subject:(Expression quantitative trait loci)

University of Georgia

1. Sprolden, Tracy Lashonda. Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/28916

► A double eQTL mapping method for identifying trans eQTLs that reduces multiple testing and increases the statistical power of eQTL mapping is described. The first… (more)

Subjects/Keywords: Single nucleotide polymorphism (SNP); Expression quantitative trait loci (eQTL); Microarray; Cis eQTL; Trans eQTL

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sprolden, T. L. (2014). Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/28916

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Sprolden, Tracy Lashonda. “Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/28916.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Sprolden, Tracy Lashonda. “Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks.” 2014. Web. 19 Jan 2021.

Vancouver:

Sprolden TL. Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/28916.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Sprolden TL. Double eQTL mapping method to improve identification of trans eQTLs and construct intermediate gene networks. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/28916

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Newcastle

2. Naudin, Crystal. The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease.

Degree: PhD, 2015, University of Newcastle

URL: http://hdl.handle.net/1959.13/1305765

►

Research Doctorate - Doctor of Philosophy (PhD)

Glomerular diseases represent a major burden for both patients and the community. They are responsible for a significant… (more)

▼

Research Doctorate - Doctor of Philosophy (PhD)

Glomerular diseases represent a major burden for both patients and the community. They are responsible for a significant proportion of chronic kidney disease, which can ultimately progress to end stage renal disease, requiring dialysis or transplantation. Glomerular diseases are associated with leakage of proteins across the glomerular filtration barrier into the primary urine (proteinuria or albuminuria – as albumin is the major protein involved). The glomerular filtration barrier is composed of three interconnected layers: podocyte foot processes, the glomerular basement membrane (GBM) and a fenestrated endothelium. The tetraspanin protein CD151 is a crucial component of the glomerular filtration barrier, where it is known to complex with integrins to strengthen podocyte foot process anchorage to the GBM. In addition, previous findings in our laboratory have shown that in FVB/N Cd151^-/- mice the disruption and abnormal development of the GBM precedes podocyte foot process abnormalities, suggesting that CD151 also plays a role in the maturation and remodelling of the GBM. In other settings CD151 has been shown to regulate the proteolytic activity of matrix metalloproteinases (MMPs), important players in the homeostasis of basement membranes, and thus CD151 has many potential roles in glomerular homeostasis and disease. Similar to human mutation, Cd151 knockout in the FVB/N mouse strain leads to severe early-onset glomerular disease associated with GBM abnormalities, whereas knockout in the C57Bl/6 mouse strain does not lead to glomerular disease with kidneys presenting healthy. This strong influence of genetic background suggests the action of modifier genes, which may have important roles in human kidney disease where the course of glomerular diseases can vary significantly between patients. It is therefore important to identify the genes modulating progression as they could be used as biomarkers to predict the course of these heterogeneous diseases in patients or as potential therapeutic targets. In order to understand the molecular mechanisms contributing to progression and onset of glomerular disease in FVB/N Cd151^-/- mice, whole genome mRNA expression profiles of glomeruli from Cd151^+/+ and Cd151^-/- mice were investigated on both the C57Bl/6 and FVB/N backgrounds. Analysis was conducted at 3 weeks of age, at this stage in FVB/N Cd151^-/- mice changes to the GBM are evident but secondary changes such as glomerulosclerosis are not yet significant or widespread, and therefore allows the identification of genes relevant to early stage disease. The FVB/N Cd151^-/- mouse glomeruli showed 24 highly significant transcript changes compared to FVB/N Cd151^+/+, including changes in transcription factors, inflammatory factors and extracellular matrix regulators. Many of these changes did not occur in the corresponding comparison in the C57Bl/6 strain (Cd151^-/- versus Cd151^+/+)…

Advisors/Committee Members: University of Newcastle. Faculty of Health & Medicine, School of Biomedical Sciences and Pharmacy.

Subjects/Keywords: glomerular disease; tetraspanin; CD151; quantitative trait loci; gene expression; matrix metalloproteinases; inflammation

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APA (6^th Edition):

Naudin, C. (2015). The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease. (Doctoral Dissertation). University of Newcastle. Retrieved from http://hdl.handle.net/1959.13/1305765

Chicago Manual of Style (16^th Edition):

Naudin, Crystal. “The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease.” 2015. Doctoral Dissertation, University of Newcastle. Accessed January 19, 2021. http://hdl.handle.net/1959.13/1305765.

MLA Handbook (7^th Edition):

Naudin, Crystal. “The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease.” 2015. Web. 19 Jan 2021.

Vancouver:

Naudin C. The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease. [Internet] [Doctoral dissertation]. University of Newcastle; 2015. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1959.13/1305765.

Council of Science Editors:

Naudin C. The tetraspanin CD151’s role in the kidney and mapping of genetic modifiers of glomerular disease. [Doctoral Dissertation]. University of Newcastle; 2015. Available from: http://hdl.handle.net/1959.13/1305765

University of Maryland

3. YU, CHEN-HSIN. ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES.

Degree: Molecular and Cell Biology, 2014, University of Maryland

URL: http://hdl.handle.net/1903/16079

► Genome-wide association studies of human complex disease have identified a large number of disease associated genetic loci. However, most of these risk loci do not… (more)

▼ Genome-wide association studies of human complex disease have identified a large number of disease associated genetic loci. However, most of these risk loci do not provide direct information on the biological basis of a disease or on the underlying mechanisms. Recent genome-wide expression quantitative trait loci (eQTLs) association studies have provided information on genetic factors, especially SNPs, associated with gene expression variation. These eQTLs might contribute to phenotype diversity and disease susceptibility, but interpretation is handicapped by low reproducibility of the expression results. Our first major goal was to establish a list of consensus eQTLs by integrating publicly available data for specific human populations and cell types. We used linkage disequilibrium data from Hapmap and the 1000 Genomes Project to integrate the results of eQTL studies. Overall, we find over 4000 genes that are involved in high confidence eQTL relationships. We also assessed the possible underlying mechanisms of tissue dependent eQTLs by mapping these to known genome sites of functional elements. Results of comparison of eQTLs across studies on the same cell type versus those on different cell types suggest that tissue specific eQTLs are less common than pan-tissue eQTLs. Our second major goal was to use these results to elucidate the role eQTLs play in human common diseases. For this purpose, we matched the high confidence eQTLs to a set of 335 disease risk loci identified from the Wellcome Trust Case Control Consortium (WTCCC1) genome-wide association study and follow-up studies for seven human common diseases. Our results show that the data are consistent with approximately 50% of these disease loci arising from an underlying expression change mechanism. In many cases, the results provide a proposed expression mechanism for genes previously suggested as disease relevant, in others, new disease relevant genes are identified. A web-based database, ExSNP, was designed to provide comprehensive access to the eQTL data and results from our analysis, including original eQTLs, high-confidence eQTLs, cell type dependent eQTLs, population dependent eQTLs, disease associated eQTLs, and functionally annotated eQTLs. The website also incorporates a genome browser that allows visualization of the relative positions of eQTL SNPs to their associated genes and other neighboring genes, as well as the relationship to functional elements and disease associations. Advisors/Committee Members: Moult, John (advisor).

Subjects/Keywords: Bioinformatics; Genetics; Systematic biology; eQTL; expression quantitative trait loci; genome-wide association study; GWAS

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APA (6^th Edition):

YU, C. (2014). ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/16079

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

YU, CHEN-HSIN. “ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES.” 2014. Thesis, University of Maryland. Accessed January 19, 2021. http://hdl.handle.net/1903/16079.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

YU, CHEN-HSIN. “ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES.” 2014. Web. 19 Jan 2021.

Vancouver:

YU C. ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES. [Internet] [Thesis]. University of Maryland; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1903/16079.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

YU C. ANALYSIS OF CONSENSUS GENOME-WIDE EXPRESSION-QTLS AND THEIR RELATIONSHIPS TO HUMAN COMPLEX TRAIT DISEASES. [Thesis]. University of Maryland; 2014. Available from: http://hdl.handle.net/1903/16079

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Toronto

4. Chadha, Kartikay. Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits.

Degree: 2018, University of Toronto

URL: http://hdl.handle.net/1807/91487

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Genome-wide association studies and expression quantitative trait loci (eQTL) studies have identified thousands of variants associated with complex diseases and gene expression levels. The frequency… (more)

Subjects/Keywords: Algorithm; Alzheimer's Disease; DNA words; Expression Quantitative Trait Loci (eQTLs); Gene-Tissue Expression (GTEx) Project; Genome wide association studies (GWAS); 0308

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APA (6^th Edition):

Chadha, K. (2018). Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits. (Masters Thesis). University of Toronto. Retrieved from http://hdl.handle.net/1807/91487

Chicago Manual of Style (16^th Edition):

Chadha, Kartikay. “Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits.” 2018. Masters Thesis, University of Toronto. Accessed January 19, 2021. http://hdl.handle.net/1807/91487.

MLA Handbook (7^th Edition):

Chadha, Kartikay. “Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits.” 2018. Web. 19 Jan 2021.

Vancouver:

Chadha K. Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits. [Internet] [Masters thesis]. University of Toronto; 2018. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1807/91487.

Council of Science Editors:

Chadha K. Investigating the Frequency of DNA Words near Loci Associated with Human Complex Traits. [Masters Thesis]. University of Toronto; 2018. Available from: http://hdl.handle.net/1807/91487

Georgia Tech

5. Wang, Lu. Transposable element polymorphisms and human genome regulation.

Degree: PhD, Biology, 2017, Georgia Tech

URL: http://hdl.handle.net/1853/59266

► Transposable elements (TEs) are DNA sequences that are capable of moving from one genomic location to another. A large proportion of the human genome is… (more)

Subjects/Keywords: Transposable elements; Bioinformatics; Alu; L1; SVA; Gene expression; Gene regulation; GWAS; Expression quantitative trait loci; Polymorphism; Genetic variation

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APA (6^th Edition):

Wang, L. (2017). Transposable element polymorphisms and human genome regulation. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/59266

Chicago Manual of Style (16^th Edition):

Wang, Lu. “Transposable element polymorphisms and human genome regulation.” 2017. Doctoral Dissertation, Georgia Tech. Accessed January 19, 2021. http://hdl.handle.net/1853/59266.

MLA Handbook (7^th Edition):

Wang, Lu. “Transposable element polymorphisms and human genome regulation.” 2017. Web. 19 Jan 2021.

Vancouver:

Wang L. Transposable element polymorphisms and human genome regulation. [Internet] [Doctoral dissertation]. Georgia Tech; 2017. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1853/59266.

