Dissertations / Theses on the topic 'QTL'
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Xing, Liqun. "Marker density, marker distribution and QTL-by-environment interaction in QTL mapping." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0034/NQ64696.pdf.
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Xing, Liqun 1962. "Marker density, marker distribution and QTL-by-environment interaction in QTL mapping." Thesis, McGill University, 1999. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=36734.
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Two studies were conducted on gene mapping analysis. For the first study, genetic simulation experiments were conducted to address the effects of marker density, method of mapping analysis, and gaps in a marker map on the efficiency of QTL detection and the accuracy of QTL parameter estimation. The simulated genome consisted of seven chromosomes with seven or eight segregating QTL affecting the simulated quantitative trait. A set of six randomly segregating QTL outside the test region was consistently used to represent 40% of phenotypic variation. An individual QTL or a linkage block of two QTL on a target chromosome contributed 10% of phenotypic variation. The marker map was either dense (with markers every 4 cM) or sparse (with markers every 20 cM). The gap in the marker map was either 32 cM or 56 cM. Interval mapping and composite interval mapping were used to map QTL on the target chromosome. A dense map provided more power of QTL detection, better accuracy of QTL parameter estimation, and higher false-positive error rates for the target chromosome than a sparse map. Composite interval mapping provided more power of QTL detection, better accuracy of QTL parameter estimation, and lower false-positive error rates than interval mapping. Presence of a large gap in a marker map affected QTL detection and QTL parameter estimation for a QTL inside or near the gap. The use of a dense map with composite interval mapping was the most efficient combination tested in this study. For the second study, a mixed factorial regression model for interval mapping was developed for conducting QTL-by-environment interaction analysis and for providing inferences about QTL that are applicable beyond the environments used in the experiments. Genetic simulation was used to test the model for the power of detecting QTL-by-environment interaction and identifying the types of such interaction as crossover or non-crossover, and for the accuracy of estimating QTL parameters. The model prov
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Bauman, Lara Elizabeth. "QTL variance component models." Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1464110531&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Yalçin, Biannaz. "QTL mapping in animal models." Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410716.
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Wahlberg, Per. "Chicken Genomics - Linkage and QTL mapping." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9502.
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Ljungberg, Kajsa. "Numerical methods for mapping of multiple QTL." Licentiate thesis, Uppsala universitet, Avdelningen för teknisk databehandling, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-86133.
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This thesis concerns numerical methods for mapping of multiple quantitative trait loci, QTL. Interactions between multiple genetic loci influencing important traits, such as growth rate in farm animals and predisposition to cancer in humans, make it necessary to search for several QTL simultaneously. Simultaneous search for n QTL involves solving an n-dimensional global optimization problem, where each evaluation of the objective function consists of solving a generalized least squares problem. In Paper A we present efficient algorithms, mainly based on updated QR factorizations, for evaluating the objective functions of different parametric QTL mapping methods. One of these algorithms reduces the computational work required for an important function class by one order of magnitude compared with the best of the methods used by other authors. In Paper B previously utilized techniques for finding the global optimum of the objective function are compared with a new approach based on the DIRECT algorithm of Jones et al. The new method gives accurate results in one order of magnitude less time than the best of the formerly employed algorithms. Using the algorithms presented in Papers A and B, simultaneous search for at least three QTL, including computation of the relevant empirical significance thresholds, can be performed routinely.
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Wang, Austin T. "Allele-Specic QTL fine-mapping with PLASMA." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/129928.
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Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, February, 2020Cataloged from student-submitted PDF of thesis.
Includes bibliographical references (pages 35-37).
We introduce PLASMA (PopuLation Allele-Specic MApping), a statistical ne- mapping method that leverages allele-specic (AS) genomic data to improve detection of quantitative trait loci (QTLs) with causal effects on molecular traits. In simulations, PLASMA accurately prioritizes causal QTL variants over a wide range of genetic architectures. Applied to RNA-Seq data from 524 kidney tumor samples, PLASMA achieves a greater power at 50 samples than conventional QTL-based ne-mapping at 500 samples: with over 17% of loci ne-mapped to within 5 causal variants compared to 2% by QTL-based ne-mapping, and a 6.9-fold overall reduction in median credible set size. PLASMA offers high accuracy even at small sample sizes, yielding a 1.3-fold reduction in median credible set size compared to QTL-based ne-mapping when applied to H3K27AC ChIP-Seq from just 28 prostate tumor/normal samples. Our results demonstrate how integrating AS activity can substantially improve the detection of causal variants from existing molecular data.
by Austin T. Wang.
M. Eng.
M.Eng. Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science
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Hu, Wei-Hua. "The use of QTL in Hebrew aphorism." Theological Research Exchange Network (TREN), 2001. http://www.tren.com.
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QUADROS, I. P. S. "MAPEAMENTO E DETECÇÃO DE QTL EM MANDIOCA." Universidade Federal do Espírito Santo, 2016. http://repositorio.ufes.br/handle/10/7844.
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tese_10266_Dissertação Final Iana Pedro da Silva Quadros.pdf: 2554686 bytes, checksum: 3716e4642d5c167349ceddb1c5ee793f (MD5)
Previous issue date: 2016-08-31A mandioca é típica dos trópicos e fonte de segurança alimentar para mais de 600 milhões de pessoas, utilizada na alimentação humana e animal e na indústria, pela extração de amido e produção de biocombustível. O Brasil é o segundo país em produção, entretanto o incremento em produção é baixo para atender o crescente mercado. A compreenção da arquitetura genética de caracteres agronomicamente importantes é útil para delinear cruzamentos e possibilita a identificação de loci controladores de características quantitativas (QTL), no intuito de seleção assistida e clonagem de genes candidatos. Neste trabalho objetivou-se identificar, mapear e caracterizar QTL para as características de altura das plantas (AP), produtividade de parte aérea (PPA), produtividade total de raízes fresca (PTR), teor de matéria seca da raiz (MS) e produtividade de amido (PROD-AMD) de mandioca. Para isto foi utilizada uma população F1 de 141 indivíduos, oriunda do cruzamento entre as cultivares Fécula Branca e BRS Formosa, mantida em delineamento em blocos, com duas repetições e 16 plantas por parcela para as análises fenotípicas. A genotipagem dos indivíduos foi realizada usando SNPs, microssatélites e minissatélites. O mapa foi construído com abordagem multiponto e a detecção dos QTL realizada por análise de contraste entre médias e intervalo, considerando os diferentes tipos de segregação do QTL. Variabilidade foi observada para todas as características e altas correlações fenotípicas, exceto para MS, com destaque para PTR e PROD-AMD (0,98), bem como alta herdabilidade para AP (74,29%). Também, segregação transgressiva foi detectada para todas as características, indicando complementariedade de alelos dos pais na progênie segregante. O mapa genético representou regiões dos 18 cromossomos da mandioca e foi composto por 283 marcadores em 32 grupos de ligação. Uma região do cromossomo 10 apresentou evidência de pleitropia. Para AP, PPA e PROD-AMD um QTL comum foi identificado, bem como para PTR e PROD-AMD, três QTL comuns foram verificados. O MS apresentou QTL exclusivos. Estes resultados indicam o controle quantitativo das características estudadas, com QTL de grande e pequeno efeito detectados. Estes são úteis no melhoramento da cultura visando maior produtividade.
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Pinto, Luis Fernando Batista. "Ocorrência de interações QTL x Sexo, de epistasias e de QTLs pleiotrópicos em aves (Gallus gallus)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/11/11139/tde-15062007-093204/.
