Relevant bibliographies by topics / Expression QTL

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Expression QTL'

Author: Grafiati
Published: 4 June 2021
Last updated: 6 February 2022

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Journal articles on the topic "Expression QTL"

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Peirce, Jeremy L., Hongqiang Li, Jintao Wang, Kenneth F. Manly, Robert J. Hitzemann, John K. Belknap, Glenn D. Rosen, et al. "How replicable are mRNA expression QTL?" Mammalian Genome 17, no. 6 (June 2006): 643–56. http://dx.doi.org/10.1007/s00335-005-0187-8.

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Penning, Bryan W., Gurmukh S. Johal, and Michael D. McMullen. "A major suppressor of cell death, slm1, modifies the expression of the maize (Zea mays L.) lesion mimic mutation les23." Genome 47, no. 5 (October 1, 2004): 961–69. http://dx.doi.org/10.1139/g04-046.

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Disease lesion mimics provide an excellent biological system to study the genetic basis of cell death in plants. Many lesion mimics show variation in phenotype expression in different genetic backgrounds. Our goal was to identify quantitative trait loci (QTL) modifying lesion mimic expression thereby identifying genetic modifiers of cell death. A recessive lesion mimic, les23, in a severe-expressing line was crossed to the maize inbred line Mo20W, a lesion-suppressing line, and an F2 population was developed for QTL analysis. In addition to locating les23 to the short arm of chromosome 2, this analysis detected significant loci for modification of lesion expression. One highly significant locus was found on the long arm of chromosome 2. The Mo20W allele at this QTL significantly delayed initiation of the lesion phenotype and decreased the final lesion severity. Other QTL with lesser effect affected severity of lesion expression without affecting lesion initiation date. Our results demonstrate that dramatic change in lesion phenotype can be controlled by a single major QTL. The presumed function of this QTL in normal plants is to regulate some aspect of the cell death pathway underlying the les23 phenotype.Key words: genetic background, quantitative trait locus, phenotype suppression, Mo20W, corn.
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Han, Bing, Naomi S. Altman, Jessica A. Mong, Laura Cousino Klein, Donald W. Pfaff, and David J. Vandenbergh. "Comparing Quantitative Trait Loci and Gene Expression Data." Advances in Bioinformatics 2008 (September 16, 2008): 1–6. http://dx.doi.org/10.1155/2008/719818.

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We develop methods to compare the positions of quantitative trait loci (QTL) with a set of genes selected by other methods, such as microarray experiments, from a sequenced genome. We apply our methods to QTL for addictive behavior in mouse, and a set of genes upregulated in a region of the brain associated with addictive behavior, the nucleus accumbens (NA). The association between the QTL and NA genes is not significantly stronger than expected by chance. However, chromosomes 2 and 16 do show strong associations suggesting that genes on these chromosomes might be associated with addictive behavior. The statistical methodology developed for this study can be applied to similar studies to assess the mutual information in microarray and QTL analyses.
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Viñuela, Ana, L. Basten Snoek, Joost A. G. Riksen, and Jan E. Kammenga. "Aging Uncouples Heritability and Expression-QTL inCaenorhabditis elegans." G3: Genes|Genomes|Genetics 2, no. 5 (May 2012): 597–605. http://dx.doi.org/10.1534/g3.112.002212.

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Zou, Wei, and Zhao-Bang Zeng. "Multiple interval mapping for gene expression QTL analysis." Genetica 137, no. 2 (May 9, 2009): 125–34. http://dx.doi.org/10.1007/s10709-009-9365-z.

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Wu, Wei-Ren, Wei-Ming Li, Ding-Zhong Tang, Hao-Ran Lu, and A. J. Worland. "Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice." Genetics 151, no. 1 (January 1, 1999): 297–303. http://dx.doi.org/10.1093/genetics/151.1.297.

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Abstract Using time-related phenotypic data, methods of composite interval mapping and multiple-trait composite interval mapping based on least squares were applied to map quantitative trait loci (QTL) underlying the development of tiller number in rice. A recombinant inbred population and a corresponding saturated molecular marker linkage map were constructed for the study. Tiller number was recorded every 4 or 5 days for a total of seven times starting at 20 days after sowing. Five QTL were detected on chromosomes 1, 3, and 5. These QTL explained more than half of the genetic variance at the final observation. All the QTL displayed an S-shaped expression curve. Three QTL reached their highest expression rates during active tillering stage, while the other two QTL achieved this either before or after the active tillering stage.
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McIntyre, C. Lynne, David Seung, Rosanne E. Casu, Gregory J. Rebetzke, Ray Shorter, and Gang Ping Xue. "Genotypic variation in the accumulation of water soluble carbohydrates in wheat." Functional Plant Biology 39, no. 7 (2012): 560. http://dx.doi.org/10.1071/fp12077.