Council of Science Editors:

Wang L. Transposable element polymorphisms and human genome regulation. [Doctoral Dissertation]. Georgia Tech; 2017. Available from: http://hdl.handle.net/1853/59266

Mississippi State University

6. Smith, Jesse Spencer. Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717.

Degree: PhD, Plant and Soil Sciences, 2017, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-06282017-082324/ ;

► Pre-harvest contamination of maize grain with aflatoxin is a chronic problem worldwide and particularly in the southeastern U.S. Aflatoxin is a mycotoxin produced by… (more)

▼ Pre-harvest contamination of maize grain with aflatoxin is a chronic problem worldwide and particularly in the southeastern U.S. Aflatoxin is a mycotoxin produced by the fungus <i>Aspergillus flavus</i>, an opportunistic ear-rot pathogen of maize (<i>Zea mays</i>). Resistance to aflatoxin accumulation is heritable, and resistant germplasm-lines are available. These lines are derived from exotic genetic backgrounds and were released as sources of resistance, not parental inbreds. However, all current sources of resistance are quantitative, which complicates conventional efforts to introgress resistance alleles from unadapted but resistant donor lines to adapted but susceptible recipient lines. Mapping quantitative trait loci (QTL) and their linked markers enables targeted introgression of the desired alleles via marker-assisted selection. Quantitative trait loci were identified in two F2:3 mapping populations, derived from crossing resistant inbreds Mp715 and Mp717 to a common susceptible parent (Va35). The Mp715 x Va35 population was phenotyped for aflatoxin accumulation under artificial inoculation in replicated field trials at Mississippi State (MSU) in 2015 and 2016. The Mp717 x Va35 population was phenotyped at MSU and Lubbock, TX in 2016. Populations were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers and linkage maps created in JoinMap4. To locate QTL, linkage maps, genotypes, and phenotypes were analyzed jointly in QTL Cartographer 2.5 using composite interval mapping (CIM) and multiple interval mapping (MIM) procedures. Five QTL with the beneficial allele contributed by Mp715 were identified during CIM in bins 5.01, 6.06, 7.03 10.04 and 10.05. Three QTL with the beneficial allele contributed by Mp717 were identified during CIM in bins 3.07/3.08, 7.02/7.03, and 10.05. In both populations, QTL were identified with the beneficial allele contributed by Va35. Those QTL did not co-locate across populations but four of the six were on chromosome 1. Significant QTL effects from CIM were used as the initial model terms in MIM, where all QTL effects were fit simultaneously and their gene-action and epistatic interactions estimated. Advisors/Committee Members: W. Paul Williams (chair), Janice Dubien (committee member), Brian S. Baldwin (committee member), Marilyn Louise Warburton (committee member), Matthew D. Krakowsky (committee member).

Subjects/Keywords: maize; aflatoxin; quantitative trait loci (QTL)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Smith, J. S. (2017). Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717. (Doctoral Dissertation). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-06282017-082324/ ;

Chicago Manual of Style (16^th Edition):

Smith, Jesse Spencer. “Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717.” 2017. Doctoral Dissertation, Mississippi State University. Accessed January 19, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-06282017-082324/ ;.

MLA Handbook (7^th Edition):

Smith, Jesse Spencer. “Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717.” 2017. Web. 19 Jan 2021.

Vancouver:

Smith JS. Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717. [Internet] [Doctoral dissertation]. Mississippi State University; 2017. [cited 2021 Jan 19]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-06282017-082324/ ;.

Council of Science Editors:

Smith JS. Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbreds in Mp715 and Mp717. [Doctoral Dissertation]. Mississippi State University; 2017. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-06282017-082324/ ;

University of Alberta

7. Asif, Muhammad. Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement.

Degree: PhD, Department of Agricultural, Food, and Nutritional Science, 2014, University of Alberta

URL: https://era.library.ualberta.ca/files/02870x13k

► Efficiency is important in wheat breeding programs. A series of studies were conducted to determine genetic differentials, map genomic regions affecting various agronomic and quality… (more)

▼ Efficiency is important in wheat breeding programs. A series of studies were conducted to determine genetic differentials, map genomic regions affecting various agronomic and quality traits in conventional and organic management systems and to improve doubled haploid (DH) technology in spring wheat. A mapping population developed from a cross between Attila x CDC Go performed differently in the two management systems. Heritability estimates differed between systems for five of the nine traits including grain yield, tillers, plant height, kernel weight and grain protein content. Direct selection in each management system resulted in 50% or less lines selected in common for eight of the nine (except for flowering time) traits. Overall, we mapped 46 QTL for various agronomic and quality traits across organic and conventional management systems for three years. Most of these QTL were specific to the management systems; however, consistent QTL for grain yield, test weight, kernel weight and days to flowering were mapped in both systems on chromosomes 6A, 1B, 3A and 5B, respectively. These consistent QTL also behaved differently in both systems with respect to their phenotypic variation and additive effects leading to the conclusion that selection and testing of genotypes for production and quality traits should be done within environmental conditions which are comparable to where candidate lines are intended to perform. The technique of isolated microspore culture (IMC) is being used in many species to produce DH plants; however, low frequency of green plant production, microbial contamination and albinism limit its use in wheat breeding programs. A series of experiments were conducted to improve microspore embryogenesis. In four different experiments, induction medium (NPB-99+10% Ficoll) was supplemented with various organelle antioxidants, antibiotics and phytosulfokine alpha (PSK-α) along with optimization of induction medium osmolality. Glutathione (2 µM), PSK-α (10-7 M) and osmolality of induction medium at 350 mOsm kg-1 enhanced the efficiency of microspore embryogenesis in wheat and triticale. Cefotaxime at 100 and 50 mg L-1 also helped to control recurrent bacterial contamination in our laboratory, reduce the occurrence of albinism and substantially increase the formation of embryo/embryo like structures and green plant production in wheat and triticale, respectively. The systematic use of these treatments in IMC of wheat and triticale is recommended.

Subjects/Keywords: Quantitative trait loci; wheat; doubled haploid

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APA (6^th Edition):

Asif, M. (2014). Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/02870x13k

Chicago Manual of Style (16^th Edition):

Asif, Muhammad. “Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement.” 2014. Doctoral Dissertation, University of Alberta. Accessed January 19, 2021. https://era.library.ualberta.ca/files/02870x13k.

MLA Handbook (7^th Edition):

Asif, Muhammad. “Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement.” 2014. Web. 19 Jan 2021.

Vancouver:

Asif M. Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement. [Internet] [Doctoral dissertation]. University of Alberta; 2014. [cited 2021 Jan 19]. Available from: https://era.library.ualberta.ca/files/02870x13k.

Council of Science Editors:

Asif M. Quantitative trait loci (QTL) mapping and doubled haploid technology for spring wheat improvement. [Doctoral Dissertation]. University of Alberta; 2014. Available from: https://era.library.ualberta.ca/files/02870x13k

Colorado State University

8. Heiliger, Annie. Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments.

Degree: MS(M.S.), Soil and Crop Sciences, 2012, Colorado State University

URL: http://hdl.handle.net/10217/71637

► Rapeseed (Brassica napus L.) is an oilseed crop that has a variety of uses, including applications in industry as well as for food, feed, and… (more)

▼ Rapeseed (Brassica napus L.) is an oilseed crop that has a variety of uses, including applications in industry as well as for food, feed, and fuel. Improved B. napus cultivars with decreased levels of two disease-causing compounds are known commonly as canola or double-low cultivars, and are approved for human and animal consumption in the U.S., Canada, and Europe. Canola is currently grown in the northern U.S. and in several areas of Canada and Europe, but has potential to be grown in other areas of the U.S., including Colorado, either for biodiesel or to be sold in a canola commodity food oil market at the discretion of the seed producer. Additionally, the cake meal left after oil extraction has a high protein concentration and can be added as a supplement to animal feed. In recent years, water availability for crop production in the western U.S. has declined due to competition with non-agricultural water uses, and the increasing demands for water will likely increase with global climate change. Therefore, in order to be sustainable, crops grown in Colorado must be high-yielding with limited or no irrigation inputs, and consequently canola cultivars adapted to the semi-arid climate of Colorado and the U.S. High Plains will need to be drought tolerant. To provide information relevant to improving adaptation of canola to Colorado conditions, a study was conducted with the following objectives: 1) to evaluate yield, yield components, and days to flowering (DTF) in two doubled haploid (DH) canola mapping populations under rainfed and irrigated conditions; 2) to determine relationships among yield and yield components by analyzing trait correlations and to study trait inheritance patterns; 3) to determine areas of the B. napus genome that are implicated in yield and yield component traits under both rainfed and irrigated conditions by quantitative trait locus (QTL) analysis; and 4) to study the sensitivity of yield and yield component traits to drought stress by performing analysis of variance and by performing a QTL analysis on the difference in trait values from the rainfed and irrigated treatments. Two DH canola mapping populations were grown in side-by-side irrigated and rainfed treatments near Fort Collins, Colorado: population SE1 in 2010 (n=183) and population DHYB (n=150) in 2011. DTF, seed yield, and yield-related traits were measured in order to understand relationships among these traits under different water regimes, to study trait heritabilities, and to better understand genotype, treatment, and treatment by genotype interaction effects. QTL mapping was conducted separately for each treatment in each population using R-QTL software to detect additive and epistatic effects. Yield components that were studied included siliques per main inflorescence (SMI), seeds per silique (SS), and thousand seed weight (TSW). Seed coat color was also classified for the DHYB population. Analysis of variance revealed an influence of genotype (P<0.0001) on all traits in both populations, treatment effects on seed yield,… Advisors/Committee Members: Byrne, Patrick (advisor), Johnson, Jerry (committee member), McKay, John (committee member).

Subjects/Keywords: canola; seed yield; quantitative trait loci

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APA (6^th Edition):

Heiliger, A. (2012). Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments. (Masters Thesis). Colorado State University. Retrieved from http://hdl.handle.net/10217/71637

Chicago Manual of Style (16^th Edition):

Heiliger, Annie. “Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments.” 2012. Masters Thesis, Colorado State University. Accessed January 19, 2021. http://hdl.handle.net/10217/71637.

MLA Handbook (7^th Edition):

Heiliger, Annie. “Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments.” 2012. Web. 19 Jan 2021.

Vancouver:

Heiliger A. Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments. [Internet] [Masters thesis]. Colorado State University; 2012. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10217/71637.

Council of Science Editors:

Heiliger A. Quantitative trait locus mapping of yield and yield components in canola (Brassica napus L.) under irrigated and rainfed treatments. [Masters Thesis]. Colorado State University; 2012. Available from: http://hdl.handle.net/10217/71637

University of Edinburgh

9. Logeswaran, Sayanthan. Mapping quantitative trait loci in microbial populations.

Degree: PhD, 2011, University of Edinburgh

URL: http://hdl.handle.net/1842/4881

► Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny… (more)

Subjects/Keywords: 572.8; QTL; mapping; quantitative trait loci

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APA (6^th Edition):

Logeswaran, S. (2011). Mapping quantitative trait loci in microbial populations. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/4881

Chicago Manual of Style (16^th Edition):

Logeswaran, Sayanthan. “Mapping quantitative trait loci in microbial populations.” 2011. Doctoral Dissertation, University of Edinburgh. Accessed January 19, 2021. http://hdl.handle.net/1842/4881.