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Este estudo teve por objetivo mapear QTLs para características de desempenho e de carcaça em Gallus gallus . Foram estudadas 350 aves F2 oriundas de um cruzamento, na primeira geração, de machos de corte da linhagem TT com fêmeas de postura da linhagem CC. O peso vivo com 1, 35 e 42 dias de idade; o ganho de peso, o consumo de ração e a conversão alimentar de 35 a 41 dias de idade; os pesos dos pulmões, fígado, coração, moela, peito, coxas (peso de coxas e sobre-coxas), carcaça (sem vísceras, pés e cabeça), carcaça residual (peso da carcaça sem peito, asas e coxas), asas, cabeça, pés e gordura abdominal; o comprimento do intestino e o percentual de hematócrito, foram os fenótipos analisados. Foram utilizados 79 marcadores microssatélites, os quais cobriram 1510,7 cM dos cromossomos 1, 2, 3, 4, 5, 8, 11 e 13. Primeiramente, foram realizadas análises isoladas de cada fenótipo original e de variáveis canônicas obtidas por análise de componentes principais dos fenótipos. O teste razão de verossimilhanças (LRT) entre um modelo incompleto (apenas com efeitos fixos de sexo, incubação e o efeito aleatório de valor genético infinitesimal) e um completo (todos os efeitos anteriores mais os efeitos de QTL) foi o procedimento utilizado nas análises, exceto para testar modelos com interações epistáticas, onde a metodologia de quadrados mínimos foi utilizada. Modelos com interação QTL x sexo também foram testados. Posteriormente, foram feitas análises de múltiplos fenótipos simultaneamente, onde foi possível testar a hipótese de QTL pleiotrópico x QTLs ligados, além dos testes descritos acima, com exceção de efeitos epistáticos. As análises descritivas e de componentes principais foram obtidas no SAS, enquanto o mapeamento de QTL foi realizado no programa QxPak, exceto para análise de efeitos epistáticos, em que um código em Fortran 90 foi empregado. O modelo univariado, sem interações, permitiu mapear oito QTLs altamente significativos (cinco no GGA1 para PV35, PV42, gordura abdominal, comprimento do intestino e peso da cabeça; dois QTLs no GGA2 para PV35 e PV42; e um QTL no GGA3 para gordura abdominal) seis significativos (dois no GGA1 para conversão alimentar e ganho de peso; dois no GGA3 para peso das asas e das coxas; um no GGA4 para peso da cabeça; e um no GGA8 para peso da moela), além de 13 ligações sugestivas para diversas características. Dez QTLs apresentaram interação com sexo, sendo cinco específicos para machos. O modelo com busca simultânea de dois QTLs mapeou seis QTLs anteriormente perdidos (cinco para PV35 e PV42; e um para peso da cabeça). Interações epistáticas foram observadas para PV35 e PV42 entre um QTL em 69 cM do GGA1 com QTLs em 333 cM do GGA1, 272 cM do GGA3 e 77 cM do GGA5. Dois QTLs e seis ligações sugestivas foram mapeados na análise de variáveis canônicas, os quais não haviam sido mapeados com as variáveis originais. Com o procedimento de múltiplas características foi possível mapear nove QTLs pleiotrópicos e o aumento de poder do teste foi evidenciado, principalmente, no GGA2.This study aim to map QTL for performance and carcass traits in (Gallus gallus) . There were used 350 F2 chickens developed by crossing a broiler male line (TT) with a layer line (CC). The body weight with 1, 35 and 42 days of age, weight gain, feed intake and feed conversion from 35 to 41 days, weights of lung, liver, heart, gizzard, breast, drums and thighs, carcass (without giblets, feet and head), residual carcass (weight of carcass without breast, drums, thighs, and wings), wings, head, feet, and abdominal fat, intestine length and hematócrito value were the phenotypes analyzed. Seventy nine microssatellite markers were used, which covered 1510.7 cM of chromosomes 1, 2, 3, 4, 5, 8, 11, and 13. Firstly, QTL analysis was carried out for each original trait and for canonical variables, obtained from principal components analysis of the phenotypes. The likelihood ratio test (LRT) between a reduced model (only fixed effects of sex, hatch and random effect of infinitesimal genetic value) and a full model (all anterior effects and QTL effects) was applied to map QTL, but mean square approach was used for mapping QTL with epistatic effect. Besides, models with QTL by sex interaction were also tested. Finally, multi-trait analysis was used to test the hypothesis of pleiotropic x linkage QTLs, besides of the tests previously described, except models with epistatic effects. For descriptive and principal components analysis the SAS software was used. QTL mapping was carried out with QxPak software and a fortran 90 source code to test models with epistatic effect. The univariate model, without interactions, allowed to map eight highly significant QTLs (five in the GGA1, for PV35, PV42, abdominal fat, intestine length, and head weight; two QTLs in the GGA2, for PV35 and PV42; and one QTL in the GGA3 for abdominal fat), six significant QTLs (two in the GGA1 for feed conversion and weight gain; two in the GGA3 for wings and drums and thighs weights; one in the GGA4 for head weight; and one in the GGA8 for gizzard weight), besides 13 suggestive linkages for several traits. Ten QTLs interacted with sex, being five of them male specific QTLs. The model with simultaneous search for two QTLs was important to map six QTLs previously lost (five for body weight at 35 and 42 days; and one for head weight). Epistatic Interactions were observed for body weight among a QTL in 69 cM of GGA1 with QTLs in 333 cM of GGA1, 272 cM of GGA3 and 77 cM of GGA5. Two QTLs and six suggestive linkages were mapped with the analysis on canonical variables, which have not been mapped with the original variables. With the multi-trait approach nine pleiotropic QTLs were mapped and an increase in the test power was observed mainly in the GGA2 chromosome.
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Ma, Junwu. "Genome-wide QTL mapping for complex traits in pigs and focusing analysis on fatness QTL on porcine chromosome X." Toulouse 3, 2009. http://thesesups.ups-tlse.fr/584/.
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Les buts de cette thèse étaient l'acquisition de connaissances sur l'architecture génétique de caractères complexes et l'étude de la variabilité des taux de recombinaison chez le porc. La première partie de cette thèse présente une analyse sur l'ensemble du génome des locus influençant des caractères quantitatifs (QTL) au sein de croisements F2 entre des verrats de race Duroc blanc et des truies Erhulian, protocole développé en Chine à l'université d'agriculture du Jiangxi (JXAU). La population étudiée dans le cadre de cette thèse regroupe de 750 à 1030 animaux F2 mesurés sur 80 caractères concernant la composition de la carcasse (17 caractères), la qualité de la viande (58 caractères) et les caractères morphologiques des oreilles (5 caractères). Au total nous avons identifié 253 QTL pour ces caractères, dont la moitié est significatif au niveau du génome entier. Les chromosomes rassemblant le plus de QTL pour ces caractères sont les chromosomes 4, 7, 8 & X. Les niveaux de signification les plus élevés sont observés pour un (ou des) QTL affectant la longueur de carcasse, le poids de la tête et le poids des oreilles situé au sein d'un intervalle de 3 cM situé sur le chromosome 7 (Sw1856-S0066) expliquant jusqu'à 50 % de la variance phénotypique. L'allèle Duroc blanc étant l'allèle favorable pour une majorité des QTL affectant la composition de la carcasse, tandis que les allèles favorables pour la qualité de la viande présentent des origines tantôt asiatique tantôt européenne. L'INRA avait réalisé il y a près de 20 ans un programme de détection de QTL entre animaux Large White & Meishan. La localisation parallèle sur le chromosome X de QTL influençant l'engraissement et la muscularité des animaux au sein des pédigrées français et chinois nous a amené a travaillé sur la cartographie fine de ce(s) QTL qui a été développée dans la deuxième partie de cette thèse réalisée en cotutelle. Dans un premier temps afin de préciser la position du QTL située sur le chromosome X, nous avons étudié les variations de taux de recombinaison entre différentes régions du chromosome ainsi que les variations inter individuelles. .The aims of this thesis are to gain knowledge on genetic architecture of complex traits and on fine-scale structure of recombination rate variation in pigs. The first part of this thesis presents a genome-wide scan for quantitative trait loci (QTL) in a cross between White Duroc boars and Erhualian sows that was developed at Jiangxi Agricultural University (JXAU) in China. The mapping population comprised 750-1030 F2 individuals that were evaluated for a total of 80 traits related to carcass composition (17 traits), meat quality (58 traits) and ear traits (5 traits). In total, we identified 253 QTL for these traits, of which about half reached genome-wide significance level. Numerous QTL for these traits have been found on porcine chromosomes 4, 7, 8 and X. The greatest significance levels were found for a QTL affecting carcass length, head weight and ear weight on SSC7 in an interval of 3 cM (SW1856-S0666), which explained up to 50% of the phenotypic variance. White Duroc alleles at a majority of QTL detected were favorable for carcass composition, while favorable QTL alleles for meat quality originated from both White Duroc and Erhualian. INRA performed a genome scan to reveal QTL in a Large White × Meishan cross 8 years ago. Coincidently, both INRA and JXAU mapped strong QTL for fatness and muscling traits in a similar region of the porcine chromosome X (SSCX). Thus, both sides wished to collaborate to fine map the QTL. .
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Winn, Jennifer Ann. "QTL mapping of high digestibility trait in sorghum bicolor (L.) Moench." Thesis, [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-2582.
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Prashar, Ankush. "Arabidopsis QTL analysis using stairs and gene expression." Thesis, University of Birmingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435316.
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Edwards, Kieron David. "Mapping circadian temperature compensation QTL in Arabidopsis thaliana." Thesis, University of Warwick, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396973.
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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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Guzman, Jessica Lorena Gonzalez. "Análise genômica de associação global e prospecção de genes relacionados à características de tipo de bubalinos leiteiros /." Jaboticabal, 2017. http://hdl.handle.net/11449/190828.
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Orientador: Humberto TonhatiResumo: No primeiro capítulo foi proposto um estudo de associação das informações genômicas com características de tipo, a fim de identificar regiões cromossômicas e genes possivelmente relacionados à altura, peso, crescimento e fatores de conformação corporal. Utilizou-se um painel de 49.010 marcadores SNPs (322 animais) conjuntamente com informações de pedigree (674 animais). As analises foram processadas através do programa Blup.f90, utilizando-se a metodologia de single-step (ssGBLUP). Somente as janelas com 10 SNPs adjacentes e que explicavam acima de 1,5% de variância genética aditiva, foram considerados. Os genes SYT10, GKAP1, C9orf64 e PHLPP1 foram identificados para a característica altura da cernelha (ALTC) e apresentam influência para crescimento, altura e desenvolvimento ósseo. Também foi reportado um QTL para ALTC influenciando crescimento e fertilidade. Foram encontrados SNPs localizados em regiões cromossômicas que ainda não foram previamente descritos com QTL para as características em estudo em búfalos. No segundo capítulo, foram estimados os parâmetros genéticos/genômicos para as características produção de leite acumulada aos 305 dias (PLDC) e caracteristicas de tipo altura da cernelha (ALTC), altura da garupa (ALTG), comprimento do corpo (COMPC), comprimento da garupa (COMPG), Largura entre os íleos (LILE), Largura entre os ísquios (LISQ) e perímetro torácico (PERTOR) em búfalos da raça Murrah utilizando modelos bicaracterísticos. As estimativas de herdabilidade f... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: In the first chapter we proposed a study of the association of genomic information with type characteristics, in order to identify chromosomal regions and genes possibly related to height, weight, growth and body conformation factors. Were used one panel of 49,010 SNPs markers (322 animals) together with pedigree information (674 animals). The analyzes were processed through the Blupf90 program, using the singlestep methodology (ssGBLUP). Only the windows with 10 adjacent SNPs and, that explained above 1.5% of additive genetic variance, were considered. The genes SYT10, GKAP1, C9orf64 and PHLPP1 were identified for the characteristic height of the withers (ALTC) and presented influence on growth height and bone development. It has also been reported a QTL for ALTC influencing growth and fertility. SNPs were found located in chromosomal regions which have not previously been described with QTL for the characteristics under study in buffaloes. In the second chapter, were estimated the genetic / genomic parameters for the characteristics accumulated milk production at 305 days (AMP) and characteristics of the withers height (WH), croup height (CH), body length (BL), croup length (CL), Width between hip bones (WBHB), Width between pin bones (WBPB) and thoracic perimeter (TP) in Murrah buffaloes using characteristic models. Genetic correlations were 0.603 between AMP and WH, 0.898 between WBHB and BL, 0.867 betwwen AMP and CL, 0.887 between AMP and TP, 0.774 between WBHB and WBPB,... (Complete abstract click electronic access below)
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Laere, Anne-Sophie van. "From QTL to QTN : identification of a quantitative trait nucleotide influencing muscle development and fat deposition in pig /." Uppsala : Dept. of Animal Breeding and Genetics, Swedish Univ. of Agricultural Sciences, 2005. http://epsilon.slu.se/200509.pdf.
