• We carried out an expression quantitative trait loci (eQTL) study of primary human osteoblasts (HOb) derived from 95 unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. (nih.gov)
  • In the process called quantitative trait loci (QTL) mapping, attempts are made to find significant correlations between marker alleles and the phenotypic variation, or disease state. (bmj.com)
  • The standard expression quantitative trait loci (eQTL) detects polymorphisms associated with gene expression without revealing causality. (nih.gov)
  • This report summarizes published research across the world in 2008 that placed additional markers, genes and quantitative trait loci (QTLs) on barley chromosome 7H. (usda.gov)
  • The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. (nature.com)
  • Twenty‐seven quantitative trait loci ( QTL ) were detected for manually collected traits associated with biomass production. (osti.gov)
  • Quantitative trait locus (QTL) mapping locates and estimates the effect of genetic loci that regulate quantitative traits. (jax.org)
  • We applied a leaf imprinting method for rapid and non-destructive phenotyping to explore genetic variation and identify quantitative traits loci (QTL) for stomatal traits in wheat grown under greenhouse and field conditions. (biomedcentral.com)
  • This suggested that stomatal traits could be an underlying mechanism increasing yield at specific loci and used as a proxy to track a target QTL in recombinant lines. (biomedcentral.com)
  • The same quantitative trait loci were identified with all models. (springer.com)
  • Mutic and Wolf [ 7 ] identified 13 quantitative trait loci (QTL) for IGE associated with size, development, and fitness related traits in Arabidopsis . (springer.com)
  • Heritable differences in transcribed RNA levels can be mapped as quantitative trait loci (QTLs). (biomedcentral.com)
  • Included among these fields is the classical field of quantitative genetics, which is a subfield of statistical genetics, that is devoted to traits that can be quantified on some continuous scale and are often influenced by alleles at many loci. (ccsenet.org)
  • From the point of view of quantitative genetics, the regions of a genome that have some influence on a quantitative trait may be viewed as loci, and variations among these loci at the $DNA$ level, such as nucleotide substitutions or other markers, may be used as working definitions of alleles, and, therefore, can be used to determine whether an individual carries a particular allele at some locus. (ccsenet.org)
  • Two major quantitative trait loci (QTL) for log-transformed HDL-C adjusted for age and gender were identified onto chromosomes 7p22 and 15q25 with maximum multipoint logarithm of odds (LOD) scores of 3.76 and 6.69, respectively. (elsevierpure.com)
  • We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. (bilkent.edu.tr)
  • Expression quantitative trait loci (eQTLs), genetic variants associated with gene expression levels, are identified in eQTL mapping studies. (escholarship.org)
  • Non-coding SNPs can also alter the level of expression of a gene, as an eQTL (expression quantitative trait locus). (wikipedia.org)
  • By integrating expression quantitative trait locus (eQTL) and genome-wide association study (GWAS) data, we demonstrate that long-range chromatin interactions between variant regulatory elements and their target genes contribute to variations in gene expression, metabolic phenotypes, and agronomic traits. (nature.com)
  • Examples of 2-omics analyses include expression quantitative trait locus eQTL (Franke & Jansen, 2009) and methylation quantitative trait locus meQTL (Smith, Kilaru, Kocak, Almli, & Mercer, 2014) that, respectively, assess the influence of genetic and epigenetic markers on gene expression. (researchgate.net)
  • We previously localized a Quantitative Trait Locus for HPFH in an extensive Asian-Indian kindred to chromosome 6q23. (biomedcentral.com)
  • TreeSNPs is a laboratory information management system with a user-friendly Web interface for the gathering and display of data generated through medium- to large-scale single nucleotide polymorphism (SNP) identification by resequencing, in the context of whole genome association, outlier detection, quantitative trait locus, and genetic mapping studies. (gc.ca)
  • RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. (biomedcentral.com)
  • Here, we present an analytical approach that uses summary-level data from cohort-based DNA methylation (DNAm) quantitative trait locus (mQTL) studies to predict PAIs. (ox.ac.uk)
  • We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. (escholarship.org)
  • However, this dramatically improved after performing genotyping-by-sequencing in the first round of selfing, followed by high-resolution-melting single nucleotide polymorphism genotyping in subsequent selection steps. (frontiersin.org)
  • An extensive expression marker map was created and additional single nucleotide polymorphism markers were developed. (usda.gov)
  • plural SNPs /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). (wikipedia.org)