MLA Handbook (7^th Edition):

Logeswaran, Sayanthan. “Mapping quantitative trait loci in microbial populations.” 2011. Web. 19 Jan 2021.

Vancouver:

Logeswaran S. Mapping quantitative trait loci in microbial populations. [Internet] [Doctoral dissertation]. University of Edinburgh; 2011. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1842/4881.

Council of Science Editors:

Logeswaran S. Mapping quantitative trait loci in microbial populations. [Doctoral Dissertation]. University of Edinburgh; 2011. Available from: http://hdl.handle.net/1842/4881

University of Georgia

10. Kong, Wenqian. Genetic analysis of plant architecture in sorghum.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/28791

► Plant architecture is the three-dimensional organization of the plant body. Above-ground architecture is determined by the size, shape and positions of leaves, stems and flowers;… (more)

Subjects/Keywords: Vegetative branching; Rhizomes; Quantitative trait loci

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APA (6^th Edition):

Kong, W. (2014). Genetic analysis of plant architecture in sorghum. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/28791

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Kong, Wenqian. “Genetic analysis of plant architecture in sorghum.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/28791.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Kong, Wenqian. “Genetic analysis of plant architecture in sorghum.” 2014. Web. 19 Jan 2021.

Vancouver:

Kong W. Genetic analysis of plant architecture in sorghum. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/28791.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Kong W. Genetic analysis of plant architecture in sorghum. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/28791

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Tennessee – Knoxville

11. Cunicelli, Mia Justina. Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping.

Degree: 2020, University of Tennessee – Knoxville

URL: https://trace.tennessee.edu/utk_graddiss/5906

► Soybean [Glycine max (L.) Merr.] is the world’s leading source of vegetable oil and high quality protein meal. However, soybean protein and oil and protein… (more)

▼ Soybean [Glycine max (L.) Merr.] is the world’s leading source of vegetable oil and high quality protein meal. However, soybean protein and oil and protein and yield are negatively genetically correlated. Agronomic and seed quality traits of soybean lines are important because they lead to increased soybean value. Molecular markers have played and will continue to play a major role in the genetic characterization and improvement of soybeans. Quantitative trait loci (QTL) are regions within a genome that contain genes that influence particular quantitative traits. Identification of QTLs through phenotypic evaluation only is not possible; therefore, to locate, identify, and characterize these regions within a genome, DNA or molecular markers are used. A major objective in soybean breeding is to develop high yielding cultivars. Unfortunately, soybean seed yield, as well as protein and oil content, are complex quantitative traits to characterize from the phenotypic and genotypic perspectives. The objectives of this study are to detect soybean genomic regions that increase protein content, while maintaining oil content and seed yield, and to successfully identify soybean QTL associated with these seed quality traits. To achieve these objectives, a population of 138 F8:10 [eighth filial generation advanced to the tenth filial generation] and 138 F8:11 [eighth filial generation advanced to the eleventh filial generation] recombinant inbred lines (RIL) of soybean were created from a cross between 5601T and U99-310255. These RILs were grown in a replicated six environment field trial across the state of Tennessee in the 2017 and 2018 field seasons. Data from the 138 RIL were used to perform QTL detection analyses in search of significant genomic regions affecting soybean seed protein, oil, and yield. A total of 21 QTL were successfully identified through QTL analysis of the population. Of these, there were three for yield, two for protein, five for oil, one for methionine, two for threonine, five for maturity, one for lodging, and two for meal. Knowledge of their locations and flanking markers will aid in marker assisted selection for plant breeders. This will lead to a more valuable soybean for farmers, processors, and animal nutritionists.

Subjects/Keywords: Soybean; Protein; Oil; Yield; Quantitative trait loci

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Cunicelli, M. J. (2020). Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/5906

Chicago Manual of Style (16^th Edition):

Cunicelli, Mia Justina. “Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping.” 2020. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed January 19, 2021. https://trace.tennessee.edu/utk_graddiss/5906.

MLA Handbook (7^th Edition):

Cunicelli, Mia Justina. “Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping.” 2020. Web. 19 Jan 2021.

Vancouver:

Cunicelli MJ. Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2020. [cited 2021 Jan 19]. Available from: https://trace.tennessee.edu/utk_graddiss/5906.

Council of Science Editors:

Cunicelli MJ. Mapping and Identification of QTL Associated with Soybean Seed Protein, Oil, and Yield in 5601T × U99-310255 RIL Population Using SNP Genotyping. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2020. Available from: https://trace.tennessee.edu/utk_graddiss/5906

Texas A&M University

12. Kim, Seung Kyum. Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training.

Degree: PhD, Kinesiology, 2015, Texas A&M University

URL: http://hdl.handle.net/1969.1/156421

► Endothelial dysfunction is a fundamental component of cardiovascular disease. Exercise training is known to prevent/improve endothelial dysfunction. However, the genetic basis for endothelial function is… (more)

▼ Endothelial dysfunction is a fundamental component of cardiovascular disease. Exercise training is known to prevent/improve endothelial dysfunction. However, the genetic basis for endothelial function is yet to be fully elucidated and the genetic contribution to endothelial responses to exercise training is largely unknown. The purposes of this research were 1) to identify quantitative trait loci (QTL)/candidate genes residing in the QTL responsible for intrinsic endothelial function and 2) to determine the interaction between genetic background and training intensity on the endothelial adaptations to exercise training. In the first study, vasoreactivity was assessed in aortic rings of male mice from 27 inbred strains. Strain-dependent differences were found for vasoreactivity including responses to ACh. Genome-wide association study for responses to ACh revealed four significant and several suggestive QTL, most of which are regions of shared synteny for cardiovascular traits in rats and/or humans. In the second study, a strain survey for the effect of traditional exercise training on vasoreactivity was performed in aortic rings of male mice from 20 inbred strains. Traditional exercise training had subtle effects on vasoreactivity including responses to ACh. Based on the strain survey, four inbred mouse strains (129S1, B6, SJL, and NON) were chosen to examine endothelial responses to two different training intensities [high (HIT) vs. moderate intensity (MOD)]. There was a significant interaction between mouse strain and training intensity on responses to ACh after exercise training. The transcriptional activation of endothelial genes was also influenced by the interaction. There was little overlap between genes altered by HIT and MOD. HIT was associated with pathways for inflammatory responses, while NON MOD genes showed enrichment for vessel growth pathways. In conclusion, the present findings provide strong evidence that genetic background influences endothelial function and its responses to exercise training. Several QTL/candidate genes are suggested as new targets for elucidating the genetic basis of intrinsic endothelial function. Exercise training has non-uniform effects on endothelial function and transcriptional activation of endothelial genes depending on the interaction between genetic background and training intensity. Advisors/Committee Members: Massett, Michael P (advisor), Woodman, Christopher R (committee member), Riggs, Penny K (committee member), Lightfoot, J Timothy (committee member).

Subjects/Keywords: Endothelial function; Genome-wide association study; Quantitative trait loci; Candidate genes; Exercise training; Training Intensity; Gene expression profiling; Pathway analysis

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kim, S. K. (2015). Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/156421

Chicago Manual of Style (16^th Edition):

Kim, Seung Kyum. “Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training.” 2015. Doctoral Dissertation, Texas A&M University. Accessed January 19, 2021. http://hdl.handle.net/1969.1/156421.

MLA Handbook (7^th Edition):

Kim, Seung Kyum. “Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training.” 2015. Web. 19 Jan 2021.

Vancouver:

Kim SK. Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training. [Internet] [Doctoral dissertation]. Texas A&M University; 2015. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1969.1/156421.

Council of Science Editors:

Kim SK. Genetic Regulation of Intrinsic Endothelial Function and Endothelial Responses to Exercise Training. [Doctoral Dissertation]. Texas A&M University; 2015. Available from: http://hdl.handle.net/1969.1/156421

Washington State University

13. [No author]. MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT .

Degree: 2019, Washington State University

URL: http://hdl.handle.net/2376/16783

► Winter conditions necessitate tolerance of snow mold and freezing cold among winter wheat plants. These traits involve numerous quantitative trait loci (QTL), environmental interactions, and… (more)

▼ Winter conditions necessitate tolerance of snow mold and freezing cold among winter wheat plants. These traits involve numerous quantitative trait loci (QTL), environmental interactions, and mechanisms such as carbohydrate tolerance and gene regulation, that complicate efforts to select for improved tolerance. To identify molecular markers associated with these traits, QTL analysis was performed using a population of 155 F2:5 recombinant inbred lines (RILs) from a cross between soft white wheat cultivars 'Finch' and 'Eltan', which differ in their tolerance to each of these stressors. Two novel QTL for freezing tolerance were identified on chromosomes 5A and 4B, one QTL for snow mold tolerance was identified on chromosome 6B, and a QTL conferring tolerance both mold and cold was detected on 5A and was determined to co-locate with the Fr-A2 (Frost-Resistance A2) locus. Twenty-six additional QTL for snow mold tolerance were detected in a RIL population from a cross between 'Xerpha' and 'Münstertaler'. This RIL population was also compared to a marker-assisted selection subpopulation, derived from the same cross, and was used for genomic selection to investigate the effectiveness of these selection tools. Although both methods failed to improve snow mold tolerance in the Xerpha-Münstertaler population, genomic prediction had good accuracy in the Finch-Eltan RIL population. To investigate the contribution of carbohydrate accumulation to snow mold and cold tolerance in the Finch-Eltan RIL population, eight lines, representing four combinations of tolerance, were analyzed for carbohydrate content over the cold-acclimation period. The lack of significant differences in carbohydrate content between these categories suggests that other traits are responsible for the observed segregation. RNA-seq was performed to investigate differential gene expression, which could account for the segregation. The knowledge derived from this study will facilitate efforts to breed for tolerance to snow mold and freezing cold by improving the understanding of the quantitative nature of these traits and enabling better leveraging of selection methods. Advisors/Committee Members: Carter, Arron H (advisor).

Subjects/Keywords: Plant sciences; Agriculture; Carbohydrate accumulation; Differential Gene Expression; Freezing tolerance; Quantitative trait loci; Snow mold tolerance; Winter Wheat

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

author], [. (2019). MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT . (Thesis). Washington State University. Retrieved from http://hdl.handle.net/2376/16783

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

author], [No. “MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT .” 2019. Thesis, Washington State University. Accessed January 19, 2021. http://hdl.handle.net/2376/16783.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

author], [No. “MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT .” 2019. Web. 19 Jan 2021.

