presented. The method is based on a mixed linear model including polygenic and random QTL allelic effects. The variance-covariance matrix of QTL allelic effects and its inverse is computed conditional on incomplete information from multiple linked markers. The method is implemented using interval mapping and a derivative-free algorithm, where the required coefficient matrix of the Mixed Model Equations is derived from a Reduced Animal Model. simulation studies based on a granddaughter design with 2000 sons, 20 sires and 9 ancestors were performed to evaluate parameter estimation and power of QTL detection. Daughter Yield Deviations of sons were simulated under three QTL models, a biallelic, a multiallelic (10 alleles), and a normal-effects model. A linkage group of five or nine markers located on the same chromosome was assumed, and genotypes were available on sons, sires and ancestors. Likelihood ratio statistics were used to test for the presence of one or two linked QTLs. Parameters were estimated quite accurately for all three QTL models, showing that the method is robust to the number of alleles at the QTL. The effect of considering or ignoring relationships in the analyses did not have a major impact on parameter estimates but reduced the power of QTL detection. In general, power tended to decrease as the number of sons per sire, QTL contribution to additive genetic variance, or distance between QTLs was reduced. The method allowed for detection of a single QTL explaining 25% of the additive genetic variance, and for detection of two QTLs when jointly they accounted for 50% or 12.5% of the additive genetic variance. Although the REML analysis is an approximate method incorporating an expected covariance matrix of the QTL
effects conditional on marker information, it is a computationally less expensive alternative to Bayesian analysis for accounting for the distribution of marker-QTL genotypes given marker and phenotypic information. For the designs studied, parameters were estimated accurately and QTLs mapped with satisfactory power.Ph. D.
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Lee, Yi-Chen. "MENDELIZING QUANTITATIVE TRAIT LOCI THAT UNDERLIE RESISTANCE TO SOYBEAN SUDDEN DEATH SYNDROME." OpenSIUC, 2016. https://opensiuc.lib.siu.edu/theses/1999.
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Soybean (Glycine max [L.] Merr.) cultivars differ in their resistance to sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Breeding for improve SDS response has proven challenging, possible due to interactions among the 18 known loci for resistance. Four loci for resistance to SDS (cqRfs to cqRfs3) were found clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on chromosome 18. Another locus on chromosome 20 (cqRfs5) was reported to interact with this cluster. The aims of this study were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but still segregated at 2 of the 4 loci (cqRfs1 and cqRfs) for resistance to SDS on chromosome 18; to examine the interaction with the locus on chromosome 20; and to identify candidate regions underlying quantitative trait loci (QTL). Used were a near isogenic line population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 1-40; SDS response data from 2 locations and years; four microsatellite markers and six thousand SNP markers. Polymorphic regions were found from 2,788 to 8,938 Kbp on chromosome 18 and 33,100 to 34,943 Kbp on chromosome 20. Both regions were significantly (0.005 < P > 0.0001) associated with resistance to SDS. A fine map was constructed that Mendelized the three loci. Substitution maps suggested the two loci on chromosome 18 were actually 3 loci (cqRfs, cqRfs1 and cqRfs19). Candidate genes for cqRfs19 were identified in a small region of the genome sequence of soybean. An epistatic interaction was inferred where the allele of loci on chromosome 18 determined the value of the locus on chromosome 20. It was concluded that SDS loci are both complex and interacting which may explain the slow progress in breeding for resistance to SDS.
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Brasier, Kyle Geoffrey. "Physiological Traits and Quantitative Trait Loci Associated with Nitrogen Use Efficiency in Soft Red Winter Wheat." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/89216.
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Development of winter wheat (Triticum aestivum L.) cultivars capable of more efficient uptake and utilization of applied nitrogen (N) has the potential to increase grower profitability and reduce negative environmental consequences associated with N lost from the plant-soil system. The first study sought to evaluate genotypic variation for N use efficiency (NUE) and identify lines consistently expressing high or low NUE under two or more N rates in a total of 51 N-environments. The results indicated that significant genotype by N rate interactions were frequently observed when trials utilized at least three N rates and identified wheat lines with high and stable yield potential that varied in performance under low N conditions. In addition, NUE was associated with above-ground biomass at physiological maturity were found to be both highly heritable across multiple N supplies. In the second study, two bi-parental mapping populations having a common low ('Yorktown') and two high (VA05W-151 and VA09W-52) NUE parents were characterized to dissect the genetics underlying N response. The populations were evaluated in eight N-environments and genotyped using single-nucleotide polymorphism data derived from a genotyping-by-sequencing protocol to identify quantitative trait loci (QTL) associated with high NUE. Six QTL for NUE were identified on chromosomes 1D, 2D, 4A, 6A, 7A, and 7D that were associated with N use efficiency. The QTL on 2D and 4A co-localized with known loci governing photoperiod sensitivity and resistance to Fusarium head blight (caused by the fungal pathogen Fusarium graminearum Schwabe), respectively. Three of the identified QTL (6A, 7A, and 7D) were associated with NUE in previous investigations, while the QTL on 1D was novel. The final experiment employed a small panel of soft red winter wheat lines to study the effects of photoperiod alleles on chromosome 1D (Ppd-D1) on yield-related traits under three or five N rates that were variably split over two growth stages in eight environments. The results validated the effect of a photoperiod sensitive allele (Ppd-D1b) that was associated with increased grain yield across N rates in half of the Virginia testing environments and under low N rates in all Ohio testing sites at the expense of grain N content. Yield advantages conferred by the Ppd-D1b allele were attributable to increased floret fertility and kernel number per spike. The findings from these studies have direct application for winter wheat breeding programs targeting NUE improvements.Doctor of Philosophy
Wheat (Triticum aestivum L.) products account for a significant percentage of the total dietary calories and protein consumed globally. To meet production demands, wheat requires efficient nitrogen (N) management to ensure continued grower profitability and to reduce negative environmental impacts of N lost from agricultural systems. This dissertation sought to evaluate variation among wheat lines for N use efficiency (NUE), assess the performance of wheat lines under multiple N supplies, validate traits that are associated with NUE, investigate the role of photoperiod sensitivity genes on N response, and identify regions of the wheat genome associated with high N use efficiency. These studies were conducted using panels of winter wheat lines grown under two or more N conditions over a combined 32 location-years. Results of Chapter I identified variation in cultivar response to N rates was more frequently observed when a greater number of N rates were used in trials of wheat N response. The first chapter also identified variation among wheat lines for NUE and identified lines that consistently produce high grain yields over N-location-years. In addition, above-ground biomass at physiological maturity was found to be strongly associated with grain yield under all N rates and was highly heritable in both studies. Chapter II utilized a combination of genetic and observable trait data to perform genetic analysis in two bi-parental populations grown in eight Nlocation-years. The study identified reproducible and significant genetic markers associated with NUE for application in wheat breeding programs. Upon analysis of photoperiod sensitive versus insensitive wheat lines in Chapter III, photoperiod sensitive wheat lines had a significant yield advantage under N-limited conditions in Ohio and across N treatments in half of the Virginia testing location-years. This resulted from an increased number of kernels per spike and fertile florets in photoperiod sensitive wheat lines. Results from this dissertation suggest that active breeding and selection for N response may be achieved through the employment of high NUE genes and the continued identification of adapted high NUE wheat parental lines.