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Water-soluble carbohydrates (WSC) stored in the stems and leaf sheaths of winter cereals provide an important source of assimilate for remobilisation during grain-filling. Consequently, WSC are a major contributor to wheat grain yield and grain size in all environments but especially where photosynthesis is compromised as occurs where water is limiting. Breeding programs targeting greater WSC should provide improved varieties with greater and more stable yields in stress environments. To facilitate selection for WSC, genetic and genomic approaches are being used to determine the genetic basis of – and define DNA probes for – marker-aided selection for this important drought-adaptive trait. Empirical studies have identified both WSC concentration and content to be under complex genetic control of many genes. Quantitative trait loci (QTL) for WSC have been identified in several wheat populations with individual QTL explaining small amounts of phenotypic variation, typically of less than 20%. Many of these QTL are common across multiple, genetically-unrelated wheat populations. Evaluation of gene expression in high and low WSC wheat progeny lines from a well characterised wheat population has identified significant differences in expression of genes from different gene categories. For example, high WSC progeny lines have higher levels of expression of genes involved in carbohydrate metabolism and lower levels of expression of genes involved in cell wall and amino acid metabolism than low WSC lines. Genetic mapping reveals several candidate genes co-locating with QTL for WSC. In addition, expression QTL (eQTL) for selected candidate genes co-locate with WSC QTL; co-location of the genes and eQTL with WSC QTL make these genes stronger candidate genes for the WSC trait.
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Ronald, James, and Joshua M. Akey. "The Evolution of Gene Expression QTL in Saccharomyces cerevisiae." PLoS ONE 2, no. 8 (August 1, 2007): e678. http://dx.doi.org/10.1371/journal.pone.0000678.

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Hitzemann, Robert J. "ON THE INTEGRATION OF GENE EXPRESSION AND QTL ANALYSES." Alcoholism: Clinical & Experimental Research 28, Supplement (August 2004): 54A. http://dx.doi.org/10.1097/00000374-200408002-00284.

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de Koning, Dirk-Jan, Henk Bovenhuis, and Johan A. M. van Arendonk. "On the Detection of Imprinted Quantitative Trait Loci in Experimental Crosses of Outbred Species." Genetics 161, no. 2 (June 1, 2002): 931–38. http://dx.doi.org/10.1093/genetics/161.2.931.

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Abstract In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted QTL were simulated in an F2 design and analyzed under Mendelian and imprinting models. Mode of expression was evaluated against the H0 of a Mendelian QTL as well as the H0 of an imprinted QTL. It was shown that imprinted QTL might remain undetected when analyzing the genome with Mendelian models only. Compared to testing against a Mendelian QTL, using the H0 of an imprinted QTL gave a higher proportion of correctly identified imprinted QTL, but also gave a higher proportion of false inference of imprinting for Mendelian QTL. When QTL were segregating in the founder lines, spurious detection of imprinting became more prominent under both tests, especially for designs with a small number of F1 sires.
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Dissertations / Theses on the topic "Expression QTL"

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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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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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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 – eSNP pairs for disease such as Ulcerative Colitis, Inflammatory Bowel Disease, Bechet's Disease, Sarcoidosis, Crohn's Disease, Grave’s 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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Perera, Suriya Arachchige Chandrika Nishanthi. "Fine mapping of QTL and microarray gene expression studies in arabidopsis using STAIRS." Thesis, University of Birmingham, 2005. http://etheses.bham.ac.uk//id/eprint/1652/.

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QTL mapping with segregating populations results in poor map resolution which limits the applicability of mapped QTL in further research such as gene cloning. The current research project aimed mainly at developing STepped Aligned Recombinant Inbred Strains (STAIRS) covering the top region of chromosome 3 and demonstrating the feasibility of using STAIRS in high resolution mapping of QTL in Arabidopsis. The top region of chromosome 3 of Arabidopsis had been reported to house QTL related to flowering time. This region was first saturated with 24 polymorphic microsatellite markers and 23 narrow STAIRS were produced within the region via a marker-assisted backcross breeding programme using whole chromosome substitution lines. The analysis of QTL with the narrow STAIRS revealed a major pleiotropic QTL within 2-3 cM affecting flowering time, leaf number at day 20 and rosette and cauline leaf numbers at flowering. A second QTL with less but opposite effect on the same traits were located within 15-20 cM. The search for candidate genes within 2-3 cM of chromosome 3, to locate possible candidate genes revealed COL-2, CONSTANS-Like gene which affects flowering time. Microarray gene expression profiling was performed using the two genotypically closest lines which differ for flowering time to compare the two lines at the same chronological and physiological ages in two experiments respectively. The lists of differentially expressed genes were obtained from the two experiments. Differential expression was observed for the possible candidate gene in the latter experiment. The results emphasized the power of STAIRS in fine mapping of QTL and the possibility of using them in transcriptional profiling to study the expression of genes.
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McSweeny, Andrew J. "Identification of Candidate Genes within Blood Pressure QTL Containing Regions Using Gene Expression Data." University of Toledo Health Science Campus / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=mco1212501779.