Vancouver:

author] [. MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT . [Internet] [Thesis]. Washington State University; 2019. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/2376/16783.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

author] [. MOLD & COLD: THE SOLUTION IS SWEET IN WINTER WHEAT . [Thesis]. Washington State University; 2019. Available from: http://hdl.handle.net/2376/16783

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

14. Schwartzentruber, Jeremy Andrew. Using molecular QTLs to identify cell types and causal variants for complex traits.

Degree: PhD, 2018, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/271308

► Genetic associations have been discovered for many human complex traits, and yet for most associated loci the causal variants and molecular mechanisms remain unknown. Studies… (more)

▼ Genetic associations have been discovered for many human complex traits, and yet for most associated loci the causal variants and molecular mechanisms remain unknown. Studies mapping quantitative trait loci (QTLs) for molecular phenotypes, such as gene expression, RNA splicing, and chromatin accessibility, provide rich data that can link variant effects in specific cell types with complex traits. These genetic effects can also now be modeled in vitro by differentiating human induced pluripotent stem cells (iPSCs) into specific cell types, including inaccessible cell types such as those of the brain. In this thesis, I explore a range of approaches for using QTLs to identify causal variants and to link these with molecular functions and complex traits. In Chapter 2, I describe QTL mapping in 123 sensory neuronal cell lines differentiated from human iPSCs. I observed that gene expression was highly variable across iPSC-derived neuronal cultures in specific gene categories, and that a portion of this variability was explained by commonly used iPSC culture conditions, which influenced differentiation efficiency. A number of QTLs overlapped with common disease associations; however, using simulations I showed that identifying causal regulatory variants with a recall-by- genotype approach in iPSC-derived neurons is likely to require large sample sizes, even for variants with moderately large effect sizes. In Chapter 3, I developed a computational model that uses publicly available gene expression QTL data, along with molecular annotations, to generate cell type-specific probability of regulatory function (PRF) scores for each variant. I found that predictive power was improved when the model was modified to use the quantitative value of annotations. PRF scores outperformed other genome-wide scores, including CADD and GWAVA, in identifying likely causal eQTL variants. In Chapter 4, I used PRF scores to identify relevant cell types and to fine map potential causal variants using summary association statistics in six complex traits. By examining individual loci in detail, I showed how the enrichments contributing to a high PRF score are transparent, which can help to distinguish plausible causal variant predictions from model misspecification.

Subjects/Keywords: iPSCs; gwas; genome-wide association studies; eQTLs; expression quantitative trait loci; sensory neurons; chromatin accessibility; gene regulation

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Schwartzentruber, J. A. (2018). Using molecular QTLs to identify cell types and causal variants for complex traits. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/271308

Chicago Manual of Style (16^th Edition):

Schwartzentruber, Jeremy Andrew. “Using molecular QTLs to identify cell types and causal variants for complex traits.” 2018. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://www.repository.cam.ac.uk/handle/1810/271308.

MLA Handbook (7^th Edition):

Schwartzentruber, Jeremy Andrew. “Using molecular QTLs to identify cell types and causal variants for complex traits.” 2018. Web. 19 Jan 2021.

Vancouver:

Schwartzentruber JA. Using molecular QTLs to identify cell types and causal variants for complex traits. [Internet] [Doctoral dissertation]. University of Cambridge; 2018. [cited 2021 Jan 19]. Available from: https://www.repository.cam.ac.uk/handle/1810/271308.

Council of Science Editors:

Schwartzentruber JA. Using molecular QTLs to identify cell types and causal variants for complex traits. [Doctoral Dissertation]. University of Cambridge; 2018. Available from: https://www.repository.cam.ac.uk/handle/1810/271308

15. Peters, Luciana Carla Oliva Marques. Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente.

Degree: PhD, Imunologia, 2009, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/42/42133/tde-08072009-122546/ ;

►

Camundongos AIRmax e AIRmin homozigotos para os alelos R e S do gene Slc11a1 foram avaliados para susceptibilidade à artrite induzida por pristane (PIA). A… (more)

▼

Camundongos AIRmax e AIRmin homozigotos para os alelos R e S do gene Slc11a1 foram avaliados para susceptibilidade à artrite induzida por pristane (PIA). A presença do alelo S aumentou a incidência e a gravidade nos AIRmax, sugerindo que o gene Slc11a1, ou outro próximo, esteja interagindo com os loci de resposta inflamatória na modulação de PIA. Para identificar estes loci foram realizados estudos de associação genótipo-fenótipo e de expressão gênica global. Os RNAs das patas dos animais foram isolados após 180 dias da indução por pristane. As análises de expressão gênica global foram realizadas usando a plataforma Codelink (36k genes), cujos resultados foram validados por PCR em tempo real. Os estudos de associação foram realizados através da análise de polimorfismo de microssatélites pelo programa MapManager. Foram identificadas duas regiões nos cromossomos 1 e 11. Um número grande de genes diferencialmente expressos foi verificado nos animais AIRmax SS cujos temas biológicos significativamente sobre-representados foram a resposta inflamatória e quimiotaxia. Os camundongos AIRmax SS também possuem uma ativação maior dos genes Ccl3, Ccl7, C3ar1, Il10, Stat3, Tirap, Trem 1, Trem 3, Mefv, Ptx3, Chi3l3 e Kras. Alguns desses genes co-localizam com regiões previamente mapeadas nos cromossomos 1 e 11.

AIRmax and AIRmin mice homozygous for Slc11a1 R and S allele were evaluated for pristane-induced arthritis (PIA) susceptibility. The presence of S allele increased the incidence and the arthritis severity in ARmax mice, suggesting that Slc11a1 or other closed-linked gene interacts with inflammatory loci to modulate PIA. In order to identify inflammatory modifier loci modulating experimental arthritis development, genotype-phenotype association studies and global gene expression analyses were performed. Mice received i.p. injections of pristane and the paw RNAs were isolated at day 180. Global gene expression analysis was performed on Codelink bioarrays (36k genes) and validated by real time PCR. The microsatellite polymorphism analyses were performed using MapManager program. Two regions on chromosomes 1 and 11 were identified. Higher number of differentially-expressed genes were detected in AIRmax SS subline, which significant over-represented biological themes were related to inflammatory response and chemotaxis. Susceptible AIRmax SS mice also display high up-regulation of Ccl3, Ccl7, C3ar1, Il10, Stat3, Tirap, Trem 1, Trem 3, Mefv, Ptx3, Chi3l3 e Kras genes. Some of them co-localize with previously identified regions mapped on chromosomes 1 and 11.

Advisors/Committee Members: Franco, Marcelo de.

Subjects/Keywords: Loci de traço quantitativo; Arthritis; Artrite; Camundongos; Expressão gênica; Gene expression; Immunology; Imunologia; Inflamação; Inflammation; Mice; Microarray and qPCR; Microarray e qPCR; Quantitative trait Loci; Seleção genética

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APA (6^th Edition):

Peters, L. C. O. M. (2009). Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/42/42133/tde-08072009-122546/ ;

Chicago Manual of Style (16^th Edition):

Peters, Luciana Carla Oliva Marques. “Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente.” 2009. Doctoral Dissertation, University of São Paulo. Accessed January 19, 2021. http://www.teses.usp.br/teses/disponiveis/42/42133/tde-08072009-122546/ ;.

MLA Handbook (7^th Edition):

Peters, Luciana Carla Oliva Marques. “Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente.” 2009. Web. 19 Jan 2021.

Vancouver:

Peters LCOM. Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente. [Internet] [Doctoral dissertation]. University of São Paulo; 2009. [cited 2021 Jan 19]. Available from: http://www.teses.usp.br/teses/disponiveis/42/42133/tde-08072009-122546/ ;.

Council of Science Editors:

Peters LCOM. Identificação dos loci reguladores da intensidade da resposta inflamatória aguda envolvidos no desenvolvimento da artrite induzida por pristane em camundongos selecionados geneticamente. [Doctoral Dissertation]. University of São Paulo; 2009. Available from: http://www.teses.usp.br/teses/disponiveis/42/42133/tde-08072009-122546/ ;

North Carolina State University

16. Silva, Luciano Da Costa E. Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses.

Degree: PhD, Statistics, 2010, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/4217

► Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. Most of… (more)

▼ Tremendous progress has been made in recent years on developing statistical methods for mapping quantitative trait loci (QTL) from crosses of inbred lines. Most of the recent research is focused on strategies for mapping multiple QTL and associated model selection procedures and criterion. In Chapter 1, we review the progress of research on QTL mapping on one and multiple trait by maximum likelihood and Bayesian methods. Although in many instances multiple trait are measured in the same subject, single traits analyses have been the main stream for the purpose of QTL identiÃ¯Â¬Â cation. However, single trait analyses do not take advantage of correlation between traits. Multiple trait analysis allows an investigator to assess the pattern of action of QTL on multiple trait, such as, testing the hypothesis of existence of pleiotropic QTL versus the hypothesis of close linked QTL aÃ¯Â¬â‚¬ecting multiple trait, and testing the hypothesis of QTL by environment interaction. In Chapter 2, we proposed a statistical model for mapping multiple QTL aÃ¯Â¬â‚¬ecting multiple trait, the multiple trait multiple interval mapping (MTMIM) model. We also developed a score-based threshold for assessing signiÃ¯Â¬Â cance level of QTL eÃ¯Â¬â‚¬ects on multiple trait. Our MTMIM model provides a comprehensive framework for QTL inference in multiple trait, in which the score-based threshold is built in as an essential and elegant tool for computing the signiÃ¯Â¬Â cance level of eÃ¯Â¬â‚¬ects of putative QTL in the genome-wide scan, therefore, allowing us to build a set of models containing multiple QTL. In Chapter 3, we empirically showed that the score-based threshold maintains the false discovery rate within acceptable levels and the multiple trait analysis can bring insights into the analysis of data for the purpose of QTL identiÃ¯Â¬Â cation. The analysis of data from an experiment with Drosophila showed the potential of our MTMIM model in delivering complementary information regarding the genetic architecture of complex traits, such as, estimating QTL eÃ¯Â¬â‚¬ects on a set of traits simultaneously, testing for the presence of pleiotropic QTL, and estimating the genotypic covariance between traits. A generalized expectation maximization Newton-Raphson (GEM-NR) algorithm for maximizing the likelihood function and estimating parameters in the MTMIM model was compared to the expectation-conditional maximization (ECM) algorithm. Empirical comparison showed that GEM-NR speeded up the convergence of likelihood function considerably when compared to the ECM algorithm, while still delivering stable estimates of parameters. In Chapter 4, we proposed analytical formulae to predict the length of conÃ¯Â¬Â dence interval for position of QTL and to predict shape of the LRT around the position of QTL in highly saturate linkage maps and multiple trait analysis using large sample theory. Our results generalize the results of Visscher and Goddard (2004) and they can be used to predict the length of conÃ¯Â¬Â dence interval for position of QTL with a hypothesized… Advisors/Committee Members: Zhao-Bang Zeng, Committee Chair (advisor), Howard D. Bondell, Committee Co-Chair (advisor), Trudy F.C. Mackay, Committee Member (advisor), Sujit K. Ghosh, Committee Member (advisor).

Subjects/Keywords: Quantitative trait loci; mapping; statistical method; multiple trait; inbred lines

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Silva, L. D. C. E. (2010). Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/4217

Chicago Manual of Style (16^th Edition):

Silva, Luciano Da Costa E. “Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses.” 2010. Doctoral Dissertation, North Carolina State University. Accessed January 19, 2021. http://www.lib.ncsu.edu/resolver/1840.16/4217.