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Marti, Raga Maria. "Environmental and genetic factors affecting Saccharomyces cerevisiae performance during second fermentation." Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0185/document.
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La méthode traditionnelle utilisée pour produire des vins mousseux (comme cava et champagne) est caractérisée par une seconde fermentation qui a lieu à l'intérieur de la bouteille. Cette deuxième fermentation présente des caractéristiques très spécifiques telles qu’une teneur élevée en éthanol, la pression croissante de CO2, une basse température et une faible disponibilité des nutriments. Dans cette thèse, on a tout d'abord analysé l'effet des facteurs environnementaux sur la cinétique de fermentation de Saccharomyces cerevisiae au cours de la seconde fermentation. Deuxièmement, on a analysé l'effet de pratiques communes, telles que l'ajout de nutriments au vin de base, sur la composition finale du vin mousseux. Enfin, nous avons cherché à identifier la base génétique de la variabilité phénotypique observée pendant la seconde fermentation en utilisant une approche Quantitative Trait Locus (QTL). Les résultats obtenus ont permis de déterminer la température, le vin de base utilisé, la souche de levure et la source d'azote utilisée dans l'acclimatation de levure comme les facteurs qui ont la plus grande incidence dans la cinétique de la seconde fermentation. Deuxièmement, par rapport à la composition finale du vin mousseux, nous avons trouvé que l'addition d'azote dans le vin base favorise la libération des acides aminés. Bien que l'ajout de levure sèche inactive favorise la libération des polysaccharides et les propriétés moussantes du vin mousseux. Enfin, on a pu identifier quatre gènes dont la variation allélique explique la variation phénotypique observée parmi les souchesThe traditional method used to produce sparkling wines (such as cava and champagne) is characterized by a second fermentation that takes place inside the bottle. This second fermentation has very specific characteristics such as a high ethanol content, increasing CO2 pressure, low temperature and low nutrient availability. In this thesis, we have firstly analyzed the effect of environmental factors on fermentation kinetics of Saccharomyces cerevisiae during the second fermentation, by monitoring the second fermentation development using aphrometers. Secondly, we analyzed what is the effect of common practices such as adding nutrients to the base wine on the final composition of the sparkling wine by HPLC analysis of content of amino acids and polysaccharides and its foaming capacity (mosalux) of the sparkling wine. Finally we aimed to identify the genetic basis of the second fermentation using Quantitative Trait Locus (QTL) mapping and validation approach. The results obtained enabled us to identify the temperature, the base wine used, the yeast strain and source of nitrogen used in the acclimatization of yeast as the factors that have the highest impact in the second fermentation kinetics. Secondly, with respect to the final composition of sparkling wine, we have found that the addition of nitrogen to the wine base favors the release of amino acids. While the addition of inactive dry yeast, promotes the release of polysaccharides and favors the foaming properties of the sparkling wine. Finally, could identify four genes whose allelic variation explains the phenotypic variation observed among strains
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Taenzler, Bärbel. "QTL-Analyse der Backqualität in Einkornweizen (T. m. monococcum)." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=964783304.
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Fytrou, Anastasia. "Drosophila immunity : QTL mapping, genetic variation and molecular evolution." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4742.
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Drosophila is involved in a wide range of interactions with parasites and pathogens (parasitoid wasps, bacteria, fungi, viruses). Drosophila hosts vary greatly at the species, population and individual level, in their response against such organisms, and much of this variation has a genetic basis. In this thesis I explored three aspects of this variation. First, using recombination mapping based on SNPs and a variation of bulk segregant analysis, I identified a QTL region on the right arm of the third chromosome of D. melanogaster associated with resistance to at least some of the parasitoid species / strains used in the experiments. The location of the QTL was further explored with deficiency complementation mapping and was narrowed down to the 96D1-97B1 region. The success of the deficiency mapping suggests that the resistant allele is not completely dominant. Second, I investigated patterns of molecular evolution in a set of immunity-related genes, using sequences from a D. melanogaster and a D. simulans population and a set of genes without known involvement in immunity for comparison. I found evidence that several of these genes have evolved under different selection pressure in each species, possibly indicating interactions with different parasites. The immunity genes tested appear to be evolving faster compared to non-immunity genes, supporting the idea that the immune system is evolving under strong selective pressure from parasites. Finally, in a D. melanogaster – sigma virus system, I measured genetic variation in the transmission of different virus genotypes, in different environments. There was poor correlation between temperatures, suggesting that environmental heterogeneity could constraint evolution of resistance (to virus transmission). The correlation between viral genotypes was also low, although relatively stronger for more closely phylogenetically related viral strains. Such interactions between host genotypes, virus genotypes and environmental conditions can maintain genetic variation in virus transmission.
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Gautier, Mathieu Yves Anthony. "Cartographie fine de régions QTL chez les bovins laitiers." Paris, Institut national d'agronomie de Paris Grignon, 2003. http://www.theses.fr/2003INAP0008.
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Sillanpää, Mikko. "Bayesian QTL mapping in inbred and outbred experimental designs." Helsinki : University of Helsinki, 2000. http://ethesis.helsinki.fi/julkaisut/mat/rolfn/vk/sillanpaa/.
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Sena, Juliana Stival. "Mapeamento e caracterização de microssatélites derivados de sequências expressas (EST) e análise de coincidência de QTL em Eucalyptus spp. em ambientes contrastantes." Universidade Federal de Viçosa, 2009. http://locus.ufv.br/handle/123456789/4702.
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The first part of this work involved the development and genetic mapping of a new battery of microsatellites for Eucalyptus derived from ESTs. Screening of 232 microsatellites derived from ESTs was carried out using a panel of 12 individuals corresponding to the parents used for population development in the Genolyptus project. Among the successfully amplified loci, 78% were polymorphic and showed complete inter-specific transferability. Thirty six loci were selected for mapping based on the amplicon size (< 400 pb), repeat motif and positive BLAST with interesting genes in public databases. With the objective of mapping, 36 loci were evaluated with regard to polymorphism and segregation in a reference segregating population derived from a cross between E. grandis x E. urophylla. The proportion of loci segregating in a fully informative configuration was about 40% lower than the one seen for microsatellites derived from genomic-enriched libraries. In spite of a relatively lower genetic information content, these loci are interesting for mapping, as they correspond to genes, allowing comparative mapping and potential co-location with QTL. Among the informative loci, 20 were successfully mapped in the particular reference mapping population. These mapped loci were characterized for polymorphism information content. Although EST derived microsatellites are generally less informative than those derived from non coding genomic regions they can be effectively used for individual identification, paternity analysis, evaluation of genetic diversity, certification of controlled crosses, genetic mapping and marker-assisted selection. In the second part of this work the coincidence in QTL detection was investigated by comparing the position and magnitude of effect of QTLs for wood and growth properties in three partially connected segregating populations of Eucalyptus spp. in two contrasting environments (Guanhães-MG and Guaíba-RS) over 3,000 km apart in a north-south latitude gradient. The families studied were: (E. camadulensis) x (E. urophilla x E. globulus), C1 x UGL, (E. dunnii x E. grandis) x (E. urophylla x E. globulus), DG x U2, and (E. dunnii x E. grandis) x (E. uropyilla), DG x UGL. Microsatellite markers flanking QTLs mapped in previous studies in these three families in Guaíba-RS were selected for the coincidence study. These markers were mapped using different sets of individuals from the same three families planted in Guanhães-MG. QTLs for eight quantitative traits related to wood and growth properties were studied. Two QTL (height and depth of pilodyn penetration, i.e. wood density) were detected in common for the two environments in the UGL parent (cross C1 x UGL); two (lignin content and pulp yield) in parents DG and U2 respectively (cross DG x U2) and four QTLs (two for diameter at breast height, one for height and one for volume), two of them colocalized with QTLs for biologically correlated traits (r > 0.8), in the parent UGL (cross DG x UGL). Furthermore, three QTLs (diameter at breast height, height and pilodyn penetration depth) located on linkage group 6 of the parent UGL were stable across the different genetic backgrounds and environments. Results indicate that QTLs of major effect for wood property traits are consistently detected in contrasting environments and/or different genetic backgrounds, suggesting that environmental variability and genetic background did not have a detectable impact on the action of the genes or genomic regions underlying these QTL, while other QTLs detected only in one of the environments are possibly under strong environmental interaction. These novel results are relevant, given that they provide target regions for marker assisted selection within families and starting point for association genetics studies.