  • Variant" may also be used as a general term for any single nucleotide change in a DNA sequence, encompassing both common SNPs and rare mutations, whether germline or somatic. (wikipedia.org)
  • We introduce a coupled Bayesian regression approach--eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combination of regulatory single-nucleotide polymorphisms (SNPs) that explain the gene expression variance. (nih.gov)
  • In the past few years several large-scale genome-wide association studies (GWAS) have discovered a lot of single nucleotide polymorphisms (SNPs) associated with the risk of cervical cancer ( Table S1 ) and provide new insight into the genetic architecture of this type of cancer. (jcancer.org)
  • We performed a large case-control study involving 414 patients and 1199 cancer-free controls to investigate whether single nucleotide polymorphisms (SNPs) in the WDR4 gene are associated with Wilms tumor susceptibility. (jcancer.org)
  • Approximately 30,000 single nucleotide polymorphisms (SNPs) were included in the genome-wide association study (GWAS), using a linear mixed model for survival time, a linear mixed model and a generalized linear mixed model for repeated binomial survival (0/1). (springer.com)
  • 6 ] conducted an association study using 1022 single nucleotide polymorphisms (SNPs) and identified 81 SNPs that were associated with IGE for plumage condition in laying hens. (springer.com)
  • Such studies typically test for an association between single nucleotide polymorphisms (SNPs) and expression under an additive model, which ignores interaction and haplotypic effects. (escholarship.org)
  • Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions(regions between genes). (wikipedia.org)
  • Mapping research located genes and QTL for morphological traits, resistance to several diseases, preharvest sprouting and various malting quality traits. (usda.gov)
  • Regions with high F ST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. (frontiersin.org)
  • The identification of causal or predictive variants/genes/mechanisms for disease-associated traits is characterized by 'complex' networks of molecular phenotypes. (researchgate.net)
  • However, with very rare exceptions, called monogenic diseases, which affect relatively few individuals, the genetic contribution to most diseases or traits is only about 2 to 5 percent, and multiple genes are involved in virtually every trait/disease. (huffpost.com)
  • These are traits that are complex, continuous and regulated by a group of genes interacting with each other and the environment. (jax.org)
  • Once a marker is found to be associated with a gene, or multiple genes, and determined to be significant to a target trait, it is designated an informative marker, diagnostic marker or predictive marker. (generationcp.org)
  • Some simple traits such as flower colour are controlled by one gene, but more complex traits such as drought tolerance are controlled by multiple genes. (generationcp.org)
  • GCP supported 25 projects to discover and develop markers for genes that control traits that enable key crops, including bean and chickpea, to tolerate drought and poor soils and resist pests and diseases. (generationcp.org)
  • We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. (biomedcentral.com)
  • Intermediary quantitative traits--an alternative in the identification of disease genes in asthma? (cdc.gov)
  • The genetics of stomatal traits on the adaxial surface of the flag leaf was investigated using 146 double haploid lines derived from a cross between two Australian lines of Triticum aestivum , RAC875 and Kukri. (biomedcentral.com)
  • This ability to use these working definitions to identify the genotype of each individual in a sample results in a significant change in the working paradigm of sub-field of quantitative genetics, called variance and covariance analysis, because effects and components of variance and covariance may be estimated directly in a sense that will be described in detail in the paper. (ccsenet.org)
  • Developments in plant genetics over the past 10-15 years have provided breeders with powerful tools to detect beneficial traits of plants much more quickly than ever before. (generationcp.org)
  • For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. (wikipedia.org)
  • For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
  • Prior studies paid at best lip service to the role of the environment, a perspective reified in the paradigm of gene-by-environment (G x E) interactions and its modern variants, such as genome-wide association studies, quantitative trait nucleotides, and whole-genome sequencing. (huffpost.com)
  • Results from genome-wide association studies (GWAS) on DGE show that most quantitative traits in livestock are highly polygenic and that variants tend to be associated with more than one trait [ 4 ]. (springer.com)
  • In recent years, many investigators have conducted genome wide sweeps and have used a variety of statistical criteria to judge whether identified regions of the human genome have a significant influence on the expression of some quantitative trait such as measurements on patients with Alzheimer's disease. (ccsenet.org)