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Guitton, Baptiste. "Genetic control of biennial bearing in apple." Thesis, Montpellier, SupAgro, 2011. http://www.theses.fr/2011NSAM0048.

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L'alternance de production est définie comme la charge en fruit d'un arbre irrégulière sur plusieurs années consécutives. La principale hypothèse en soulignant l'alternance est que la charge en fruits d'une année en cours inhibe la formation de fleurs pour l'année suivante. Ce phénomène génère d'importants problèmes agronomiques pour les espèces fruitières comme le pommier, en réduisant la production de fruits au cours des années 'OFF' et la qualité des fruits au cours des années 'ON', tout en augmentant les coûts de gestion des vergers, en particulier pour l'éclaircissage des fruits. Une stratégie pour atténuer l'alternance est de développer de nouvelles variétés avec une production régulière. Les principaux objectifs de ma thèse étaient: (i) d'améliorer les stratégies de phénotypage et les méthodes pour caractériser l'alternance de production, (ii) de disséquer le contrôle génétique de l'alternance de production en utilisant une descendance de pommier en ségrégation et d'identifier les principales régions génétiques responsables de la variation du caractère, et (iii) d'étudier les processus physiologiques sous-jacents à l'alternance de production. J'ai combiné des méthodes comme la modélisation, la génétique quantitative, la détection de Quantitative Trait Loci (QTL) et de gènes candidats ainsi que la cartographie et l'expression de gènes.Mon étude a utilisé une population de pommier ségrégation obtenue à partir d'un croisement entre des parents contrastés pour les caractéristiques architecturales et de floraison (‘Starkrimson' x 'Granny Smith'). Le phénotypage de la population pour l'alternance de production a été réalisée à l'échelle d'arbres entiers, en observant les occurrences de floraison pendant six années consécutives, et à l'échelle locale, en observant la succession de méristèmes floraux vs végétative en position terminale de rameaux. De ces données, de nouveaux modèles ont été développés afin de quantifier l'alternance de la production, en tenant compte de la croissance ontogénétique de la production et la présence / absence de floraison entre les années successives le long des pousses courtes. Ceci nous a conduits à proposer de nouveaux descripteurs de la tendance d'un génotype à l'alternance de production dans les premiers stades de développement des arbres et ouvre des possibilités pour une évaluation plus rapide et plus précoce de ce caractère dans les programmes de sélection de fruits à pépins.Pour identifier les régions génomiques impliquées dans l'alternance, une détection de QTL a été réalisée sur la base des données phénotypiques et des valeurs de BLUP obtenues à partir des modèles. J'ai démontré que la régularité de la production est sous contrôle polygénique. J'ai extrait une liste de gènes qui sont présents au sein de ces QTL en utilisant la séquence du génome du pommier. Les principaux gènes candidats identifiés sont liés aux gibbérellines, aux auxines, et à la floraison. J'ai étudié l'expression des gènes candidats co-localisant avec des QTLs par PCR quantitative en utilisant les méristèmes prélevés sur les arbres portant une forte charge en fruits vs une faible charge. Une analyse microarray m'a permis d'obtenir un aperçu global des processus biologiques et de l'expression des gènes qui sont modulés dans le méristème lorsque des fruits sont présents. Certains gènes liés à la floraison, au développement du méristème, aux gibbérellines et aux auxines ont montré un profil d'expression affectée par la présence de fruits.Mes résultats fournissent des éclaircissements sur le contrôle physiologique et génétique de ce caractère complexe qui est l'alternance et ouvrent la perspective d'inclure la régularité de production dans les schémas de sélection de pommier et d'autres espèces fruitières
Biennial bearing is defined as the irregular crop load of a tree over consecutive years. The main assumption underlining biennial bearing is that the fruit load of a given year inhibits flower formation for the following year. This phenomenon generates major agronomic problems for fruit species such as apple, by reducing fruit production during ‘OFF' years and fruit quality during ‘ON' years, while increasing orchard management costs, especially for fruit thinning. A strategy to attenuate biennial bearing is to develop new varieties with regular production. The main objectives of my project were (i) to improve phenotyping strategy and methodology for biennial bearing characterisation, (ii) to dissect the genetic control of biennial bearing using an apple segregating progeny and to identify key genetic regions responsible for the trait variation, and (iii) to investigate physiological processes underlying biennial bearing. I combined methodologies such as modelling, quantitative genetics, candidate gene and Quantitative Trait Loci (QTL) mapping and gene expression.My study used an apple segregating population issued from a cross between contrasting parents for architectural and flowering features (‘Starkrimson' x ‘Granny Smith'). Phenotyping of the population for biennial bearing was achieved at whole tree scale by observing flowering occurrence for six consecutive years, and at local scale, by observing the succession of floral vs. vegetative meristems in terminal position of shoots. From this data, new models were constructed to quantify the alternation of production, taking into account the ontogenetic increasing trend of production and the presence/absence of flowering between successive years along short shoots. This led us to propose new descriptors of the tendency of a genotype to biennial bearing in the early stages of tree development and opens possibilities for a faster and earlier evaluation of this character in pipfruit breeding programmes and for orchard management.To identify genomic regions involved in biennial bearing, a QTL detection was performed on the basis of phenotypic data and BLUP values obtained from the models. I demonstrated that the regularity of production is under polygenic control. I mined a list of genes that are present within these QTLs using the apple genome sequence. The main candidate genes identified are related to gibberellins, auxins, and flowering.I investigated the expression of candidate genes co-locating with QTLs by quantitative PCR using meristems collected on trees bearing heavy fruit load vs. light crop. A microarray analysis enabled me to obtain a global overview of biological processes and gene expression that are modulated in the meristem when fruits are present. Some genes related to flowering, meristem development, gibberellins and auxins showed an expression profile affected by the presence of fruit.My results provide elucidation on the physiological and genetic control of the complex trait that is biennial bearing and open up the perspective of including regular bearing in breeding schemes for apple and other fruit species
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Santos, Michelle da Fonseca. "Mapeamento de QTL e expressão gênica associados à resistência da soja ao complexo de percevejos." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-16082012-083347/.