No primeiro capítulo desta tese, foi desenvolvido e geneticamente mapeado um novo conjunto de microssatélites para Eucalyptus spp. derivados de EST (Expressed Sequence Tag). Foi feita uma triagem de 232 microssatélites derivados de EST utilizando-se um painel de 12 indivíduos correspondendo aos parentais das populações segregantes do projeto Genolyptus. Dentre os locos amplificados com sucesso, 78% foram polimórficos e apresentaram um nível elevado de transferibilidade interespecífica. Trinta e seis locos foram selecionados para mapeamento com base no tamanho dos segmentos amplificados (< 400 pb), motivos de repetição e BLAST positivo com genes de interesse em bancos públicos de dados. Com o objetivo de mapeamento, os 36 locos foram avaliados quanto ao polimorfismo e a segregação em uma população de referência envolvendo os parentais E. grandis x E. urophylla, verificando-se que a quantidade de locos totalmente informativos foi cerca de 40% menor quando comparados com microssatélites derivados de bibliotecas genômicas enriquecidas. Apesar da menor hipervariabilidade estes locos são interessantes para mapeamento, pois correspondem a regiões gênicas, possibilitando mapeamento comparativo e potencial colocalização de genes com QTLs. Dos locos em configuração informativa de segregação, 20 foram mapeados com sucesso. Estes locos mapeados foram caracterizados quanto ao seu conteúdo de informação para análise genética. Embora os microssatélites derivados de EST sejam menos polimórficos que os microssatélites derivados de sequências não codificantes, ainda assim eles podem ser utilizados com eficiência na discriminação de indivíduos, estudos de parentesco, avaliação de diversidade genética, mapeamento genético e seleção assistida por marcadores. O segundo capítulo teve como objetivo a verificação da coincidência de detecção de QTLs por meio da comparação da posição genômica e magnitude de efeito de QTLs para características silviculturais de crescimento e de qualidade da madeira em amostras de descendentes de três famílias segregantes de Eucalyptus spp. em dois locais experimentais contrastantes (Guanhães- MG e Guaíba- RS). As famílias estudadas foram: (E. camadulensis) x (E. urophilla x E. globulus), C1 x UGL, (E. dunii x E. grandis) x (E. urophilla x E. globulus), DG x U2, e (E. dunii x E. grandis) x (E. urophilla), DG x UGL. Primeiramente foram selecionados marcadores microssatélites flanqueantes e internos às regiões de QTL mapeados em experimentos anteriores para estas três famílias oriundas do ambiente de Guaíba-RS. Posteriormente mapeou-se estes marcadores utilizando-se diferentes indivíduos destas mesmas três famílias oriundos do ambiente de Guanhães-MG. Foram estudados QTLs para oito características quantitativas relacionadas com desempenho silvicultural e qualidade da madeira. Detectou-se dois QTLs (altura e profundidade de penetração do Pilodyn) em comum para os dois ambientes, no genitor UGL da família C1 x UGL; dois QTLs (teor de lignina e rendimento depurado) nos genitores DG e U2 respectivamente, do cruzamento DG x U2 e quatro QTLs (dois para diâmetro à altura do peito, um para altura e um para volume) no genitor UGL, do cruzamento DG x UGL, sendo que dois destes se colocalizaram com QTLs para características biologicamente correlacionadas (r > 0,8). Ainda, três QTLs (diâmetro à altura do peito, altura e profundidade de penetração do Pilodyn) localizados no grupo de ligação 6 do genitor UGL se mostraram estáveis entre os diferentes backgrounds genéticos e ambientes. Os resultados indicam que QTLs de maior efeito para características de qualidade da madeira são detectados em ambientes contrastantes e/ou entre diferentes backgrounds genéticos, sugerindo que a variabilidade ambiental e de background genético não teve impacto detectável sobre a expressão dos genes presentes nestes QTLs. Estes resultados inéditos para Eucalyptus são relevantes, pois fornecem regiões alvo interessantes para a seleção assistida dentro de famílias via seleção para QTLs ou ainda como ponto de partida para estudos de genética de associação.
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Mihaljević, Renata. "Biometrical Analyses of Epistasis and the Relationship between Line per se and Testcross Performance of Agronomic Traits in Elite Populations of European Maize (Zea mays L.)." [S.l. : s.n.], 2005. http://nbn-resolving.de/urn:nbn:de:bsz:100-opus-1391.
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Hohenheim, Univ., Diss., 2005.Aus: Congruency of quantitative trait loci detected for agronomic traits in testcrosses of five populations of European maize.2004.Crop Sci. 44:114-124. and QTL correspondence between line per se and testcross performance for agronomic traits in four populations of European maize.Crop Sci. 45:114-122.
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Masle, Stela. "Multistage QTL mapping strategy in an advanced backcross cattle population." Diss., [S.l.] : [s.n.], 2007. http://edoc.ub.uni-muenchen.de/archive/00007061.
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Sabry, Ahmed Mohamed-Bashir. "QTL mapping of resistance to sorghum downy mildew in maize." Diss., Texas A&M University, 2003. http://hdl.handle.net/1969.1/460.
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Sorghum downy mildew (SDM) of maize is caused by the oomycete Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw. The disease can cause devastating yield losses in maize (Zea mays L.). Quantitative trait loci (QTLs) mediating resistance to SDM were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white) and highly resistant inbred P345C4S2B46-2-2-1-2-B-B-B (yellow). The phenotypic expression was assessed on F2:3 families in a wide range of environments under natural field infection and in a controlled greenhouse screening method. Heritability estimates of disease reaction ranged from 93.3% in Thailand sit 1 to 48% in Thailand sit 2. One hundred and thirty three polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 covering about 1265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome was located within a 10 cM distance to the nearest marker. Three putative QTLs were detected in association with resistance to SDM in different environments using composite interval mapping. Despite environmental and symptom differences, one QTL on chromosome 2 bin 9 had a major effect in all trials and explained up to 70% of the phenotypic variation in Thailand where the highest disease pressure was experienced. Two other QTLs on chromosome 3 bin 5 and chromosome 9 bin 2 had a minor effect, each explaining no more than 4% of the phenotypic variation. These results revealed one major gene and two minor genes that control sorghum downy mildew resistance. These markers should be very useful in breeding programs in facilitating the introgression of the resistance genes into commercial varieties. Marker-assisted selection for these loci should be useful in incorporating SDM resistance genes in maize across environments, even in the absence of the pathogen.
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Ytournel, Florence. "Déséquilibre de liaison et cartographie de QTL en population sélectionnée." Phd thesis, AgroParisTech, 2008. http://pastel.archives-ouvertes.fr/pastel-00003789.
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Par définition le déséquilibre de liaison (Linkage Disequilibrium, LD) décrit les associations préférentielles entre allèles de deux locus. Ce concept est devenu un outil indispensable pour la cartographie fine de locus quantitatifs (QTL), par l'identification de déséquilibres d'associations entre allèles à un locus marqueur (ou à un ensemble de locus marqueurs) et à un locus impliqué dans la variation d'un caractère quantitatif. La création et l'intensité du LD sont dépendantes des forces évolutives qui ont construit la population. Parmi ces forces, la dérive génétique et la sélection sont particulièrement actives dans les populations d'animaux de rente. Cette thèse a pour but d'étudier l'influence de la sélection sur la structure du déséquilibre de liaison autour d'un locus quantitatif, ainsi que son impact sur la précision de cartographie fine des QTL. Un logiciel de simulation de populations a été développé dans le cadre de la thèse. A partir d'une population en équilibre de liaison, il permet de générer du LD dans des générations dites historiques, grâce à différentes forces évolutives. La détection de QTL est appliquée aux générations suivantes, de généalogie connue. Pour ces dernières générations, les principaux dispositifs de détection de QTL de génétique animale sont décrits dans le simulateur. Les données exploitées dans cette thèse sont issues de ce logiciel. Le LD a été mesuré par le D' et le
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Zhong, Shengqiang. "Integrating QTL analysis into plant breeding practice using Bayesian statistics." [Ames, Iowa : Iowa State University], 2008.
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Yusuf, Mohammed. "From Fat QTL to Functional Genes : A Molecular Cytogentic Strategy." Thesis, University of Kent, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.499711.
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Elisabeth, Ahlgren. "Marker generation for Fine Mapping a QTL in the chicken." Thesis, Linköpings universitet, Biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-108983.
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The purpose of this study was to design and test five SNP markers in an inbred chicken cross between Red Junglefowl and domestic White Leghorn of the 8th generation. The markers lie in a region affecting the tonic immobility behaviour which differs significantly between the two species. The markers could be identified by usage of PCR and pyrosequencing. The data obtained were further used in a small scale quantitative trait locus (QTL) analysis. QTL analysis is a statistical method to link phenotypic traits to genotypic data. Four out of five markers could be genotypes and thereby, made it possible to proceed with the QTL analysis. The results showed that there is no QTL associated with the markers identified. The two flanking markers were closest to a significant difference between genotypes and it is therefore a possibility that a QTL lies close further down or up the searched region. From the line map it is indicated that there is little recombination in the marker region.
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Cavalcanti, JoseÌ Jaime Vasconcelos. "Genetic mapping and QTL identification in cashew (Anacardium occidentale L.)." Thesis, University of Reading, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.412181.
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Ngwako, Samodimo. "QTL mapping and marker-assisted selection in Brassica and Arabidopsis." Thesis, University of Birmingham, 2003. http://etheses.bham.ac.uk//id/eprint/5265/.
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The study was aimed at applying molecular marker techniques to locate QTL and determine the efficiency of the marker-assisted selection. The research was done using Brassica oleracea and Arabidopsis thaliana. The Brassica DH lines represented a population of homozygous individuals while the F\(_2\) and F\(_3\) generations of Arabidopsis represented a segregating population. Marker-assisted selection was applied after the detection of QTL which allowed the identification of markers linked to the QTL and hence the selection for such markers. In Brassica, 40 QTL were detected using the marker regression method. Between 1 and 6 QTL were located per trait, which individually explained 2-49% of the additive genetic variance. In Arabidopsis the marker regression method detected 23 QTL in the F\(_2\), whereas 40 QTL were detected by the interval mapping method in the F\(_3\) generation. 1 7 QTL mapping to similar positions and showing similar modes of action were detected by both methods. Alleles for various QTL were dispersed between parents in both crosses. The efficiency of MAS was determined using various approaches, based on the number of top ranks, number of lines in a group, phenotypic value and as the ratio between response based on MAS and response obtained in the F\(_3\) by applying phenotypic selection to the F\(_2\) generation. The MAS gave generally better response compared to phenotypic selection, particularly when heritability was low. MAS for single QTL was always more effective while multiple QTL and QTL showing linkage posed some practical problems in MAS applications. Overall, MAS has to be applied in conjunction with phenotypic selection to get best results as QTL of minor effect cannot be tackled through marker/QTL associations.
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Ueno, Sueme. "Mapeamento de QTL para múltiplos caracteres e ambientes em milho." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-22032018-112738/.