  • Once a favourable gene for a target agronomic trait is discovered and located in the plant's genome, the next step is to find a molecular marker that will effectively tag it. (generationcp.org)
  • The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. (biomedcentral.com)
  • Single nucleotide substitutions with an allele frequency of less than 1% are sometimes called single-nucleotide variants (SNVs). (wikipedia.org)
  • Proinflammatory cytokine single nucleotide polymorphisms in nasal polyposis. (cdc.gov)
  • The common genetic variants associated with complex traits typically lie in noncoding DNA and may alter gene regulation in a cell type-specific manner. (nih.gov)
  • The characterization of genetic variants and their association with traits of interest are important initial steps to understand the biological pathways controlling these traits. (fapesp.br)
  • Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. (bilkent.edu.tr)
  • Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. (escholarship.org)
  • Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. (frontiersin.org)
  • The availability of genomic information has increased our understanding of complex traits, but studies have mainly focussed on DGE. (springer.com)
  • Future research programs can be focused on the development of transgenic plants with enhanced stress tolerance in field conditions based upon the outcome of genomic approaches and knowing the mystery of nucleotides sequences hidden in cells. (intechopen.com)
  • Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). (biomedcentral.com)
  • Thus, the detection of genomic regions and/or potentially causative mutations associated with internal organ weight traits may provide important information to poultry breeding programs, facilitating selection of chickens with proportional development of internal organs, improved feed efficiency and reduced susceptibility to metabolic disorders. (biomedcentral.com)
  • The putative IGF2 differentially methylated regions (DMR) 0, 1 and 2, a quantitative trait nucleotide (QTN) region in the intron 3 and a CpG island in the intron 4 of the IGF2 gene as well as three regions around porcine CTCF binding sites within the H19 differentially methylated domain (DMD) were selected for the DNA methylation analysis. (eurekamag.com)
  • These results indicate differences in DNA methylation patterns between breeds and it remains to be established whether variation in DNA methylation patterns impacts on phenotypic traits. (eurekamag.com)
  • Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. (nature.com)
  • This study demonstrates the use of mQTL data to predict PAIs and provides insights into the role of PAIs in complex trait variation. (ox.ac.uk)
  • Identifying genetic variation is a crucial step towards a better understanding of the molecular mechanisms responsible for traits of biological interest. (fapesp.br)
  • Integration of the predicted PAIs with GWAS data highlight interactions among 601 DNAm sites associated with 15 complex traits. (ox.ac.uk)
  • Plant area index ( PAI ) estimated from below‐canopy hemispherical images, as well as a suite of thirteen traits assessed by manual destructive harvests, were measured in a Setaria recombinant inbred line mapping population segregating for aboveground productivity and architecture. (osti.gov)
  • Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk. (escholarship.org)
  • A family-based quantitative transmission disequilibrium test (QTDT) revealed significant association between variant rs1800588 in LIPC and HDL-C in the GeneQuest population (P = 0.0067), which may account for the minor QTL on 15q22. (elsevierpure.com)
  • This is one of the first large studies investigating the genetic architecture of a socially-affected trait. (springer.com)
  • The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. (biomedcentral.com)
  • ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals. (escholarship.org)
  • In this first study to decifer genetic relationships between wheat stomatal traits and yield in response to water deficit, no significant correlations were observed among yield and stomatal traits under field conditions. (biomedcentral.com)
  • Fortunately, the raw data of many RNA-seq experiments are being deposited in public databases, and the number of available human RNA-seq samples is growing exponentially, for example, in the European Nucleotide Archive (ENA) (Figure 1 a). (biomedcentral.com)
  • However we found some overlaps between QTL for stomatal traits and yield across environments. (biomedcentral.com)
  • The horizontal line above the y axis represents a significant LOD score of 0.05 (as determined by permuting the trait values). (jax.org)
  • Significant differences between the lines were observed for stomatal densitity and size related traits. (biomedcentral.com)
  • Heterocellular hereditary persistence of fetal hemoglobin (HPFH) is a common multifactorial trait characterized by a modest increase of fetal hemoglobin levels in adults. (biomedcentral.com)