MLA Handbook (7^th Edition):

Silva, Luciano Da Costa E. “Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses.” 2010. Web. 19 Jan 2021.

Vancouver:

Silva LDCE. Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses. [Internet] [Doctoral dissertation]. North Carolina State University; 2010. [cited 2021 Jan 19]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/4217.

Council of Science Editors:

Silva LDCE. Multiple Trait Multiple Interval Mapping of Quantitative Trait Loci from Inbred Line Crosses. [Doctoral Dissertation]. North Carolina State University; 2010. Available from: http://www.lib.ncsu.edu/resolver/1840.16/4217

17. Kocmarek, Andrea. Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci.

Degree: PhD, Department of Integrative Biology, 2014, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8283

► To increase our understanding of the genetics controlling growth in rainbow trout, gene expression in the liver and white muscle of large and small rainbow… (more)

▼ To increase our understanding of the genetics controlling growth in rainbow trout, gene expression in the liver and white muscle of large and small rainbow trout was investigated using a 44K gene microarray. Three half-sibling families were created from genotypically normal September and December spawning males (Sept. and Dec. XY) and a September spawning neomale (Sept. XX). A quantitative trait loci (QTL) study with 11 linkage groups previously identified as containing growth QTL was conducted on the same families. The Dec. XY fish were larger than the Sept. XY fish and seasonal differences in gene expression were detected in the white muscle. Changes in thermal growth coefficients indicate that at the time of sampling the Dec. fish were entering a period of increased growth and the Sept. fish were entering a period of decreased growth. In the muscle genes were consistently expressed across seasons, but few genes were expressed across seasons in liver, indicating that muscle-specific genes are better predictors of growth differences. These data also indicate that sampling season needs to be considered when interpreting gene expression studies. No significant differences in the average weight or length and similar gene expression profiles were observed when the Sept XX male’s all-female offspring were compared to the mixed-sex offspring of the Sept. XY male. Some expression differences were seen in the muscle of the small all-female and mixed sex offspring. Weight and length QTL were detected on 6 of the 11 linkage groups tested in the three families. These QTL co-localized with a significant proportion of differentially expressed genes. In the mixed sex offspring of the Sept. XY and Dec. XY male, the genes co-localizing to the detected QTL were primarily expressed in the muscle of the large fish and were associated with energy usage and the stress response. Conversely, in the all-female fish the majority of genes co-localizing to QTL regions were associated with increased energy usage in the liver of the small fish. This suggests different sets of genes may be controlling growth in mixed sex and all-female fish. Advisors/Committee Members: Danzmann, Roy (advisor), Ferguson, Moira (advisor).

Subjects/Keywords: Rainbow Trout; Growth; Gene Expression; Quantitative Trait Loci

…chromosomal regions (quantitative trait loci, QTL), associated with growth related traits… …MM (2013) Comparative analysis of genetic parameters and quantitative trait loci… …Merilä J (2013) Quantitative trait loci for growth and body size in the nine-spined… …Moghadam HK, Sakhrani D, Danzmann RG (2010) Growth-related quantitative trait loci in… …heritability values [16-18] and chromosomal regions (quantitative trait loci, QTL)…

10 more images…

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kocmarek, A. (2014). Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8283

Chicago Manual of Style (16^th Edition):

Kocmarek, Andrea. “Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci.” 2014. Doctoral Dissertation, University of Guelph. Accessed January 19, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8283.

MLA Handbook (7^th Edition):

Kocmarek, Andrea. “Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci.” 2014. Web. 19 Jan 2021.

Vancouver:

Kocmarek A. Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci. [Internet] [Doctoral dissertation]. University of Guelph; 2014. [cited 2021 Jan 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8283.

Council of Science Editors:

Kocmarek A. Differential Expression of Growth Genes in the Liver and White Muscle of Small and Large Rainbow Trout (Oncorhynchus mykiss) Produced in Two Seasons and Co-localization with Quantitative Trait Loci. [Doctoral Dissertation]. University of Guelph; 2014. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8283

University of Cambridge

18. Glinos, Dafni Anna. Characterising the gene regulatory landscape of CD4+ T cells.

Degree: PhD, 2019, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/292438

► Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease… (more)

▼ Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease are not well understood. Immune susceptibility loci identified by genome wide association studies (GWAS) overlap with active regulatory elements in CD4+ T cells, and particularly in regulatory T cells (Tregs). CD4+ T cells are the orchestrators of the adaptive immune response and their dysfunction has been associated with immune-mediated disorders through uncontrolled activation and resistance to downregulation, which is usually mediated by Tregs. T cell activation requires the combination of T cell receptor (TCR) recognition of an antigen and CD28 co-stimulation. The role of CD28 co-stimulation requirement in the activation of different T cell subsets has been understudied. Here, I assessed the role of immune disease variants in modulating pathways underlying T cell activation and Treg function. For that, I activated CD4+ T cells using different intensities of CD28 and TCR signals, followed by genome-wide transcriptome and chromatin profiling of naive and memory cells. I observed that CD28 plays a critical role in the expression of genes involved in effector functions, cell cycle regulation in memory T cells and in disease susceptibility. I profiled the gene expression regulatory landscape in Tregs using a combination of genomic assays. Due to the scarce Treg numbers in peripheral blood I first optimised the ChIPmentation (ChM) sequencing protocol to profile H3K4me3 and H3K27ac histone modifications in Tregs. I combined it with chromatin accessibility and gene expression profiling in resting and stimulated Tregs from ten donors. I observed cases of alternative transcription, such as alternative splicing and promoter, induced by stimulation, which could be predicted by changes in the chromatin landscape. Finally, I assessed how genetic variability impacts the function of Tregs and how this can lead to autoimmunity. I carried a quantitative trait locus (QTL) mapping using RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChM-seq data from Tregs isolated from 100 individuals. Additionally, I processed publicly available data from naive T cells to distinguish the Treg specific effects from generic CD4+ T cell signals. I recapitulated known colocalisations between QTLs and immune GWAS loci, and identified previously unknown Treg specific colocalisations. My findings highlight the value of carrying QTL studies in rare immune cell types relevant to the disease.

Subjects/Keywords: regulatory T cell; immune system; transcriptomics; quantitative trait loci; GWAS; autoimmunity; CD4 T cell; CD28 costimulation; ChiP-seq; ATAC-seq; differential gene expression; humans

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Glinos, D. A. (2019). Characterising the gene regulatory landscape of CD4+ T cells. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/292438

Chicago Manual of Style (16^th Edition):

Glinos, Dafni Anna. “Characterising the gene regulatory landscape of CD4+ T cells.” 2019. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://www.repository.cam.ac.uk/handle/1810/292438.

MLA Handbook (7^th Edition):

Glinos, Dafni Anna. “Characterising the gene regulatory landscape of CD4+ T cells.” 2019. Web. 19 Jan 2021.

Vancouver:

Glinos DA. Characterising the gene regulatory landscape of CD4+ T cells. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Jan 19]. Available from: https://www.repository.cam.ac.uk/handle/1810/292438.

Council of Science Editors:

Glinos DA. Characterising the gene regulatory landscape of CD4+ T cells. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://www.repository.cam.ac.uk/handle/1810/292438

University of Cambridge

19. Kölling, Nils. Quantitative genetics of gene expression during fruit fly development.

Degree: PhD, 2016, University of Cambridge

URL: https://www.repository.cam.ac.uk/handle/1810/256090https://www.repository.cam.ac.uk/bitstream/1810/256090/5/Kolling_2015_PhD.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/7/Kolling_2015_Agreement.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/6/Kolling_2015_PhD.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/256090/8/Kolling_2015_Agreement.pdf.jpg

► Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes,… (more)

▼ Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also been applied to highthroughput RNA sequencing (RNA-seq) data in order to find loci associated with different levels of gene expression, called expression quantitative trait loci (eQTL). Because of the large amount of data that is required for such high-resolution eQTL studies, most of them have so far been carried out in humans, where the cost of data collection could be justified by a possible future impact in human health. However, due to the rapidly falling price of high-throughput sequencing it is now also becoming feasible to perform high-resolution eQTL studies in higher model organisms. This enables the study of gene regulation in biological contexts that have so far been beyond our reach for practical or ethical reasons, such as early embryonic development. Taking advantage of these new possibilities, we performed a high-resolution eQTL study on 80 inbred fruit fly lines from the Drosophila Genetic Reference Panel, which represent naturally occurring genetic variation in a wild population of Drosophila melanogaster. Using a 3′ Tag RNA-sequencing protocol we were able to estimate the level of expression both of genes as well as of different 3′ isoforms of the same gene. We estimated these expression levels for each line at three different stages of embryonic development, allowing us to not only improve our understanding of D. melanogaster gene regulation in general, but also investigate how gene regulation changes during development. In this thesis, I describe the processing of 3′ Tag-Seq data into both 3′ isoform expression levels and overall gene expression levels. Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene categories enriched or depleted in eQTLs. Finally, I extend the proximal eQTL calling approach to distal variants to find gene regulatory mechanisms acting in trans. Taken together, this thesis describes the design, challenges and results of performing a multivariate eQTL study in a higher model organism and provides new insights into gene regulation in D. melanogaster during embryonic development.

Subjects/Keywords: Research Subject Categories::NATURAL SCIENCES::Biology::Cell and molecular biology; genome-wide association studies; GWAS; genome; phenotypes; genetic variation; expression quantitative trait loci; eQTL; gene regulation; RNA sequencing

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kölling, N. (2016). Quantitative genetics of gene expression during fruit fly development. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/256090https://www.repository.cam.ac.uk/bitstream/1810/256090/5/Kolling_2015_PhD.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/7/Kolling_2015_Agreement.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/6/Kolling_2015_PhD.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/256090/8/Kolling_2015_Agreement.pdf.jpg

Chicago Manual of Style (16^th Edition):

Kölling, Nils. “Quantitative genetics of gene expression during fruit fly development.” 2016. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://www.repository.cam.ac.uk/handle/1810/256090https://www.repository.cam.ac.uk/bitstream/1810/256090/5/Kolling_2015_PhD.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/7/Kolling_2015_Agreement.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/6/Kolling_2015_PhD.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/256090/8/Kolling_2015_Agreement.pdf.jpg.

MLA Handbook (7^th Edition):

Kölling, Nils. “Quantitative genetics of gene expression during fruit fly development.” 2016. Web. 19 Jan 2021.

Vancouver:

Kölling N. Quantitative genetics of gene expression during fruit fly development. [Internet] [Doctoral dissertation]. University of Cambridge; 2016. [cited 2021 Jan 19]. Available from: https://www.repository.cam.ac.uk/handle/1810/256090https://www.repository.cam.ac.uk/bitstream/1810/256090/5/Kolling_2015_PhD.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/7/Kolling_2015_Agreement.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/6/Kolling_2015_PhD.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/256090/8/Kolling_2015_Agreement.pdf.jpg.