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Caracteres quantitativos possuem herança complexa, que envolvem efeitos epistáticos, pleiotrópicos e interação com ambientes. Em razão da importância desses caracteres para o melhoramento genético, diversos estudos sobre sua natureza genética e herança têm sido conduzidos. Nesse contexto, o mapeamento de QTL é uma ferramenta útil, que permite mapear e estimar os efeitos dos locos que controlam os caracteres quantitativos além de obter outras importantes informações, como a ocorrência de QTL pleiotrópicos e interações QTL x ambientes. Os objetivos do presente trabalho foram mapear QTL e obter informações sobre a interação QTL x ambientes, QTL pleiotrópicos e herança de diversos caracteres de importância agronômica em uma população de milho tropical. Foram utilizadas 250 progênies F2:3 retrocruzadas para ambos os genitores conforme proposto no delineamento III, totalizando 500 progênies, as quais foram avaliadas em até seis ambientes. Para o mapeamento de QTL foi empregado o mapeamento por intervalo composto expandido para múltiplos ambientes ou caracteres (mCIM), considerando um mapa genético com 177 marcadores microssatélite. Os caracteres analisados foram produção de grãos (PG), prolificidade (PROL), peso de 500 grãos (P500), número de fileiras da espiga (NF) e de grãos por fileira (NGF), altura de planta (AP) e espiga (AE), dias para o florescimento feminino (FF) e masculino (FM), número de ramificações do pendão (RP) e stay green (SG). Os resultados das análises do delineamento III indicaram sobredominância para o caráter PG, dominância completa para NGF e dominância parcial para os demais caracteres. Estimativas elevadas de correlações genéticas foram obtidas entre os caracteres PG, PROL, NGF, FF, FM, AP e AE, sugerindo ocorrência de pleiotropia entre tais caracteres. No mapeamento considerando múltiplos ambientes foram mapeados 260 QTL para os onze caracteres analisados, distribuídos por todos os cromossomos do milho. O grau médio de dominância dos QTL foi de sobredominância para PG e AP, e dominância completa ou parcial para os demais caracteres. Devido ao desequilíbrio de ligação nesta população e ao modelo de mapeamento empregado, as estimativas que indicaram sobredominância foram, provavelmente, superestimadas. Para os caracteres PG, NF, NGF, P500, AE e SG, a maioria dos QTL mapeados interagiu significativamente com ambientes, indicando que experimentos conduzidos em vários locais e anos são necessários para identificar genótipos e QTL estáveis. Esses resultados sugerem que devido à elevada interação QTL x ambientes dos caracteres avaliados, os programas de melhoramento e a utilização de seleção assistida por marcadores (SAM) devem ser direcionados para ambientes específicos. No mapeamento de múltiplos caracteres foram identificados 43 QTL com efeitos significativos para dois ou mais caracteres analisados, distribuídos em todos os cromossomos do milho. A quantidade de QTL pleiotrópicos para combinações entre pares de caracteres não foi consistente com as magnitudes das correlações observadas. Em geral, para cada caráter, os QTL pleiotrópicos apresentaram magnitudes e graus de dominância distintos. Portanto, embora diversos QTL pleiotrópicos tenham sido mapeados, suas magnitudes e efeitos distintos para cada caráter indicaram grande complexidade da natureza genética das correlações, constituindo-se em um desafio para uso das informações desses QTL na SAM visando o melhoramento de múltiplos caracteres.Quantitative traits have complex inheritance, including effects of epistasis, pleiotropy and interaction with environments. Due to the importance of these traits for plant breeding, many studies on their inheritance have been conducted. In this context, QTL mapping is a useful tool that allows mapping and estimating the effects of loci that control the quantitative traits besides obtaining other important information, such as the occurrence of pleiotropic QTL and QTL x environments interactions. The aims of the present study were to map QTL, obtain information about the QTL x environments interaction and the pleiotropic QTL of several relevant traits in a tropical maize population, using the design III. Two hundred and fifty F2:3 progenies backcrossed to both parents were used as proposed in the design III, totaling 500 progenies, which were evaluated in up to six environments. The components of the genetic variances and average degree of dominance were estimated using the design III. The QTL mapping was performed considering a genetic map with 177 microsatellite markers and the multi-trait composite interval mapping (mCIM). The evaluated traits were: grain yield (GY), prolificacy (PROL), 500 kernel weight (W500), kernel row number (KRN), number of kernel per row (NK), plant height (PH), ear height (EH), days to silk emergence (DS), days to anthesis (DA), number of tassel branches (NTB) and stay green (SG). The results from design III indicated occurrence of overdominance for GY, complete dominance for NK and dominance for the others traits. Higher genetic correlations were observed among GY, PROL, NK, DS, DA, PH and EH, suggesting occurrence of pleiotropy. The QTL mapping for multiple environments mapped 260 QTL for the eleven analyzed traits, distributed in all chromosomes. The average degree of QTL dominance was overdominance for GY and PH, and complete or partial dominance for the other traits. Estimates that indicated overdominance are probably biased due to the linkage disequilibrium in this population and the mapping model employed. For GY, KRN, NK, W500, EH and SG, most mapped QTL interacted significantly with environments, indicating that it is necessary to conduct experiments at many locations and years to identify stable QTL. These results suggests that, due to high number of QTL that showed significant interaction with the environment, assisted marker selection (MAS) must be targeted to specific geographic regions. The QTL mapping for multiple traits identified 43 pleiotropic QTL for two or more analyzed traits, distributed in all chromosomes of maize. The amount of pleiotropic QTL for combinations of pairs of traits was not consistent with the magnitudes of the observed correlations. In general, for each trait, the pleiotropic QTL exhibited different magnitude and estimate of the degree of dominance. Although several pleiotropic QTL have been mapped, their distinct magnitudes and effects on each trait indicated the great complexity of the genetic nature of the correlations, constituting a challenge to use QTL information in the MAS for simultaneous improvement of multiple traits.
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Antonyuk, Alexander. "Statistical methodology for QTL mapping and genome-wide association studies." Thesis, University of Oxford, 2009. https://ora.ox.ac.uk/objects/uuid:23393c76-b7ef-44c2-a06f-3b23e3a6d936.
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This work deals with statistical tests of association between genetic markers and disease phenotypes. The main criterion used for comparing the tests is statistical power. First we consider animal models and then data from association studies of humans. For the animal section, we analyse a dataset from a prominent mouse experiment which developed a heterogeneous stock of mice via multiple crosses. This stock is characterised by small distances between recombinants which allows fine mapping of genetic loci, but also by uncertainty in haplotypes. We start by highlighting the disadvantages of the currently used approach to deal with this uncertainty and suggest a method that has greater statistical power and is computationally efficient. The method applies the EM algorithm to the broad class of exponential family distributions of phenotypes. We also develop a Bayesian version of the method, for which we extend the widely used IRLS algorithm to maximisation of the weighted posterior. Then we move on to genome-wide association studies (GWAS), where two situations are considered: known and unknown minor allele frequency. First we develop an innovative Bayesian model with the optimal prior for the known population MAF. We demonstrate that not only it is more powerful than any frequentist test considered (the size of the advantage depends on prevalence of the disease and MAF), but also that the frequentist tests change ranking in terms of power. A remarkable property of the frequentist tests, the advantage of discarding part of the data to gain power, is highlighted. The second chapter on GWAS considers the currently more common situation of the unknown MAF, when the Armitage test is known to be the most powerful frequentist method. We show that the suggested model is more powerful in the broad selection of settings considered, including the three different allele effect models: additive, dominant and recessive. For both known and unknown MAF cases we point out that the parameters are constrained and demonstrate how to gain power by taking this constraint into account.
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Roldan, Dana Leticia. "Détection de QTL : interaction entre dispositif expérimental et méthodes statistiques." Toulouse 3, 2011. http://thesesups.ups-tlse.fr/1395/.
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Les régions du génome portant des polymorphismes associés à la variation des caractères quantitatifs sont nommées en anglais " quantitatif trait loci " (QTL). Jusqu'à récemment la cartographie des QTL était principalement basée sur des marqueurs microsatellites. La densité de cartes de microsatellites est telle que la détection des associations entre les marqueurs et les QTLs ne peut être basée que sur l'analyse de liaison (LA), où la structure familiale est importante. Une fois qu'une région chromosomique a été identifiée comme porteuse d'un QTL putatif, plus de marqueurs doivent être développés pour obtenir une densité plus élevée dans cette région. Cette cartographie fine doit réduire suffisamment l'incertitude sur la position du QTL pour que l'identification des mutations de(s) gène(s) devienne faisable. Les nouveaux marqueurs SNP rendent possible cet objectif et permettent la cartographie fine du QTL sur la base du déséquilibre de liaison (LD) entre certains allèles marqueurs et le QTL. Le choix de la structure génétique de la population expérimentale pour cette cartographie fine par l'analyse conjointe des transmissions intrafamille et du déséquilibre de liaison dans la population générale (approche dites LDLA) se pose après une étape de primo localisation par analyse de liaison, ou directement quand la primo détection et la localisation fine sont confondues dans une seule étape de cartographie. Cette question est abordée dans ce travail. La démarche de cette thèse a été construite en trois étapes : (i) Validation d'une nouvelle méthode LDLA de type régression linéaire (Legarra et Fernando, 2009) et comparaison numérique par simulations de cette méthode avec la méthode de composantes de variance basée sur l'estimation des probabilités IBD (identical by descendant) de Meuwissen et al. , (2002). La méthode par régression est généralement aussi précise et toujours beaucoup plus rapide que la méthode de Meuwissen et al. (2002). (ii) Optimisation, sur la base de la méthode de régression, des protocoles expérimentaux définis par le nombre de descendants par père et le type de structure (demi-frères et un mélange de pleins-et demi-frères). Nous trouvons que le QTL est localisé plus précisément en utilisant les méthodes LDLA que LA et que la structure du dispositif expérimental et la taille des haplotypes ont un impact considérable sur la précision de la localisation d'un QTL. Un équilibre entre le nombre et la taille des familles est à déterminer selon les caractéristiques de l'application pratique (longueur du segment exploré, densité en marqueurs, taille de la population totale etc. . . ). (iii) Application des méthodes de cartographie au cas de la production de laine chez le mouton, un exemple possible parmi d'autres caractères. Dans un premier temps, nous avons appliqué l'analyse de liaison à une population de Merinos Argentins sur laquelle ont été mesurés des caractères de production de laine. Cette population comprenait 617 individus répartis en 10 familles de demi-frères de père. 48 microsatellites ont été utilisés pour marquer 280,7 cM dans des régions du génome à priori intéressantes. Des QTL ont été trouvés, notamment un QTL affectant le caractère coefficient de variation du diamètre de fibres à 67,6 cM sur le chromosome 11. Dans une seconde étape, nous avons évalué, pour les caractéristiques particulières de cette population, les recommandations de la partie (ii) pour l'organisation d'un protocole LDLA de cartographie fine dans cette population réelle. Plusieurs situations ont été envisagées en changeant le nombre de descendants par famille et la densité des marqueurs. Ce travail nous a permis de faire des recommandations pratiques pour affiner la localisation des QTL de laineGenomic regions carrying polymorphisms associated with variation in quantitative traits are termed quantitative trait loci (QTL). Until recently, mapping QTL was mainly based on microsatellite markers. The density of these markers is such that detection of associations between markers and QTL can only be based on linkage analysis (LA), and a family structured design is needed. Once a chromosomal region has been identified to carry a putative QTL, more markers should be developed at a higher density within that region. Tightly linked markers are needed for sufficiently narrowing down the putative QTL position such that finding actual gene mutations becomes feasible. The new SNP markers make this objective realistic, allowing fine mapping based on linkage disequilibrium (LD) of these markers and QTL across families. Designing experiments aiming at fine mapping QTL combining LD and LA (LDLA) is a question raised after a primo localisation obtained from classical family LA, or directly where primo and fine localisation steps are confounded. Questions related to this designing problem were addressed in this thesis: how should one balance family size and number in LDLA design? What is the best LDLA protocol to fine map QTL that were previously roughly localised in a classical LA analysis?. Three steps were followed: (i) Evaluation of a new LDLA method based on regression (Legarra and Fernando, 2009) and numerical comparison of this method with a variance component IBD (identical by descendant) based method (Meuwissen et al. , 2002). The regression approach appeared to be generally as precise as the Meuwissen et al. (2002) method and always much faster. (ii) Design optimization, using this LDLA regression technique, in terms of number of progenies by sire, and type of families (half-sib to mixture full- and half-sib). We found that QTL is more exactly localised with LDLA rather than LA and that experimental structure as well as haplotypes sizes have a big impact on this localisation. A balance between family number and size must be found depending on the case characteristics (explored segment length, marker density, total population size, etc. . . ). (iii) Application of the mapping method to the wool production traits, an example among other of quantitative traits. In the first stage familial linkage analysis was applied to real half-sibs Merino sheep population measured for wool traits. This population consisted in 617 individuals belonging to 10 sire half-sibs. Forty eight microsatellites were used, covering 280. 70 cM in candidate areas. QTLs were found, in particular affecting the fibre diameter coefficient of variation at position 67. 60 cM on OAR11. In a second stage, we evaluated, considering the specificity of our ovine population, the recommendations established after the step (ii) concerning the organisation of a LDLA design. This work allowed as to make practical conclusions for a fine mapping of wool trait QTL in our population
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Mukhaimar, Maisara. "Sources naturelles de la résistance contre les nématodes à galles Meloidogyne javanica chez la plante modèle Arabidopsis thaliana." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA112033/document.