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O grupo de percevejos que mais frequentemente causa perdas econômicas à soja no Brasil é composto pelas espécies: Nezara viridula, Piezodorus guildinii e Euchistus heros. Assim, os objetivos desta pesquisa foram avaliar parâmetros genéticos e correlações entre as diferentes características de desenvolvimento e produção, mapear QTL associados à resistência da soja aos percevejos e determinar respostas de expressão gênica associadas à alimentação do inseto. Uma população F2:3 foi desenvolvida através do cruzamento de IAC- 100 (resistente) e CD-215 (suscetível) e avaliada em campo experimental. As características agronômicas avaliadas foram: número de dias para o florescimento (NDF), altura da planta no florescimento (APF), número de dias para a maturidade (NDM), altura da planta na maturidade (APM), acamamento (AC), valor agronômico (VA) e produtividade de grãos (PG). As características de resistência a percevejos avaliadas foram: período de enchimento de grãos (PEG), retenção foliar (RF), índice percentual de danos nas vagens (IPDV), número de vagens por planta (NVP), número de sementes (NS), peso de sementes manchadas (PSM), peso de sementes boas (PSB), e peso de cem sementes (PCS). Para se ter um total de 96 amostras, os dois pais foram genotipados juntamente com as 12 mais resistentes e 12 mais suscetíveis plantas F2 para as características PEG, PCS e PSB, e as 11 mais resistentes e 11 mais suscetíveis para a característica RF. Para determinar o tempo de resposta de expressão gênica nas vagens à alimentação de percevejos, um estudo de microarranjo foi realizado com CD-215 avaliando a expressão relativa 5.5, 21, 24 e 41 horas após infestação em condições de casa-de-vegetação. Dentre as características de resistência, os maiores valores de herdabilidade foram observados para PCS e PEG. O caráter PCS apresentou correlação genética positiva e significativa com PSM e PEG. Neste estudo, 337 SNP, 28 SSR, 13 TRAP e 41 AFLP foram mapeados em 20 grupos de ligação. Quatorze QTL foram encontrados usando o modelo restrito de múltiplos QTL e análise de Kruskal-Wallis. A maioria dos QTL foi detectada para mais de uma característica e composta por genes com efeito menor. Na análise de microarranjo foi observada uma expressão diferencial clara para as amostras de 21, 24 e 41 horas com P. guildinii. Assim, para o experimento de campo as vagens foram infestadas com esta espécie e amostras de vagens foram coletadas 0, 8, 24 e 46 horas após infestação. Nesta etapa foi sequenciado somente o RNA mensageiro da amostra 24 horas. Na análise de RNA-seq realizada nas vagens sem nenhum tratamento, a cultivar resistente (IAC- 100) apresentou 39,4% dos genes com maior expressão e 11,68% dos genes com menor expressão do que a cultivar suscetível (CD-215). Baseado nos resultados, a seleção indireta para PCS associado com PSB pode ser realizada com sucesso para a obtenção de genótipos resistentes a percevejo. Além disso, os resultados de mapeamento de QTL foram parcialmente consistentes com estudos anteriores para característica agronômicas, sugerindo que QTL reais foram mapeados.
The group of stink bugs most frequently causing economic losses in soybean in Brazil consists of the species: Nezara viridula, Piezodorus guildinii, and Euchistus heros. Therefore, the objectives of the current research were to evaluate genetic parameters and correlations among distinct development and yield traits, map QTL associated with soybean resistance to stink bugs, and determine plant gene expression profiles associated to insect feeding. An F2:3 population was developed by crossing IAC-100 (resistant) and CD-215 (susceptible) and it was evaluated at an experimental field. The agronomic traits evaluated were number of days to flowering (NDF), plant height at flowering (PHF), number of days to maturity (NDM), plant height at maturity (PHM), lodging (L), agronomic value (AV), and grain yield (GY). The characteristics of stink bug resistance evaluated were grain filling period (GFP), leaf retention (LR), percentage index of pod damage (PIPD), number of pods per plant (NPP), number of seeds (NS), weight of spotted seeds (WSS), healthy seed weight (HSW), and weight of a hundred seeds (WHS). To have a total of 96 samples, the two parent lines were genotyped along with the 12 most resistant and 12 most susceptible F2 plants for the traits GFP, WHS, and HSW, and the 11 most resistant and 11 most susceptible for the trait LR. In order to determine the timing of gene expression response in pods under stink bug feeding, a microarray study was carried out with the cultivar CD-215, evaluating relative transcription levels at 5.5, 21, 24, and 41 hours post-infestation under greenhouse conditions. Among the characteristics of resistance, the highest values of heritability were observed for WHS and GFP. The trait WHS exhibited positive and significant genotypic correlation with WSS and GFP. In this study, 337 SNP, 28 SSR, 13 TRAP, and 41 AFLP markers were mapped to 20 linkage groups. Fourteen QTL were found using the restricted multiple QTL model and Kruskal-Wallis analyses. The majority of the QTL was detected for more than one trait and consisted of genes with minor effects. A clear differential gene expression was observed in the microarray analysis for the samples at time points 21, 24, and 41 hours infested with P. guildinii. Thus, in field trials the pods were infested with this species and samples of pods were taken at 0, 8, 24, and 46 hours. In this study, only RNA from the 24 hour sample was sequenced. From RNA-seq analysis performed on pods without treatment, the resistant cultivar (IAC-100) showed 39.4% of genes with induced expression and 11.68% of genes with repressed expression in comparison to the susceptible cultivar (CD-215). Based on the results, indirect selection for WHS associated with HSW can be successfully employed for obtaining stink bug resistant genotypes. Moreover, mapping QTL results were partially consistent with previous studies for agronomic traits, suggesting that real QTL were mapped.
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Pumphrey, Michael Odell. "Towards map-based cloning of Fusarium head blight resistance QTL Fhb1 and non-additive expression of homoeologous genes in allohexaploid wheat." Diss., Kansas State University, 2007. http://hdl.handle.net/2097/32793.