Council of Science Editors:

Kölling N. Quantitative genetics of gene expression during fruit fly development. [Doctoral Dissertation]. University of Cambridge; 2016. Available from: https://www.repository.cam.ac.uk/handle/1810/256090https://www.repository.cam.ac.uk/bitstream/1810/256090/5/Kolling_2015_PhD.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/7/Kolling_2015_Agreement.pdf.txt ; https://www.repository.cam.ac.uk/bitstream/1810/256090/6/Kolling_2015_PhD.pdf.jpg ; https://www.repository.cam.ac.uk/bitstream/1810/256090/8/Kolling_2015_Agreement.pdf.jpg

Duke University

20. Acharya, Chaitanya Ramanuj. Efficient analysis of complex, multimodal genomic data .

Degree: 2016, Duke University

URL: http://hdl.handle.net/10161/13390

► Our primary goal is to better understand complex diseases using statistically disciplined approaches. As multi-modal data is streaming out of consortium projects like Genotype-Tissue… (more)

▼ Our primary goal is to better understand complex diseases using statistically disciplined approaches. As multi-modal data is streaming out of consortium projects like Genotype-Tissue Expression (GTEx) project, which aims at collecting samples from various tissue sites in order to understand tissue-specific gene regulation, new approaches are needed that can efficiently model groups of data with minimal loss of power. For example, GTEx project delivers RNA-Seq, Microarray gene expression and genotype data (SNP Arrays) from a vast number of tissues in a given individual subject. In order to analyze this type of multi-level (hierarchical) multi-modal data, we proposed a series of efficient-score based tests or score tests and leveraged groups of tissues or gene isoforms in order map genomic biomarkers. We model group-specific variability as a random effect within a mixed effects model framework. In one instance, we proposed a score-test based approach to map expression quantitative trait loci (eQTL) across multiple-tissues. In order to do that we jointly model all the tissues and make use of all the information available to maximize the power of eQTL mapping and investigate an overall shift in the gene expression combined with tissue-specific effects due to genetic variants. In the second instance, we showed the flexibility of our model framework by expanding it to include tissue-specific epigenetic data (DNA methylation) and map eQTL by leveraging both tissues and methylation. Finally, we also showed that our methods are applicable on different data type such as whole transcriptome expression data, which is designed to analyze genomic events such alternative gene splicing. In order to accomplish this, we proposed two different models that exploit gene expression data of all available gene-isoforms within a gene to map biomarkers of interest (either genes or gene-sets) in paired early-stage breast tumor samples before and after treatment with external beam radiation. Our efficient score-based approaches have very distinct advantages. They have a computational edge over existing methods because they do not need parameter estimation under the alternative hypothesis. As a result, model parameters only have to be estimated once per genome, significantly decreasing computation time. Also, the efficient score is the locally most powerful test and is guaranteed a theoretical optimality over all other approaches in a neighborhood of the null hypothesis. This theoretical performance is born out in extensive simulation studies which show that our approaches consistently outperform existing methods both in statistical power and computational speed. We applied our methods to publicly available datasets. It is important to note that all of our methods also accommodate the analysis of next-generation sequencing data. Advisors/Committee Members: Allen, Andrew S (advisor).

Subjects/Keywords: Bioinformatics; Genetics; Biostatistics; DNA methylation; efficient score test; expression quantitative trait loci; genome wide study; multimodal genomic data; next-generation sequencing data

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Acharya, C. R. (2016). Efficient analysis of complex, multimodal genomic data . (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/13390

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Acharya, Chaitanya Ramanuj. “Efficient analysis of complex, multimodal genomic data .” 2016. Thesis, Duke University. Accessed January 19, 2021. http://hdl.handle.net/10161/13390.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Acharya, Chaitanya Ramanuj. “Efficient analysis of complex, multimodal genomic data .” 2016. Web. 19 Jan 2021.

Vancouver:

Acharya CR. Efficient analysis of complex, multimodal genomic data . [Internet] [Thesis]. Duke University; 2016. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10161/13390.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Acharya CR. Efficient analysis of complex, multimodal genomic data . [Thesis]. Duke University; 2016. Available from: http://hdl.handle.net/10161/13390

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge

21. Kölling, Nils. Quantitative genetics of gene expression during fruit fly development.

Degree: PhD, 2016, University of Cambridge

URL: https://doi.org/10.17863/CAM.26 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.685469

► Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes,… (more)

▼ Over the last ten years, genome-wide association studies (GWAS) have been used to identify genetic variants associated with many diseases as well as quantitative phenotypes, by exploiting naturally occurring genetic variation in large cohorts of individuals. More recently, the GWAS approach has also been applied to highthroughput RNA sequencing (RNA-seq) data in order to find loci associated with different levels of gene expression, called expression quantitative trait loci (eQTL). Because of the large amount of data that is required for such high-resolution eQTL studies, most of them have so far been carried out in humans, where the cost of data collection could be justified by a possible future impact in human health. However, due to the rapidly falling price of high-throughput sequencing it is now also becoming feasible to perform high-resolution eQTL studies in higher model organisms. This enables the study of gene regulation in biological contexts that have so far been beyond our reach for practical or ethical reasons, such as early embryonic development. Taking advantage of these new possibilities, we performed a high-resolution eQTL study on 80 inbred fruit fly lines from the Drosophila Genetic Reference Panel, which represent naturally occurring genetic variation in a wild population of Drosophila melanogaster. Using a 3′ Tag RNA-sequencing protocol we were able to estimate the level of expression both of genes as well as of different 3′ isoforms of the same gene. We estimated these expression levels for each line at three different stages of embryonic development, allowing us to not only improve our understanding of D. melanogaster gene regulation in general, but also investigate how gene regulation changes during development. In this thesis, I describe the processing of 3′ Tag-Seq data into both 3′ isoform expression levels and overall gene expression levels. Using these expression levels I call proximal eQTLs both common and specific to a single developmental stage with a multivariate linear mixed model approach while accounting for various confounding factors. I then investigate the properties of these eQTLs, such as their location or the gene categories enriched or depleted in eQTLs. Finally, I extend the proximal eQTL calling approach to distal variants to find gene regulatory mechanisms acting in trans. Taken together, this thesis describes the design, challenges and results of performing a multivariate eQTL study in a higher model organism and provides new insights into gene regulation in D. melanogaster during embryonic development.

Subjects/Keywords: 572.8; Cell and molecular biology; genome-wide association studies; GWAS; genome; phenotypes; genetic variation; expression quantitative trait loci; eQTL; gene regulation; RNA sequencing

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Kölling, N. (2016). Quantitative genetics of gene expression during fruit fly development. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.26 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.685469

Chicago Manual of Style (16^th Edition):

Kölling, Nils. “Quantitative genetics of gene expression during fruit fly development.” 2016. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://doi.org/10.17863/CAM.26 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.685469.

MLA Handbook (7^th Edition):

Kölling, Nils. “Quantitative genetics of gene expression during fruit fly development.” 2016. Web. 19 Jan 2021.

Vancouver:

Kölling N. Quantitative genetics of gene expression during fruit fly development. [Internet] [Doctoral dissertation]. University of Cambridge; 2016. [cited 2021 Jan 19]. Available from: https://doi.org/10.17863/CAM.26 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.685469.

Council of Science Editors:

Kölling N. Quantitative genetics of gene expression during fruit fly development. [Doctoral Dissertation]. University of Cambridge; 2016. Available from: https://doi.org/10.17863/CAM.26 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.685469

University of Cambridge

22. Glinos, Dafni Anna. Characterising the gene regulatory landscape of CD4+ T cells.

Degree: PhD, 2019, University of Cambridge

URL: https://doi.org/10.17863/CAM.39595 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.774781

► Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease… (more)

▼ Despite the high prevalence of immune-mediated diseases, the molecular mechanisms by which they arise and the influence of genetic variation in the predisposition to disease are not well understood. Immune susceptibility loci identified by genome wide association studies (GWAS) overlap with active regulatory elements in CD4+ T cells, and particularly in regulatory T cells (Tregs). CD4+ T cells are the orchestrators of the adaptive immune response and their dysfunction has been associated with immune-mediated disorders through uncontrolled activation and resistance to downregulation, which is usually mediated by Tregs. T cell activation requires the combination of T cell receptor (TCR) recognition of an antigen and CD28 co-stimulation. The role of CD28 co-stimulation requirement in the activation of different T cell subsets has been understudied. Here, I assessed the role of immune disease variants in modulating pathways underlying T cell activation and Treg function. For that, I activated CD4+ T cells using different intensities of CD28 and TCR signals, followed by genome-wide transcriptome and chromatin profiling of naive and memory cells. I observed that CD28 plays a critical role in the expression of genes involved in effector functions, cell cycle regulation in memory T cells and in disease susceptibility. I profiled the gene expression regulatory landscape in Tregs using a combination of genomic assays. Due to the scarce Treg numbers in peripheral blood I first optimised the ChIPmentation (ChM) sequencing protocol to profile H3K4me3 and H3K27ac histone modifications in Tregs. I combined it with chromatin accessibility and gene expression profiling in resting and stimulated Tregs from ten donors. I observed cases of alternative transcription, such as alternative splicing and promoter, induced by stimulation, which could be predicted by changes in the chromatin landscape. Finally, I assessed how genetic variability impacts the function of Tregs and how this can lead to autoimmunity. I carried a quantitative trait locus (QTL) mapping using RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChM-seq data from Tregs isolated from 100 individuals. Additionally, I processed publicly available data from naive T cells to distinguish the Treg specific effects from generic CD4+ T cell signals. I recapitulated known colocalisations between QTLs and immune GWAS loci, and identified previously unknown Treg specific colocalisations. My findings highlight the value of carrying QTL studies in rare immune cell types relevant to the disease.

Subjects/Keywords: regulatory T cell; immune system; transcriptomics; quantitative trait loci; GWAS; autoimmunity; CD4 T cell; CD28 costimulation; ChiP-seq; ATAC-seq; differential gene expression; humans

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Glinos, D. A. (2019). Characterising the gene regulatory landscape of CD4+ T cells. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.39595 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.774781

Chicago Manual of Style (16^th Edition):

Glinos, Dafni Anna. “Characterising the gene regulatory landscape of CD4+ T cells.” 2019. Doctoral Dissertation, University of Cambridge. Accessed January 19, 2021. https://doi.org/10.17863/CAM.39595 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.774781.

MLA Handbook (7^th Edition):

Glinos, Dafni Anna. “Characterising the gene regulatory landscape of CD4+ T cells.” 2019. Web. 19 Jan 2021.

Vancouver:

Glinos DA. Characterising the gene regulatory landscape of CD4+ T cells. [Internet] [Doctoral dissertation]. University of Cambridge; 2019. [cited 2021 Jan 19]. Available from: https://doi.org/10.17863/CAM.39595 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.774781.