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Les nématodes phytoparasites constituent une menace réelle pour la production alimentaire mondiale. Ils sont responsables de 14% des pertes de rendement de la production alimentaire globale, ce pourcentage est l’équivalent de 100 milliards de dollar américain par an. La lutte contre ces phytoparasites est devenue un défit majeur, notamment après l'interdiction de l'utilisation du nématicide le plus efficace, en raison de ses effets nocifs sur l’environnement. Par conséquent, des nouvelles sources pour la gestion des nématodes phytoparasites sont nécessaires et urgentes. Ce travail vise à déterminer si la plante modèle Arabidopsis thaliana pourrait servir comme une source naturelle de gènes de la résistance aux nématodes phytoparasites. Parmi des accessions d’Arabidopsis, on a trouvé une variation génétique naturelle de la résistance contre les nématodes à galles Meloidogyne javanica, on a également identifié plusieurs QTL de résistance aux nématodes, et finalement, on a réalisé une cartographie fine d’un des QTL détectésPlant-parasitic nematodes are a serious threat for global food production. They are responsible for 14% of global yield loss, equivalent to an economic value of more than 100 billion US$ per year. Pest management is challenging, in particular since the most efficient nematicide has been banned due to its devastating effect on the environment. Hence, novel sources for nematode management are urgently required. This work investigates whether the model plant Arabidopsis thaliana could serve as a natural source for resistance genes against plant-parasitic nematodes. It finds natural genetic variation among Arabidopsis accessions for resistance against the root-knot nematode Meloidogyne javanica, identifies several QTL for nematode resistance, and fine-maps one of these resistance QTL
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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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Noble, Jessica. "Identification des bases moléculaires de propriétés technologiques de levures oenologiques." Thesis, Montpellier, SupAgro, 2011. http://www.theses.fr/2011NSAM0014.
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Les bases moléculaires responsables des propriétés technologiques des levures œnologiques sont pas ou peu connues. Or, ces connaissances sont nécessaires pour mettre en œuvre des stratégies d'amélioration génétique des capacités fermentaires ou de l'impact organoleptique des levures par croisements et une meilleure exploitation de la biodiversité. Ces travaux de thèse ont visé à l'identification des bases génétiques de plusieurs propriétés d'intérêt, telles que la production de sulfites, la capacité fermentaire en milieu carencé en azote ou la formation d'esters. Une approche de recherche de QTL a été mise en œuvre en s'appuyant sur la création d'une population de ségrégants méiotiques issus du croisement de deux souches œnologiques aux caractéristiques contrastées. Une caractérisation des phénotypes des ségrégants associé à leur génotypage a permis d'identifier des QTL pour les différents traits étudiés. L'implication d'une région du génome dans le contrôle de la voie d'assimilation des sulfates a été démontrée. Ce locus est responsable de la variation phénotypique de plusieurs métabolites de cette voie et de métabolites indirectement connectés. D'autres QTL ont également pu être mis en évidence pour les capacités fermentaires sur un milieu carencé en azote et la production de différents composés volatils. Leur analyse a permis d'identifier plusieurs gènes candidats dont les fonctions sont liées directement ou indirectement aux phénotypes étudiésThe molecular basis of technological properties of wine yeasts are not or poorly known. However, this knowledge is required for the improvement of the fermentation capacity and of the organoleptic impact of wine yeasts by breeding strategies and a better exploitation of the yeast biodiversity. This thesis aimed at identifying the genetic bases of several traits of interest such as: sulfite production, fermentation ability in low nitrogen medium or esters formation. A QTL mapping approach has been implemented from a population of meiotic segregants derived from the cross of two strains with contrasting oenological characteristics. Phenotyping of the a population of meiotic segregants was combined with a genotyping to identify QTL for these traits. The involvement of a region of the genome in the control of sulphate assimilation pathway has been demonstrated. This locus is responsible for the phenotypic variation of several metabolites of this pathway and indirectly connected metabolites. Other QTLs have also been demonstrated for the fermentation capacities on a nitrogen limiting medium and production of various volatile compounds. Their analysis revealed several candidate genes whose functions are related directly or indirectly to the studied phenotypes
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Zimmer, Daisy [Verfasser]. "Modified random models for QTL discovery in F2 populations / Daisy Zimmer." Kiel : Universitätsbibliothek Kiel, 2011. http://d-nb.info/1020201770/34.
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Cai, Jin. "Mapping QTL for fusarium head blight resistance in Chinese wheat landraces." Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/13703.
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Master of ScienceDepartment of Agronomy
Allan Fritz
Fusarium head blight (FHB) is one of the most devastative diseases in wheat. Growing resistant cultivars is one of the most effective strategies to minimize the disease damage. Huangcandou (HCD) is a Chinese wheat landrace showing a high level of resistance to FHB spread within a spike (type II). To identify quantitative traits loci (QTL) for resistance in HCD, a population of 190 recombinant inbred lines (RILs) were developed from a cross between HCD and Jagger, a susceptible hard winter wheat (HWW) released in Kansas. The population was evaluated for type II resistance at the greenhouses of Kansas State University. After initial marker screening, 261 polymorphic simple-sequence repeats (SSR) between parents were used for analysis of the RIL population. Among three QTL identified, two from HCD were mapped on the short arms of chromosomes 3B (3BS) and 3A (3AS). The QTL on the distal end of 3BS showed a major effect on type II resistance in all three experiments. This QTL coincides with a previously reported Fhb1, and explained 28.3% of phenotypic variation. The QTL on 3AS explained 9.7% of phenotypic variation for mean PSS over three experiments. The third QTL from chromosome 2D of Jagger explained 6.5% of phenotypic variation. Allelic substitution using the closest marker to each QTL revealed that substitution of Jagger alleles of two QTL on 3AS and 3BS with those from HCD significantly reduced the PSS. HCD containing both QTL on 3AS and 3BS with a large effect on type II resistance can be an alternative source of FHB resistance for improving FHB type II resistance in wheat. Besides, meta-analyses were used to estimate 95% confidence intervals (CIs) of 24 mapped QTL in five previously mapped populations derived from Chinese landraces: Wangshuibai (WSB), Haiyanzhong (HYZ), Huangfangzhu (HFZ), Baishanyuehuang (BSYH) and Huangcandou (HCD). Nineteen QTL for FHB type II resistance were projected to 10 QTL clusters. Five QTL on chromosomes 1A, 5A, 7A, and 3BS (2) were identified as confirmed QTL that have stable and consistent effects on FHB resistance and markers in these meta-QTL regions should be useful for marker-assisted breeding.
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Kamogawa, Karen Pallotta Tunin. "Modelos estatísticos para mapeamento de QTL associados a dados de contagem." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/11/11139/tde-06082009-081116/.