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Doctor of Philosophy
Department of Plant Pathology
Bikram S. Gill
Wheat is the most widely grown and consumed grain crop in the world. In order to meet future agricultural production requirements of a growing population, it is essential that we achieve an increased understanding of the basic components and mechanisms shaping growth and productivity of the polyploid wheat plant. Fusarium head blight (FHB) (syn. "scab") poses a serious threat to the quantity and safety of the world's food supply. The resistance locus Fhb1 has provided partial resistance to FHB of wheat for nearly four decades. Map-based cloning of Fhb1 is justified by its significant and consistent effects on reducing disease levels, the importance of FHB in global wheat production and food safety, and because this gene confers partial resistance to this disease and does not appear to behave in a gene-for-gene manner. A bacterial artificial chromosome (BAC) contig spanning the Fhb1 region was developed from the cultivar 'Chinese Spring', sequenced and seven candidate genes were identified in an ~250 kb region. Cosmid clones for each of the seven candidate genes were isolated from a line containing Fhb1 and used for genetic transformation by biolistic bombardment. Transgenic lines were recovered for five candidate genes and evaluated for FHB resistance. All failed to complement the Fhb1 phenotype. Fhb1 is possibly one of the two remaining candidate genes, an unknown regulatory element in this region, or is not present in Chinese Spring. Traditional views on the effects of polyploidy in allohexaploid wheat have primarily emphasized aspects of coding sequence variation and the enhanced potential to acquire new gene functions through mutation of redundant loci. At the same time, the extent and significance of regulatory variation has been relatively unexplored. Recent investigations have suggested that differential expression of homoeologous transcripts, or subfunctionalization, is common in natural bread wheat. In order to establish a timeline for such regulatory changes and estimate the frequency of non-additive expression of homoeologous transcripts in newly formed T. aestivum, gene expression was characterized in a synthetic T. aestivum line and its T. turgidum and Aegilops tauschii parents by cDNA-SSCP and microarray expression experiments. The cDNA-SSCP analysis of 30 arbitrarily selected homoeologous transcripts revealed that four (~13%) showed differential expression of homoeoalleles in seedling leaf tissue of synthetic T. aestivum. In microarray expression experiments, synthetic T. aestivum gene expression was compared to mid-parent expression level estimates calculated from parental expression levels. Approximately 16% of genes were inferred to display non-additive expression in synthetic T. aestivum. Six homoeologous transcripts classified as non-additively expressed in microarray experiments were characterized by cDNA-SSCP. Expression patterns of these six transcripts suggest that cis-acting regulatory variation is often responsible for non-additive gene expression levels. These results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and non-additive gene expression in synthetic T. aestivum.
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Nguyen, Le Khanh. "Caractérisation fonctionnelle d'un QTL de développement racinaire détecté par GWAS dans une collection de variétés vietnamiennes de riz." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTG044.