Council of Science Editors:

Glinos DA. Characterising the gene regulatory landscape of CD4+ T cells. [Doctoral Dissertation]. University of Cambridge; 2019. Available from: https://doi.org/10.17863/CAM.39595 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.774781

University of Otago

23. Wiggins, George Andrew Ross. Gene expression variability in breast tumour development .

Degree: University of Otago

URL: http://hdl.handle.net/10523/10587

► Breast cancer is the most common female malignancy and presents a major health issue both worldwide and in New Zealand. Individuals with a family history… (more)

▼ Breast cancer is the most common female malignancy and presents a major health issue both worldwide and in New Zealand. Individuals with a family history of either breast or ovarian cancer have an increased lifetime risk of breast cancer. Furthermore, approximately 10% of breast cancers are thought to be caused by rare inherited genetic variants, of which variants in BRCA1 and BRCA2 are the most prominent. Individuals carrying a pathogenic BRCA1 or BRCA2 variant have up to a 87% and 84% lifetime risk of developing breast cancer compared to 12% for the general population. BRCA1 and BRCA2 functions are critical to genomic stability, which is essential to maintaining a healthy cell state in all tissues. However, there is a lack of disease risk in the majority of non-breast and ovarian tissues. Additionally, there are thousands of different sequence variants across each gene that present distinct risk profiles ranging from benign to pathogenic. A large proportion of these are considered variants of uncertain significance (VUS) resulting in no additional information to aid clinical management. The effect of pathogenic variants on gene expression is a potential source of information that can help to identify genes involved in tissue-specific risk and a phenotype that can be used to help classify VUS. Previous studies have explored BRCA1- and BRCA2-associated gene expression profiles, however, there has been a lack of consistency between genes identified as associated with BRCA1- and BRCA2 variant status. These studies have typically focused on identifying differences by comparing the mean level of gene expression, however, the variability of gene expression is also under genetic control and has been under-explored in BRCA1- and BRCA2-associated tissues. BRCA1 and BRCA2-associated gene expression variability was calculated across three familial breast tumours datasets. Additionally, as BRCA1-associated tumours are typically subtyped as basal-like, gene expression variability was calculated between basal and non-basal breast tumours in four datasets. BRCA1- associated and basal-like tumours exhibited greater global gene expression variability compared to familial breast tumour with no BRCA1 or BRCA2 pathogenic variant (BRCAx) and non-basal tumours. By comparison, the mean level of gene expression was similar between all tumour-types. Three genes (DSC3, EN1 and IGF2BP3) were found to be differentially variable in BRCA1-associated and basal-like breast tumours compared to BRCAx and non-basal tumours, respectively. RNA in situ hybridisation (RNA ISH) was used to explore EN1 expression in 503 breast tumour cores, including 151 BRCA1-associated tumours. Consistent with mircoarray analyses, RNA ISH found the expression of EN1 was variable in BRCA1-associated tumours. Two breast cell lines were used to measure gene expression variability in BRCA1 heterozygous models. In contrast to tumour analysis, MCF-10A BRCA1mut/+ cells displayed less global gene expression variability compared to wild type MCF-10A cells. Additionally,… Advisors/Committee Members: Walker, Logan (advisor).

Subjects/Keywords: Gene expression; variability; breast cancer; familial; BRCA1; Quantitative Trait Loci

Record Details Similar Records Cite « Share

❌

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Wiggins, G. A. R. (n.d.). Gene expression variability in breast tumour development . (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/10587

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Chicago Manual of Style (16^th Edition):

Wiggins, George Andrew Ross. “Gene expression variability in breast tumour development .” Doctoral Dissertation, University of Otago. Accessed January 19, 2021. http://hdl.handle.net/10523/10587.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

MLA Handbook (7^th Edition):

Wiggins, George Andrew Ross. “Gene expression variability in breast tumour development .” Web. 19 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

Wiggins GAR. Gene expression variability in breast tumour development . [Internet] [Doctoral dissertation]. University of Otago; [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10523/10587.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Council of Science Editors:

Wiggins GAR. Gene expression variability in breast tumour development . [Doctoral Dissertation]. University of Otago; Available from: http://hdl.handle.net/10523/10587

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Mississippi State University

24. Guo, Yufang. QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS.

Degree: PhD, Plant and Soil Sciences, 2008, Mississippi State University

URL: http://sun.library.msstate.edu/ETD-db/theses/available/etd-11062007-142438/ ;

► Cotton is a very important economical crop in the U.S. and throughout the world. The developments in molecular biology offer new and innovative approaches toward… (more)

▼ Cotton is a very important economical crop in the U.S. and throughout the world. The developments in molecular biology offer new and innovative approaches toward evaluating and understanding genetic mechanisms of important agronomical traits. Bacterial artificial chromosome (BAC) libraries have rapidly become the preferred choice for physical mapping. BAC-derived microsatellite or simple sequence repeats (SSRs) markers facilitate the integration of physical and genetic recombination maps. The first objective in this research was to identify chromosome locations of a set of BAC-derived SSR markers in tetraploid cotton. A total of 192 SSR primer pairs were derived from BAC clones of an Upland cotton (Gossypium hirsutum L.) genetic standard line TM-1. Using deletion analysis method, we assigned 39 markers out of the 192 primer pairs to 18 different chromosomes or chromosome arms. Chromosomal assignment of these markers will help to improve the current cotton genetic linkage maps and facilitate positional candidate gene cloning, comparative genome analysis, and the coordination of chromosome-based genome sequencing projects. Wild race stocks (Gossypium spp.) represent valuable resources for genetic improvement. Most primitive accessions are photoperiod sensitive; they do not flower under the long days of the U.S. cotton belt. Molecular markers were used to locate quantitative trait loci (QTLs) for node of first fruiting branch (NFB), node of first open boll (NOB), and fruiting score (FS). An F2 population consisted of 251 plants from the cross of a day neutral cultivar Deltapine 61, and a photoperiod sensitive accession Texas 701, were used in this study. For each trait, three major QTLs were mapped to chromosome 16, 21, and 25. QTL analysis was also conducted in two F2 populations generated from the cross between Deltapine 61 and two photoperiod sensitive accessions (T1107, PI 607174; T1354, PI 530082) of Upland cotton (G. hirsutum L.). QTL analysis indicated that NFB differed between the two F2 populations. Two major QTLs (q-NFB-c21-1 and q-NFB-c25-1) were found in population 1107; whereas, only one (q-NFB-c25-1) was important in population 1354. Discovering QTLs associated with flowering time may have the potential to facilitate day neutral conversion of wild photoperiod sensitive accessions. Advisors/Committee Members: Johnie N. Jenkins (chair), Sukumar Saha (chair), Din-Pow Ma (committee member), Jack C. McCarty, Jr (committee member), Frank B. Matta (committee member), Ted Wallace (committee member), John A. Boyle (committee member).

Subjects/Keywords: quantitative trait loci; flowering time

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APA (6^th Edition):

Guo, Y. (2008). QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS. (Doctoral Dissertation). Mississippi State University. Retrieved from http://sun.library.msstate.edu/ETD-db/theses/available/etd-11062007-142438/ ;

Chicago Manual of Style (16^th Edition):

Guo, Yufang. “QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS.” 2008. Doctoral Dissertation, Mississippi State University. Accessed January 19, 2021. http://sun.library.msstate.edu/ETD-db/theses/available/etd-11062007-142438/ ;.

MLA Handbook (7^th Edition):

Guo, Yufang. “QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS.” 2008. Web. 19 Jan 2021.

Vancouver:

Guo Y. QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS. [Internet] [Doctoral dissertation]. Mississippi State University; 2008. [cited 2021 Jan 19]. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-11062007-142438/ ;.

Council of Science Editors:

Guo Y. QUANTITATIVE GENETIC ANALYSIS OF FLOWERING TIME IN PRIMITIVE UPLAND COTTON GOSSYPIUM HIRSUTUM L., AND CHROMOSOME ASSIGNMENT OF BAC-DERIVED SSR MARKERS. [Doctoral Dissertation]. Mississippi State University; 2008. Available from: http://sun.library.msstate.edu/ETD-db/theses/available/etd-11062007-142438/ ;

25. Chen, Hua. Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.).

Degree: PhD, Department of Agricultural, Food, and Nutritional Science, 2016, University of Alberta

URL: https://era.library.ualberta.ca/files/c08612n615

► Early maturity, grain yield and grain protein content are some of the important traits in western Canadian wheat breeding programs. A series of experiments were… (more)

▼ Early maturity, grain yield and grain protein content are some of the important traits in western Canadian wheat breeding programs. A series of experiments were conducted to explore the genetic basis of days to heading, and maturity, plant height, grain protein, grain yield and related traits. In a spring wheat population of 187 recombinant inbred lines genotyped with 341 Diversity Array Technology (DArT) polymorphic markers, a total of 21 quantitative trait loci (QTLs) were identified for all phenotypic traits recorded, except plant height and grain protein content. Two earliness per se QTLs were mapped on chromosomes 1A (QEps.dms-1A) and 4A (QEps.dms-4A) in all three growing seasons, contributing 15-27% and 8-10%, respectively, to the total genetic variation in days to maturity. The two earliness QTLs and Vrn-B1 exhibited additive interaction. In the same population, lines carrying the resistant allele of Lr34/Yr18 were taller, matured earlier, yielded less grain with lower test weights than lines without Lr34/Yr18. Lines with Lr34/Yr18 also exhibited lower leaf and stripe rust infection than lines with the susceptible allele. The failure to combine Lr34/Yr18 with high yield, protein, and SDS sedimentation suggested single seed descent or doubled haploid populations for the combined selection of multiple quantitatively inherited traits, and simply one molecular marker, would require population sizes in excess of at least 500 to have any possibility of selection success. Genetic diversity analysis for earliness related and plant height reducing genes in 82 spring wheat cultivars registered in western Canada through eight diagnostic DNA markers suggested breeding efforts in western Canada have resulted in the incorporation of vernalization and photoperiod insensitive and height reducing genes in modern cultivars to promote early maturity, to make use of off-season nurseries in other parts of the world and to improve lodging tolerance. Using genome-wide association mapping (GWAS). we identified a total of 152 significant marker-trait associations; however, there were only 18 genomic regions that consisted of clusters of 3 to 20 significant single nucleotide polymorphisms (SNPs) across 12 chromosomes, including two regions each for grain yield, test weight and protein content, six regions for plant height and six other coincident regions that were associated with two or three traits. The genomic region associated with plant height on chromosome 4B showed high linkage disequilibrium (r2 > 0.80) with the semi-dwarfing gene Rht-B1. Results of these studies suggest that besides the widely used semi-dwarf and early maturity related genes, there is a wide spectrum of loci available that could be used for modulating plant height, days to maturity, grain yield and grain protein content in western Canadian wheat germplasm.

Subjects/Keywords: genomewide association mapping; quantitative trait loci; early maturity; wheat

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APA (6^th Edition):

Chen, H. (2016). Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.). (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/c08612n615

Chicago Manual of Style (16^th Edition):

Chen, Hua. “Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.).” 2016. Doctoral Dissertation, University of Alberta. Accessed January 19, 2021. https://era.library.ualberta.ca/files/c08612n615.