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Este estudo teve por objetivo analisar e comparar metodologias estatísticas para fins de mapeamento de QTL associados à resistência a ectoparasitas em bovinos. Os animais, submetidos à infestação artificial, foram periodicamente avaliados por contagens, como número de carrapatos. Estes dados se caracterizam como medidas repetidas e, via de regra, não atendem ou atendem parcialmente as exigências usuais da análise, para mapeamento de QTL, dentre elas a de apresentar distribuição normal e independência dos erros. Ainda não está bem definido qual seria a melhor estratégia para analisar dados com o perfil descrito. Algumas alternativas seriam transformações de dados que permitam o uso dos programas já disponíveis, ou o desenvolvimento de programas que utilizem outras distribuições como Poisson ou Poisson inflada de zeros (ZIP). Esta proposta está inserida na parceria entre EMBRAPA - Gado de Leite e a ESALQ/USP, para desenvolvimento do projeto de mapeamento de QTL em bovinos mestiços (Gir x Holandês), para várias características incluindo a resistência a parasitas. Foram utilizados 263 animais F2, genotipados com 5 marcadores moleculares no cromossomo 23, na tentativa de mapear QTL para característica de resistência a carrapatos. Dados coletados naquela população F2 e dados simulados em diferentes cenários, serão a base para a comparação de estratégias de análise e mapeamento de QTL. Os modelos de mapeamento clássico, assim como a utilização de transformações dos dados originais foram comparados a modelos de regressão Poisson e modelo ZIP. Os modelos Poisson e ZIP apresentaram os melhores resultados quando trabalhamos com dados de contagem inflacionados de zeros, porém em outros cenários a transformação dos dados originais se mostrou igualmente eficiente. Dependendo do propósito do mapeamento (seja ele localizar ou estimar o efeito), cada modelo possui suas vantagens e suas limitações. Assim, sempre é recomendável uma prévia análise descritiva dos dados para que o melhor modelo seja utilizado.This study has as main objective to analyze and compare statistical approaches to QTL mapping for parasites resistance in bovines. The animals, under artificial infestation, were periodically evaluated by counting, as ticks count. These data are characterized as repeated measures and, usually, dont follow or partially follow the usual requirements for the analysis, for QTL mapping, that is to present normal distribution and error independence. It is not clear yet which will be the best strategy to analyze this kind of data. Some alternatives could be data transformation that allows the use of software available on the web, or the development of specific programs that use other types of distribution like Poisson or Zero Inflated Poisson (ZIP).This work is an association between EMBRAPA Gado de Leite and ESALQ/USP, to the development of the QTL mapping project for crossbred bovines (Gyr x Holstein), for different characteristics including the parasite resistance. Were used 263 animals F2, genotyped for 5 molecular markers on the chromosome 23, aiming to map QTL for characteristics of parasite resistance. Data collected on this F2 population and simulated data in different scenarios will be the base for the strategies of the QTL mapping approaches comparison. The classical mapping models and the use of data transformation of the original data were compared to Poisson regression and ZIP models. The Poisson and ZIP models presented the best results when working with zero inflated count data however in some other scenarios the data transformation showed similar efficiency. Depending on the purpose of the mapping (this meaning locate or estimate the QTL effect) each model has its vantages and its limitations. This way, it is always advisable to make a previous descriptive analysis of the data to better choose the model.
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Guess, Adam Joseph. "QTL analysis of ray pattern in Caenorhabditis elegans recombinant inbred lines." Wright State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=wright1205197070.
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Ousova, Olga. "Analyse d'un QTL d'hypercortisolémie chez le porc : rôle de la transcortine." Bordeaux 2, 2001. http://www.theses.fr/2001BOR28867.
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Cette thèse avait pour but de préciser les facteurs génétiques responsables des différences de cortisolémie entre les races de porc Meishan et Large White. Lors d'études précédentes d'analyse de liaisons génétiques sur le croisement F2 Meishan x Large White, un QTL influençant les taux de cortisol basal et induit par un stress a été cartographié sur le chromosome 7 porcin. Par l'analyse comparative des cartes humaine, murine et porcine nous avons révélé la présence d'un gène candidat positionnel codant pour la transcortine ou CBG (corticosteroid binding globulin). En premier lieu nous avons vérifié la localisation de ce gène chez le porc. Cela a été réalisé d'abord par cartographie sur des panels d'hybrides somatiques et irradiés à l'aide d'un fragment du gène Cbg. De plus ce fragment de Cbg porcin nous a servi pour isoler un clone BAC que nous avons utilisé pour cartographier ce gène par hybridation in situ sur un étalement de chromosomes porcins. L'ensemble de ces techniques nous a permis de localiser la CBG porcine en 7q26, entre les marqueurs flanquant le QTL de cortisolémie. L'évaluation de paramètres de liaison de la transcortine pour le cortisol (fait par la technique de radioliaison en utilisant la Concanavaline A-Sepharose) a montré que les porcs de race Meishan possédaient une capacité maximale de la CBG plasmatique pour le ligand 1. 6 fois supérieure à celle des porcs de race Large White. Les mêmes mesures biochimiques sur la population de porcs F2 ont abouti à l'établissement d'une liaison génétique forte entre les taux de la CBG et la même région du chromosome 7q24-q26 où le QTL de cortisolémie a été placé. Les études moléculaires ont montré l'absence de variation de l'expression des ARNm Cbg entre les deux races porcines. Nous avons déterminé la séquence de la partie codante et promotrice du gène Cbg porcin. Les premiers résultats d'analyse d'haplotype du gène Cbg (partie promotrice, codante et 3'UTR) chez les porcs F1 et leurs parents sont discutésThis thesis was directed to precise the genetic factors underlying the variations of cortisol levels vetween pig races Large White and Meishan. Previous studies had identified on chromosome 7 a QTL associated with the levels of cortisol, basal and after a novelty stress. Comparative mapping data between human, mouse and pig genomes has suggested that transcortine or CBG (corticosteroid binding globulin) incoding gene might be a causal gene for this QTL. Firstly, using a porcine Cbg gene fragment we have mapped the porcine Cbg gene on somatic cell hybrid and radiation hybrid panels. Thereafter isolation of a BAC Cbg clone using the same DNA probe has allowed us to localise the gene Cbg on pig metaphase chromosomes by FISH. These methods together has assigned the Cbg gene to band q26 of pig chromosome 7, between the markers flanking the QTL associated with cortisol levels. Estimation of transcortin binding parameters realised using cortisol binding capacity assay after absorption on solid phase (concanacalin A-Sepharose) revealed that Meishan pigs had a maximal CBG binding capacity 1. 6 times higher than Large White pigs. Using the same biochemical measures on the F2 pig population, we showed a strong genetic linkage between CBG binding capacity and the chromosomal region 7q24-7q26 where the QTL associated with cortisol levels was localised. Molecular expression studies indicated no differences in Cbg mRNA expression in the liver of the two parental breeds. The sequence of exons and promoter region of porcine Cbg gene has been determined. The preliminary results of haplotype analysis of Cbg gene (proximal promoter, coding sequence, 3'UTR) of F1 pigs and their parents are discussed
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Szalma, Stephen J. "QTL and association analyses of the phenylpropanoid pathway in maize silks /." free to MU campus, to others for purchase, 2003. http://wwwlib.umi.com/cr/mo/fullcit?p3091971.
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Grace, Christopher Philip. "Detection and exploitation of expression QTL in drug discovery and development." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:7b174e64-d17f-4e2c-b366-065684bfd813.
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Expression quantitative trait loci (eQTLs) are genetic markers associated with transcription of Ribonucleic Acid (RNA). eQTLs are detected using association analysis to detect correlations between RNA expression data (microarray or RNA-SEQ) and the genotypes of individuals within a study. Trans-ethnic meta-analysis can increase power to detect genetic variants for eQTLs and improve fine-mapping resolution because of differential patterns of linkage disequilibrium (LD) between diverse populations. Lymphoblastoid cell lines (LCLs) from samples in the Phase II and III HapMap populations have been used to detect cis eQTLs using association analysis followed by meta-analysis. Phase III HapMap samples have also been imputed using the 1000 Genomes March 2012 "all ancestries" panel. The goals of this thesis are to perform meta-analysis on multi-ethnic association summary statistics in order to: Increase the power to detect eQTLs, leverage differences in LD between ancestry groups to fine map eQTL variants and investigate and characterize heterogeneity in allelic effect sizes on expression between diverse populations. In addition to this, eQTLs identified are used to perform integration with signals from genome-wide association studies (GWAS) of complex human traits. A pipeline has been developed where eSNPs from the eQTL datasets are integrated with disease SNPs (dSNPs) from the NHGRI GWAS catalog using reciprocal conditional analysis to determine whether eSNP and dSNP tag or are the same causal variant. Also, eQTLs which are also "absorption, distribution, metabolism, and excretion" (ADME) genes are studied in more detail, specifically looking for heterogeneity and enrichment in this dataset. The analysis shows that combining association analysis summary statistics using meta-analysis leads to an increase in power to detect eQTLs. Differences in LD between ancestry groups can be used to improve fine mapping resolution, as measured by "credible sets" of variants most likely to drive the eQTL signal, when all ancestry groups are combined. Considerable heterogeneity between ancestry groups has been detected, much of which is due to differing LD between tag SNP and causal variants across ancestry groups. Furthermore, the GWAS integration has led to the identification of several dSNP â eSNP pairs for disease such as Ulcerative Colitis, Inflammatory Bowel Disease, Bechet's Disease, Sarcoidosis, Crohn's Disease, Graveâs Disease and Primary Biliary Cirrhosis, and have provided potential novel insights of genes through which these disease association signals are mediated. Several eQTLs for genes within the ADME dataset have also been identified some of which have significant heterogeneity.
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Schiavini, F. "MAPPING QTL IN THE BROWN SWISS BREED FOR MILK QUALITY TRAITS." Doctoral thesis, Università degli Studi di Milano, 2011. http://hdl.handle.net/2434/155478.
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Mastitis is a multifactorial infectious disease, mainly caused by bacteria that infect the mammary gland. It is one of the major diseases in dairy ruminants, with respect to industry and public concern, economic impact, and animal welfare. The high genetic correlation of Somatic Cell Count (SCC) and bacterial infection described in many studies and the availability in most countries of SCC data routinely recorded within the milk recoding system, have lead the suggestion to use SCC in selection against udder infection and to incorporate selection for lower SCC content in the overall selection indexes for dairy cattle. Objective of this study is to map QTL for SCC in the Italian Brown Swiss breed population using a selective DNA pooling design with Single Marker Mapping (SMM) and Multi Marker Mapping analysis (MMM). This will be the first complete SCC QTL mapping in this population and will serve as base information for further confirmation studies using dense marker chip design.
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Strillacci, M. G. "GENOME-WIDE DETECTION OF QTL AND CNVS IN DAIRY CATTLE POPULATION." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/243633.
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The QTL involved in susceptibility/resistance of infectious diseases and in the productive traits variations, are characterized by genetic heterogeneity and multifactorial inheritance, involving gene polymorphisms from different alternative pathways. With the availavility of single nucleotide polymorphism (SNP) genotyping arrays, the genome-wide association studies (GWAS) have been frequently used to determine the genetic component of complex trait. The Copy Number Variations (CNVs) are another genomic marker that can be possibly used in GWAS and that can be identified from SNP chips themselves.