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Le riz est l'une des céréales les plus importantes au monde. Au Vietnam, le riz est également considéré comme un produit agronomique clé pour l'exportation. Cependant, le stress dû à la sécheresse menace la production de riz de plus en plus fréquemment et sur de plus longues périodes. Les racines coronaires constituent une partie importante du système racinaire du riz et jouent un rôle crucial dans le maintien du rendement en cas de sécheresse. Le nombre de racines coronaires affecte la biomasse de racines et détermine la capacité de la plante à extraire les ressources du sol. Un QTL de NRC, qNCR11, localisé sur le chromosome 11, avait été détecté dans une étude d’association précédente utilisant un panel de riz vietnamiens. Dans notre étude, son effet sur le NCR, léger, a été validé par cartographie de QTL en utilisant une population biparentale . Afin de déterminer les gènes sous-jacents à qNCR11 et régissant l'initiation et le développement des racines coronaires, une étude de séquençage du génome entier et une étude d'expression ont été réalisées. Deux gènes candidats, NCR2 (NBS-LRR) et NCR3 (OsbHLH014) ont été identifiés. NCR2 portait un SNP non synonyme dans son ORF, provoquant un codon stop prématuré corrélé avec un NCR élevé; NCR3 était moins exprimé dans les bases de la tige des plantes à haplotype NCR élevé que chez les plantes à haplotype NCR faible. Des mutations dans ces gènes ont été obtenues à l'aide du système CRISPR / Cas9 et le phénotypage des lignées obtenues est en cours. Le QTL qNCR11 à effet mineur pourrait être utile aux sélectionneurs pour produire des variétés de riz avec un NCR augmenté ou diminué pour les différents écosystèmes-cibles, afin de favoriser l'extraction de l'eau dans des conditions de sécheresse
Rice is one of the most important cereals worldwide. In Vietnam, rice is also known as a key agronomic product for exportation. However, drought stresses threaten rice production with an increasing frequency and for longer periods. Crown roots are a major component of rice root system and play a crucial role in maintaining yield under drought. The number of crown roots (NCR) impacts on root biomass and determines the ability of a plant to acquire soil resources. qNCR11, a QTL for NCR located on chromosome 11, was detected in a previous genome-wide association study using a Vietnamese rice panel. qNCR11 was validated to have a slight effect on NCR by QTL mapping using a biparental population in this study. To determine the genes underlying qNCR11 and governing crown root initiation and development, whole genome sequencing and expression study were performed. Two candidate genes, NCR2 (NBS-LRR) and NCR3 (OsbHLH014) were identified. NCR2 carried a non-synonymous SNP inside its ORF, causing a premature stop-codon that correlates with the high NCR trait; NCR3 was less expressed in stem bases of the high NCR haplotype plants relative to the low NCR haplotype plants. Mutations in these genes were obtained using the CRISPR/Cas9 system and the phenotyping of the obtained lines is on-going. The minor-effect qNCR11 could be useful for breeders to generate rice varieties with increased or decreased NCR for different target agro-systems, in order to enhance water extraction under drought stress
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Rubin, Carl-Johan. "Functional Genomics of Bone Metabolism : Novel Candidate Genes Identified by Studies in Chicken Models." Doctoral thesis, Uppsala University, Department of Medical Sciences, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8498.