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McClure, Matthew Charles Taylor J. "Genome scan in commercial angus cattle for quantitative trait loci influencing growth, carcass, and reproductive traits." Diss., Columbia, Mo. : University of Missouri-Columbia, 2009. http://hdl.handle.net/10355/7006.
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The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from PDF of title page (University of Missouri--Columbia, viewed on January 6, 2010). Vita. Thesis advisor: Jeremy Taylor. "July 2009" Includes bibliographical references.
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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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Wambach, Tina. "Effects of epistatic interaction on detection and parameter analysis of quantitative trait loci." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33039.
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Recent scientific support for the involvement of genetic locus interaction in quantitative trait variation and the widespread use of quantitative trait locus (QTL) mapping has resulted in the need to examine those aspects concurrently. Computer software was written to simulate interacting quantitative trait loci (QTLs) in plant populations. Using this software, interacting QTLs were simulated to examine effects of epistasis on the detection of QTLs and the quality of QTL parameter estimates. Simulations involved doubled haploid populations exhibiting two non-epistatic traits and seven epistatic traits, each trait at four levels of heritability. Detection efficiency of QTL main and interaction effects decreased with decreasing heritability. At a given level of broad-sense heritability, traits differed with respect to the relative quality of main-effect detection and interaction-effect detection. Main-effect detection was notably poor for one epistatic locus that has a relatively small additive effect. Position estimates were accurate but their precision deteriorated with decreasing heritability. The quality of QTL effect estimates declined consistently with decreasing heritability, and loss in the accuracy was associated with losses in power of detection.
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Schneerman, Martha June Cook Weber David F. "Identification of quantitative trait loci (QTLs) of corn oil in Zea mays L." Normal, Ill. Illinois State University, 1996. http://wwwlib.umi.com/cr/ilstu/fullcit?p9720812.
Full textAbstract:
Thesis (Ph. D.)--Illinois State University, 1996.Title from title page screen, viewed May 31, 2006. Dissertation Committee: David F. Weber (chair), Alan J. Katz, Marjorie A. Jones, Radheshyam K. Jayaswal, Jefferey A. Dole. Includes bibliographical references (leaves 96-108) and abstract. Also available in print.
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Rickett, Daniel Viner. "Identification and characterisation of phenolic based quantitative trait loci from wild tomato relatives." Thesis, Royal Holloway, University of London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.594163.
Full textAbstract:
Quality traits associated with consumer health are an important aspect of modem plant breeding programmes. Of particular interest are phenolic compounds, a group that includes phenylpropanoids, flavonoids and anthocyanins. Previous studies have shown an inverse correlation between the incidence of chronic disease states and the intake of fruits and vegetables rich in phenolics. Molecular linkage mapping populations that utilise wild tomato relatives in traditional breeding strategies exploit wild germplasm for the identification of novel quantitative trait loci (QTL) without the use of genetic modification. In this study, the Solanum neorickii backcross inbred line population was screened for novel phenolic profiles. Marker data available within the EU Sol consortium were used to identify chromosomes 5 and 10 as possible QTL-containing regions for high rutin and p-coumaric acid phenotypes, and accessions neo-lll and neo- 123 were selected as candidate lines, respectively. Accession 3939 was incorporated from the Solanum habrochaites near isogenic line population because of its similarities with neo-ili. Each accession was characterised for metabolomic and physiological properties throughout fruit development and ripening. Results indicated multiple metabolic pathways were affected, including increases in isoprenoid intermediates; fruit ripening time was increased; and fruit size was altered. Antioxidant capacity of polar extracts increased, especially in fruit tissues accumulating phenolics. Transcriptomic analysis throughout fruit development identified 186 differentially expressed transcription factor (TF) genes. The promoter regions of two of these TF genes. a MYB-related in chromosome 5 and a LLM family in chromosome 10, were sequenced for differences between the wild relative and Solanum lycopersicum parents. These differences provide candidate QTL identities for the previously characterised phenotypes, and offer the potential for future utilisation in plant breeding programmes for high phenolic commercial lines.