The aims and related discussions for each of the studies presented in this thesis were grouped into three different chapters.
• Chapter 1 described the QTL mapping analysis to identify the existence of genetic variability associated to the CLA, VA and D9D contents in milk of the Italian Brown Swiss dairy cattle breed. For this study a selective DNA pooling in a daughter design was adopted, using the Illumina Bovine SNP50 Bead Chip to genotype the pools. Milk samples from 60 animals with higher values (after correction for environmental factors) and 60 animals with lower values for each of these traits from each of five half-sib families were pooled separately. Allele frequencies were compared between pools of high and low value at the sire and marker level for each SNPs for which the sires were heterozygous. An R procedure was implemented to perform data analysis. A correction for multiple tests was applied using the proportion of false positives approach. BTA 19 showed the largest number of markers in association with CLA. Associations between SNPs and the VA and D9-desaturase traits were found on several chromosomes. A bioinformatics survey identified genes with an important role in pathways for milk fat and fatty acids metabolism within 1 Mb distance from SNP markers associated with fatty acids contents. This is the first available mapping for fatty acid content in the Brown Swiss population.
• Chapter 2 described a genome-wide association study for somatic cell score (SCS) in the Valdostana Red Pied cattle, with a selective DNA pooling analysis, using the Illumina BovineHD BeadChip. The phenotypes of 275 sires for SCS were expressed as Deregressed Proofs (DP-EBVs) for SCS. The sires were ranked according to DP-EBVs for SCS and the 20% high and 20% low sires included in the pools. The multiple marker test was performed in R software. On BTAs 1, 2, 3, 4, 9, 13, 15, 17, 21 and 22 the largest number of markers in association to the trait was found identifying novel genomic regions related to mastitis (1-Mb SNP windows) and confirming others already mapped. The largest number of significant SNPs exceeding the threshold for genome-wide significant signal was found on BTA 15, located at 50.43-51.63 Mb. The genomic regions identified in this study contribute to a better understanding of the genetic control of the mastitis immune response in cattle and may allow the inclusion of more detailed QTL information in selection programs.
• Chapter 3 described a genome wide CNVs discovery in 651 bulls of the Italian Brown Swiss breed using the Illumina Bovine SNP50 BeadChip data. Hidden Markov Model (HMM) of PennCNV and SVS7 software (Golden Helix) were used for the identification of the CNVs and Copy Number Variation Regions (CNVRs). A total of 5,099 and 1,289 CNVs were identified using PennCNV and SVS7 software, respectively. These were grouped at the population level into 1,101 (220 losses, 774 gains, 107 complex) and 277 (185 losses, 56 gains and 36 complex) CNVRs, covering 682 Mb (27.14%) and 33.7 Mb (1.35%) of the autosome, respectively. Ten of the selected CNVRs were experimentally validated with qPCR and the proportions of confirmed positive samples for each region varied from 50% to 100%. The GO and pathway analyses identified genes (false discovery rate corrected) in the CNVRs related to biological processes, cellular component, molecular function and metabolic pathways. Although there is variability in the CNVRs detection across methods, platforms, this study allowed the identification CNVRs in Italian Brown Swiss, overlapping those already detected in other breeds and finding additional ones.
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Souza, Gustavo Henrique de. "Detecção de QTLs em famílias de meios-irmãos por meio de genes idênticos por descendência, utilizando simulação." Universidade Federal de Viçosa, 2003. http://www.locus.ufv.br/handle/123456789/10513.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
Para muitas espécies de animais domésticos, árvores frutíferas perenes e especialmente seres humanos, a formação de linhagens endogâmicas é impraticável, sendo uma alternativa para o mapeamento de QTL a execução de análises de marcadores moleculares entre famílias existentes dentro de uma população segregante. O procedimento de mapeamento por intervalo baseado em modelo aleatório foi aplicado para estudar a robustez e propriedades no mapeamento de QTL, em populações simuladas, constituídas de famílias de meios-irmãos, variando o número de famílias, o tamanho da família , o número de alelos do QTL e a percentagem da variância genética explicada pelo QTL. As famílias de meios-irmãos foram simuladas considerando um segmento cromossômico de 100 cM, com seis marcadores igualmente distribuídos no cromossomo, a intervalos de 20 cM, com seis alelos de mesma freqüência. O número de alelos do suposto QTL foi de 2, 4, 6 ou 10, sempre com as mesmas freqüências. O número de famílias foi de 10 ou 100 e os tamanhos de famílias foram de 25 ou 50 com 10, 50 ou 100 % da proporção da variância genética devida ao QTL. Sob o modelo aleatório, a localização e os componentes de variância foram estimados, usando o método da máxima verossimilhança. As estimativas dos parâmetros foram baseadas na metodologia de pares de irmão. A proporção de genes idênticos por descendência (IBD) do QTL foi estimada pelo algoritmo proposto por MARTINEZ e VUKASINOVIC (2000). Na estimação dos parâmetros do QTL, que são a localização e os componentes de variância observou-se pouca influencia do número de alelos do QTL, sendo a proporção da variância genética devida ao QTL e ao número de indivíduos analisados, o que mais influenciou nas estimativas. Quando havia apenas 10 famílias, as estimativas de localização dos componentes de variância do QTL e da variância poligênica foram sempre viesadas. O mapeamento por intervalo estabelecido em modelos aleatórios em populações de meios-irmãos para a identificação de QTL parece não ser apropriado para investigar a presença de QTL, quando existem apenas 10 famílias com 25 ou 50 filhos. O número de alelos do QTL parece não influenciar na estimação da localização ou na estimação dos componentes de variância. O método indicou corretamente o intervalo do suposto QTL. Por ser simples e robusto, o modelo aleatório pode ser recomendado para a varredura rápida do genoma, aplicando-se, em seguida, análises mais refinadas no intervalo em que for indicada a existência de um suposto QTL. O modelo aleatório não consegue separar eficientemente a variância poligênica e as variâncias dos QTLs, propondo-se o uso de métodos mais sofisticados para estimar as variâncias devidas ao QTL.
For many species of domestic animals, perennial fruit trees and especially in human beings, the formation of inbred lines is impracticable, being an alternative for the mapping of QTL the execution of analyses of molecular markers among existent families of a outbred population. The mapping procedure by interval based on random model was applied to study the robustness and properties in the mapping of QTL in simulated populations of half-sibs families, varying the number of families, the family size, number of QTL allele and the percentage of the genetic variance explained by QTL. The half-sibs families were simulated considering a chromosomal segment of 100 cM, with six markers equally distributed in the chromosome at intervals of 20 cM, with six allele of same frequency. The number of allele of the putative QTL was 2, 4, 6 or 10 allele, always with the same frequencies. The number of families was 10 or 100 and the sizes of families were 25 or 50 with 10, 50 or 100% of the proportion of the genetic variance due to QTL. Under the random model the location and the variance components were estimated using the maximum likelihood method. The estimates of the parameters were based on the brother's pairs methodology. The proportion of identical-by- descent (IBD) of QTL was estimated by the algorithm proposed by MARTINEZ and VUKASINOVIC (2000). In the estimate of the QTL parameters, which are location and variance components, it was observed little influences of the number of allele of QTL being the proportion of the genetic variance due to QTL and the number of analyzed individuals what more influenced in the estimates. When there had been only 10 families, the location estimates of the components of QTL variance and polygenic variance were always biased. The mapping by interval based on random models in half-sibs populations for the identification of QTL is not appropriate to investigate the presence of QTL when there are only 10 families with 25 or 50 children. The number of allele of QTL does not influence in the estimate of the location or in the estimate of the variance components. The method indicated correctly the interval of the putative QTL. Since it is simple and robust, the random model can be recommended for a fast sweeping of the genome, being applied, soon after, more refined analyses in the interval that the existence of a putative QTL is indicated. The random model is not able to separate the polygenic variance and the QTL variance efficiently, being proposed the use of more sophisticated methods to estimate the variances due to QTL.
Dissertação importada do Alexandria
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Ben, jemaa Slim. "Cartographie fine de qtl de fertilite femelle chez les bovins laitiers franÇais." Phd thesis, AgroParisTech, 2009. http://pastel.archives-ouvertes.fr/pastel-00005162.
Full textAbstract:
L'objectif de la thèse est la cartographie fine de QTL de fertilité femelle (FF) chez les races bovines Françaises : la Prim'Holstein (PH), la Normande (NO) et la Montbéliarde (MO). La première étape du projet consiste en une primo-localisation, sur un dispositif de 78 familles, de QTL de FF dans 12 régions génomiques. Six QTL de FF ont été détectés chez la PH et deux chez la NO. La deuxième étape consiste en une cartographie des QTL détectés sur les chromosomes BTA01, BTA02, BTA03 et BTA21 sur un échantillon de 41 familles des trois races. La localisation de ces QTL a été confirmée et précisée pour les QTL détectés sur les chromosomes BTA01 et BTA03. Le QTL sur le chromosome BTA03 a été finement cartographié en utilisant 437 SNP ce qui a permis de réduire son intervalle de localisation à quelques centimorgans et de sélectionner six gènes candidats. Les régions flanquant les exons de ces six gènes ont été séquencées sur quatre pools d'ADN d'individus de phénotypes extrêmes afin de trouver des polymorphismes intéressants dans les régions séquencées qui pourront ensuite être validés sur l'ensemble du dispositif. La mise à disposition récente d'une puce de 54000 SNP situés dans tout le génome bovin a changé la stratégie de cartographie de QTL de FF. Des gènes pouvant influencer la FF ont été sélectionnés et suggérés comme étant des gènes candidats positionnels et fonctionnels responsables de la dégradation de la FF chez les bovins laitiers.
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Nettelblad, Carl. "Two Optimization Problems in Genetics : Multi-dimensional QTL Analysis and Haplotype Inference." Doctoral thesis, Uppsala universitet, Avdelningen för beräkningsvetenskap, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-180920.
Full textAbstract:
The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools. The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures. The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).eSSENCE