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Osteoporosis is a disease that leads to decreased bone mineral density (BMD), an altered bone micro-architecture and fragile bones. The disease is highly heritable and numerous genes are thought to be involved, making it difficult to identify the causative genetic elements.

Animal models, mainly intercrosses between laboratory strains of mice, have been succesfully used to map genes affecting these traits, but may not mirror the multifactorial genetic etiology of highly complex traits such as osteoporosis.

Over the course of tens of thousand years humans have kept domestic animals whose phenotypic repertoires have been tailored to meet our needs. Wild-type red junglefowl (RJ) and domestic White Leghorn (WL) chicken differ for several bone traits.

In this thesis Quantitative Trait Loci (QTL) mapping was used to trace the inheritance of bone traits in two separate intercrosses between RJ and WL. In these studies we identified several QTL that contributed to differences in BMD, bone size and biomechanical strength of bone. In a comparison of QTL identified in the two intercrosses it was observed that nine QTL had overlapping genomic positions, implicating these loci as important to bone phenotypic variation in chicken.

In two separate studies, microarray technology was used to compare global gene expression in bone tissue from RJ and WL. In these studies, differential expression was observed for 779 and 560 genes, respectively. Many differentially expressed genes were co-localized with QTL, which implicates them as QTL-candidates.

Results presented in this thesis link several genomic regions and genes to variation in bone traits. Increased knowledge about these identified genes and regions will contribute to a better understanding of the mechanisms underlying inter-individual differences in bone metabolism, both in chicken and man.

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Books on the topic "Expression QTL"

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Walsh, Bruce, and Michael Lynch. The Neutral Divergence of Quantitative Traits. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0012.

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The joint action of genetic drift and mutation results in the divergence of trait means over time. This chapter examines the expected amount of divergence, which forms the basis for a number of tests on whether an observed pattern is either too large relative to drift (suggesting directional selection) or two small (suggesting stabilizing selection). It then applies these results to examine tests for selection over a very diverse range of data sets, ranging from a stratophenetic series of fossils to divergence in gene expression over time. It also examines a number of trait-augmented marked-based tests (such as using the QTLs or GWAS hits for a trait) for departures from neutrality.
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Book chapters on the topic "Expression QTL"

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Abberton, Michael T., Athole Marshall, Rosemary P. Collins, Charlotte Jones, and Matthew Lowe. "QTL Analysis and Gene Expression Studies in White Clover." In Molecular Breeding of Forage and Turf, 1–10. New York, NY: Springer New York, 2008. http://dx.doi.org/10.1007/978-0-387-79143-2_15.

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Abberton, Michael T., Athole Marshall, Rosemary P. Collins, Charlotte Jones, and Matthew Lowe. "QTL Analysis and Gene Expression Studies in White Clover." In Molecular Breeding of Forage and Turf, 163–72. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-79144-9_15.

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Rustenholz, Camille, and Patrick S. Schnable. "Integrating “Omics” Data and Expression QTL to Understand Maize Heterosis." In Polyploid and Hybrid Genomics, 85–103. Oxford, UK: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118552872.ch5.

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Alberts, Rudi, and Klaus Schughart. "High-Throughput Gene Expression Analysis and the Identification of Expression QTLs." In Gene Discovery for Disease Models, 11–30. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470933947.ch2.

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Kumar, Pardeep, Mukesh Choudhary, B. S. Jat, M. C. Dagla, Vishal Singh, Abhijit Kumar Das, Santosh Kumar, Ningthaipuilu Longmei, Robert J. Henry, and Shabir Hussain Wani. "Isolation of genes/quantitative trait loci for drought stress tolerance in maize." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 267–81. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0015.

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Abstract This chapter focuses on target traits for drought stress, progress in mapping for drought tolerance-associated genes/QTLs identification and expression studies and introgression strategies followed by the possibilities of integrating the concept of speed breeding in maize drought breeding programmes for better utilization of wild relatives.
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Imprialou, Martha, Enrico Petretto, and Leonardo Bottolo. "Expression QTLs Mapping and Analysis: A Bayesian Perspective." In Methods in Molecular Biology, 189–215. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6427-7_8.

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Arcangeli, Annarosa. "Expression and Role of hERG Channels in Cancer Cells." In The hERG Cardiac Potassium Channel: Structure, Function and Long QT Syndrome, 225–34. Chichester, UK: John Wiley & Sons, Ltd, 2008. http://dx.doi.org/10.1002/047002142x.ch17.

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Iehisa, Julio C. M., Yoichi Motomura, Fuminori Kobayashi, and Shigeo Takumi. "Abiotic Stress Signal Network with Expression QTLs for Cold-Responsive Genes in Common Wheat." In Plant and Microbe Adaptations to Cold in a Changing World, 219–29. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-8253-6_19.

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Liu, Bing, Ina Hoeschele, and Alberto de la Fuente. "Inferring Gene Regulatory Networks from Genetical Genomics Data." In Handbook of Research on Computational Methodologies in Gene Regulatory Networks, 79–107. IGI Global, 2010. http://dx.doi.org/10.4018/978-1-60566-685-3.ch004.

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In this chapter, we review the current state of Gene Regulatory Network inference based on ‘Genetical Genomics’ experiments (Brem & Kruglyak, 2005; Brem, Yvert, Clinton & Kruglyak, 2002; Jansen, 2003; Jansen & Nap, 2001; Schadt et al., 2003) as a special case of causal network inference in ‘Systems Genetics’ (Threadgill, 2006). In a Genetical Genomics experiment, a segregating or genetically randomized population is DNA marker genotyped and gene-expression profiled on a genomewide scale. The genotypes are regarded as natural, multifactorial perturbations resulting in different gene-expression ‘phenotypes’, and causal relationships can therefore be established between the measured genotypes and the gene-expression phenotypes. In this chapter, we review different computational approaches to Gene Regulatory Network inference based on the joint analysis of DNA marker and expression data and additionally of DNA sequence information if available. This includes different methods for expression QTL mapping, selection of regulator-target pairs, construction of an encompassing network, which strongly constrains the network search space, and pairwise and multivariate methods for Gene Regulatory Network inference, such as Bayesian Networks and Structural Equation Modeling.
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"Finding Genes in Spite of Heterogeneity: Endophenotypes, QTL Mapping, and Expression Profiling in Autism." In Understanding Autism, 95–114. CRC Press, 2006. http://dx.doi.org/10.1201/9781420004205-9.

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Conference papers on the topic "Expression QTL"

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Lu, Hong, Huaijin Guan, Hui Chen, and Lu Lu. "Expression QTL and genetic regulatory network analysis of Col11a1." In 2012 5th International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2012. http://dx.doi.org/10.1109/bmei.2012.6512879.

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Loo, Lenora W. M., Iona Cheng, Maarit Tiirikainen, Annette Lum-Jones, Ann Seifried, Lucas M. Dunklee, Steve Gallinger, Stephen N. Thibodeau, Graham Casey, and Loic Le Marchand. "Abstract 4732: Cis-expression QTL analysis of established risk variants for colorectal cancer." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4732.

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Yu, Xiaoqing, and Xuefeng Wang. "Abstract 4974: Germline prognostic SNPs and tumor-immunity-specific expression QTL (tis-eQTL) in cancer." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-4974.

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Yu, Xiaoqing, and Xuefeng Wang. "Abstract 4974: Germline prognostic SNPs and tumor-immunity-specific expression QTL (tis-eQTL) in cancer." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-4974.

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Slob, Elise M. A., Alen Faiz, Susanne Vijverberg, Cristina Longo, Merve Kutlu, Patricia Soares, Fook Tim Chew, et al. "Bronchial airway inducible expression and methylation QTL mapping identifies a single nucleotide polymorphism predicting inhaled corticosteroids response heterogeneity." In ERS International Congress 2020 abstracts. European Respiratory Society, 2020. http://dx.doi.org/10.1183/13993003.congress-2020.4920.

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Choudhury, Nirupam, Rosy Sarmah, and Suranjon Sarma. "A modified QT-clustering algorithm over Gene Expression data." In 2012 1st International Conference on Recent Advances in Information Technology (RAIT). IEEE, 2012. http://dx.doi.org/10.1109/rait.2012.6194618.

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Hao, Ke, and Andrew Kasarskis. "Empirical Data Indicates a Primarily Additive Genetic Model for Expressional QTLs." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5517911.

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Bergau, Dennis M., Cong Liu, and Hui Lu. "Prediction of human QT prolongation liability based on pre-clinical RNA expression profiles." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217701.

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Hao, Ke. "Notice of Retraction: Normal and Obese Liver Expressional QTLs Reveal Genes and Pathways Underlying Metabolic Disorders." In 2011 5th International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2011. http://dx.doi.org/10.1109/icbbe.2011.5780092.

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Thompson, Jeffrey A., and Carmen J. Marsit. "Abstract 783: Methylation-expression QTLs (meeQTLs) as part of an integrated model of the disruption of gene regulation in cancer." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-783.

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