MLA Handbook (7^th Edition):

Chen, Hua. “Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.).” 2016. Web. 19 Jan 2021.

Vancouver:

Chen H. Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.). [Internet] [Doctoral dissertation]. University of Alberta; 2016. [cited 2021 Jan 19]. Available from: https://era.library.ualberta.ca/files/c08612n615.

Council of Science Editors:

Chen H. Quantitative trait loci and genomewide association mapping in western Canadian spring wheat (Triticum aestivum L.). [Doctoral Dissertation]. University of Alberta; 2016. Available from: https://era.library.ualberta.ca/files/c08612n615

North Carolina State University

26. Tarter, Jennifer Ann. Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L).

Degree: PhD, Crop Science, 2005, North Carolina State University

URL: http://www.lib.ncsu.edu/resolver/1840.16/5039

► Epistasis effects estimated in conjunction with quantitative trait locus (QTL) mapping are often confounded by segregating background genomes or QTL x background interactions. To improve… (more)

▼ Epistasis effects estimated in conjunction with quantitative trait locus (QTL) mapping are often confounded by segregating background genomes or QTL x background interactions. To improve the precision of estimating QTL epistatic effects, 16 near-isogenic lines (NILs), resulting from the introgression of chromosomal segments of Tx303 into the genetic background of inbred line B73, were crossed in all pairwise combinations. Marker-assisted selection and self-fertilization were employed to create double-introgression NILs (dNILs) homozygous for two introgressed segments. The resulting 127 dNILs, their 16 parental, single-introgression NILs, and inbred lines B73 and Tx303 were evaluated as inbred lines, per se, as well as in testcross combinations with Mo17, in replicated field trials to measure the effects of introgressions singly (additive effects) and in pairs (epistatic effects). Across traits tested, significant additive effects involving single NILs were detected in 2% to 28% of the tests in the inbred trials and between 2% and 40% of the tests involving single NILs in testcross in the hybrid trials. Significant epistatic effects were identified in 2% to 19% of the tests including inbred dNILs and in 2% to 27% of the tests including testcross dNILs. Generally, the frequency and magnitude of epistatic interactions were less than those of additive effects for both the inbred and hybrid trials. Across traits, between 0% and 100% of the significant epistatic interactions involved chromosomal segments that did not display independent significant additive effects. There was minimal congruency between chromosomal regions displaying significant genetic effects in the inbred and hybrid trials. These results suggest that epistatic interactions can affect predictions of phenotypic performance based solely on additive effects detected either in inbred lines or hybrid combinations. Such predictions might be biased and warrant testing in both population types. Advisors/Committee Members: James B. Holland, Committee Co-Chair (advisor), Major M. Goodman, Committee Co-Chair (advisor).

Subjects/Keywords: quantitative trait loci; maize; epistasis

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APA (6^th Edition):

Tarter, J. A. (2005). Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L). (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/5039

Chicago Manual of Style (16^th Edition):

Tarter, Jennifer Ann. “Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L).” 2005. Doctoral Dissertation, North Carolina State University. Accessed January 19, 2021. http://www.lib.ncsu.edu/resolver/1840.16/5039.

MLA Handbook (7^th Edition):

Tarter, Jennifer Ann. “Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L).” 2005. Web. 19 Jan 2021.

Vancouver:

Tarter JA. Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L). [Internet] [Doctoral dissertation]. North Carolina State University; 2005. [cited 2021 Jan 19]. Available from: http://www.lib.ncsu.edu/resolver/1840.16/5039.

Council of Science Editors:

Tarter JA. Additive Genetic Effects of Single Chromosomal Segment Introgressions and Epistatic Effects of Paired Introgressions on Quantitative Traits in Maize (Zea mays. L). [Doctoral Dissertation]. North Carolina State University; 2005. Available from: http://www.lib.ncsu.edu/resolver/1840.16/5039

University of Guelph

27. Richardson, Colin. GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS).

Degree: MS, Department of Integrative Biology, 2011, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2977

► Co-variation in the genetic architecture, and co-localization of quantitative trait loci (QTL), for embryonic developmental rate and age at maturation in male rainbow trout (Oncorhynchus… (more)

Subjects/Keywords: embryonic developmental rate; precocious maturation; Quantitative Trait Loci; rainbow trout

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APA (6^th Edition):

Richardson, C. (2011). GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS). (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2977

Chicago Manual of Style (16^th Edition):

Richardson, Colin. “GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS).” 2011. Masters Thesis, University of Guelph. Accessed January 19, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2977.

MLA Handbook (7^th Edition):

Richardson, Colin. “GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS).” 2011. Web. 19 Jan 2021.

Vancouver:

Richardson C. GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS). [Internet] [Masters thesis]. University of Guelph; 2011. [cited 2021 Jan 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2977.

Council of Science Editors:

Richardson C. GENETIC COVARIATION BETWEEN EMBRYONIC DEVELOPMENTAL RATE AND PRECOCIOUS MATURATION IN RAINBOW TROUT (ONCORHYNCHUS MYKISS). [Masters Thesis]. University of Guelph; 2011. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2977

University of Guelph

28. Rossi, Maria Eugenia. Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean.

Degree: MS, Department of Plant Agriculture, 2011, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3184

► The main goal of soybean breeding is to increase yield with improved seed quality characters. The objectives of this thesis were: i) to identify yield… (more)

Subjects/Keywords: Quantitative trait loci (QTL); Yield; Agronomic traits; Adaptation; Mega-environments

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APA (6^th Edition):

Rossi, M. E. (2011). Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3184

Chicago Manual of Style (16^th Edition):

Rossi, Maria Eugenia. “Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean.” 2011. Masters Thesis, University of Guelph. Accessed January 19, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3184.

MLA Handbook (7^th Edition):

Rossi, Maria Eugenia. “Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean.” 2011. Web. 19 Jan 2021.

Vancouver:

Rossi ME. Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean. [Internet] [Masters thesis]. University of Guelph; 2011. [cited 2021 Jan 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3184.

Council of Science Editors:

Rossi ME. Adaptation to Mega-environments: Introgression of novel alleles for yield using Canadian x Chinese crosses in Soybean. [Masters Thesis]. University of Guelph; 2011. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3184

University of Guelph

29. Magee, Riley. The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss).

Degree: MS, Department of Integrative Biology, 2012, University of Guelph

URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3224

► I examined the influence of cyclic feeding regime on fillet yield and quality and their genetic architecture in rainbow trout (Oncorhynchus mykiss). Two lots of… (more)

Subjects/Keywords: Quantitative trait loci; Rainbow trout; Fat deposition; Cyclic feeding

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APA (6^th Edition):

Magee, R. (2012). The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss). (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3224

Chicago Manual of Style (16^th Edition):

Magee, Riley. “The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss).” 2012. Masters Thesis, University of Guelph. Accessed January 19, 2021. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3224.

MLA Handbook (7^th Edition):

Magee, Riley. “The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss).” 2012. Web. 19 Jan 2021.

Vancouver:

Magee R. The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss). [Internet] [Masters thesis]. University of Guelph; 2012. [cited 2021 Jan 19]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3224.

Council of Science Editors:

Magee R. The Effect of Cyclic Feeding Regime on Growth-Related Traits, Estimates of Fat Deposition and Their Genetic Architecture in Rainbow Trout (Oncorhynchus mykiss). [Masters Thesis]. University of Guelph; 2012. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/3224

University of KwaZulu-Natal

30. Chaminuka, Michael. Humanitarian military interventions in developing countries and the role of self interest : an ethical critique.

Degree: 2017, University of KwaZulu-Natal

URL: http://hdl.handle.net/10413/14917

► This study was an ethical investigation of humanitarian military interventions in developing countries. The main argument which is proffered in the study is that the… (more)

▼ This study was an ethical investigation of humanitarian military interventions in developing countries. The main argument which is proffered in the study is that the issue of humanitarian military intervention is extremely controversial from an array of perspectives. Some of the controversies that have been identified in this study are as follows; that humanitarian military interventions which are mostly undertaken in developing countries by developed countries have worsened the political and security situation far much more than before the intervention, that humanitarian military interventions do violate international law especially on those instances when they are undertaken without the authorisation from the multilateral bodies such as the United Nations (UN) and its organ – the United Nations Security Council (UNSC), without authorisation from the UNSC the humanitarian military interventions do violate International law, whether humanitarian military interventions are acceptable or not, especially in the light that such interventions in most cases do violate nation-state sovereignty just to mention a few. For conceptualization purposes, the study set the scene by providing a conceptual definition of humanitarianism with the aim of delineating the meaning of this term from its use in other disciplines. It was asserted that when humanitarian is suffixed with military intervention the implication is that of the military intervening in particular socio-political context with the aim of alleviating human suffering. After providing this conceptual definition, the study went to provide a brief historical account of humanitarian military interventions from ancient times up to modern times. Within the modern era, the study provided examples in which it was shown that most of the literature on humanitarian military interventions which have been undertaken to date have been entangled in controversies showing that these interventions have often worsened the security situation of the intervened country far much more than what it was before intervention. The study went on to argue that the humanitarian military interventions that have been undertaken by powerful countries have been undertaken with the aim of protecting geo-strategic interests in those intervened countries. These geo-strategic interests included political influence, extraction of natural resources such as petroleum and minerals which are indispensable to the flourishing of the economies of powerful countries. In this regard interventions that have been undertaken in the Middle East, North and West Africa by powerful countries were based on the need to preserve traditional areas of influence for marketing and extraction of raw materials by powerful countries. As an example, it was argued that the current Syrian civil war has resulted in USA and Russia fighting a proxy war for geo-strategic influence in the Middle East. This proxy war has caused an unprecedented refugee pool since the end of World War 2. Multilateral efforts to transform humanitarian military… Advisors/Committee Members: Murove, Munyaradzi Felix. (advisor).

Subjects/Keywords: Cajanus cajan.; Seed protein content.; Genomics.; Quantitative trait loci.; Candidate genes.

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APA (6^th Edition):

Chaminuka, M. (2017). Humanitarian military interventions in developing countries and the role of self interest : an ethical critique. (Thesis). University of KwaZulu-Natal. Retrieved from http://hdl.handle.net/10413/14917

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chaminuka, Michael. “Humanitarian military interventions in developing countries and the role of self interest : an ethical critique.” 2017. Thesis, University of KwaZulu-Natal. Accessed January 19, 2021. http://hdl.handle.net/10413/14917.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chaminuka, Michael. “Humanitarian military interventions in developing countries and the role of self interest : an ethical critique.” 2017. Web. 19 Jan 2021.

Vancouver:

Chaminuka M. Humanitarian military interventions in developing countries and the role of self interest : an ethical critique. [Internet] [Thesis]. University of KwaZulu-Natal; 2017. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10413/14917.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chaminuka M. Humanitarian military interventions in developing countries and the role of self interest : an ethical critique. [Thesis]. University of KwaZulu-Natal; 2017. Available from: http://hdl.handle.net/10413/14917

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations