Genetic loci associated with a QUANTITATIVE TRAIT.
A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)
Any method used for determining the location of and relative distances between genes on a chromosome.
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
A form of gene interaction whereby the expression of one gene interferes with or masks the expression of a different gene or genes. Genes whose expression interferes with or masks the effects of other genes are said to be epistatic to the effected genes. Genes whose expression is affected (blocked or masked) are hypostatic to the interfering genes.
Animals that are produced through selective breeding to eliminate genetic background differences except for a single or few specific loci. They are used to investigate the contribution of genetic background differences to PHENOTYPE.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
The mating of plants or non-human animals which are closely related genetically.
The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
Genotypic differences observed among individuals in a population.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.
A phenotypic outcome (physical characteristic or disease predisposition) that is determined by more than one gene. Polygenic refers to those determined by many genes, while oligogenic refers to those determined by a few genes.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
Mouse strains constructed to possess identical genotypes except for a difference at a single gene locus.
The functional hereditary units of PLANTS.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.
Computer-based representation of physical systems and phenomena such as chemical processes.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.
Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations, or by parent x offspring matings carried out with certain restrictions. All animals within an inbred strain trace back to a common ancestor in the twentieth generation.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
The capacity of an organism to defend itself against pathological processes or the agents of those processes. This most often involves innate immunity whereby the organism responds to pathogens in a generic way. The term disease resistance is used most frequently when referring to plants.
Animals that are generated from breeding two genetically dissimilar strains of the same species.
A phenomenon in which multiple and diverse phenotypic outcomes are influenced by a single gene (or single gene product.)
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.
Diseases of plants.
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The reproductive organs of plants.
The adaptive superiority of the heterozygous GENOTYPE with respect to one or more characters in comparison with the corresponding HOMOZYGOTE.
Tops of plants when in flower, including the stems, leaves and blooms.
Cultivated plants or agricultural produce such as grain, vegetables, or fruit. (From American Heritage Dictionary, 1982)
The systematic study of the complete DNA sequences (GENOME) of organisms.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
Animals produced by the mating of progeny over multiple generations. The resultant strain of animals is virtually identical genotypically. Highly inbred animal lines allow the study of certain traits in a relatively pure form. (Segen, Dictionary of Modern Medicine, 1992)
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A plant species of the family BRASSICACEAE best known for the edible roots.
A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The edible portions of any animal used for food including domestic mammals (the major ones being cattle, swine, and sheep) along with poultry, fish, shellfish, and game.
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
A plant genus of the family Phrymaceae. Members contain 6-geranylflavanones and mimulone.
Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.
Deoxyribonucleic acid that makes up the genetic material of plants.
Substituted thioglucosides. They are found in rapeseed (Brassica campestris) products and related cruciferae. They are metabolized to a variety of toxic products which are most likely the cause of hepatocytic necrosis in animals and humans.
A species of SWINE, in the family Suidae, comprising a number of subspecies including the domestic pig Sus scrofa domestica.
The transmission of traits encoded in GENES from parent to offspring.
A plant species cultivated for the seed used as animal feed and as a source of canola cooking oil.
A plant genus of the family SOLANACEAE. Members contain SOLANACEOUS ALKALOIDS. Some species in this genus are called deadly nightshade which is also a common name for ATROPA BELLADONNA.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family composed of spouses and their children.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
Inbred rats derived from Sprague-Dawley rats and used for the study of salt-dependent hypertension. Salt-sensitive and salt-resistant strains have been selectively bred to show the opposite genetically determined blood pressure responses to excess sodium chloride ingestion.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
A plant species of the family SOLANACEAE, native of South America, widely cultivated for their edible, fleshy, usually red fruit.
A hereditary disease of the hip joints in dogs. Signs of the disease may be evident any time after 4 weeks of age.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA.
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.
Geographic variety, population, or race, within a species, that is genetically adapted to a particular habitat. An ecotype typically exhibits phenotypic differences but is capable of interbreeding with other ecotypes.
Databases devoted to knowledge about specific genes and gene products.
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.
Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.
Sequential operating programs and data which instruct the functioning of a digital computer.
A statistical technique that isolates and assesses the contributions of categorical independent variables to variation in the mean of a continuous dependent variable.
An individual having different alleles at one or more loci regarding a specific character.
A genus of trees of the Myrtaceae family, native to Australia, that yields gums, oils, and resins which are used as flavoring agents, astringents, and aromatics.
Procedures for finding the mathematical function which best describes the relationship between a dependent variable and one or more independent variables. In linear regression (see LINEAR MODELS) the relationship is constrained to be a straight line and LEAST-SQUARES ANALYSIS is used to determine the best fit. In logistic regression (see LOGISTIC MODELS) the dependent variable is qualitative rather than continuously variable and LIKELIHOOD FUNCTIONS are used to find the best relationship. In multiple regression, the dependent variable is considered to depend on more than a single independent variable.
An individual in which both alleles at a given locus are identical.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A principle of estimation in which the estimates of a set of parameters in a statistical model are those quantities minimizing the sum of squared differences between the observed values of a dependent variable and the values predicted by the model.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The total process by which organisms produce offspring. (Stedman, 25th ed)
The physical measurements of a body.
An annual legume. The SEEDS of this plant are edible and used to produce a variety of SOY FOODS.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
The experimental study of the relationship between the genotype of an organism and its behavior. The scope includes the effects of genes on simple sensory processes to complex organization of the nervous system.
A plant genus of the family POACEAE. The seed is one of the millets used in EDIBLE GRAIN. It contains vitexin. The common name of buffelgrass is also used for CENCHRUS.
The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)
A genus herbs of the Asteraceae family. The SEEDS yield oil and are used as food and animal feed; the roots of Helianthus tuberosus (Jerusalem artichoke) are edible.
Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.
A strain of Rattus norvegicus with elevated blood pressure used as a model for studying hypertension and stroke.
Those characteristics that distinguish one SEX from the other. The primary sex characteristics are the OVARIES and TESTES and their related hormones. Secondary sex characteristics are those which are masculine or feminine but not directly related to reproduction.
Any of a group of bone disorders involving one or more ossification centers (EPIPHYSES). It is characterized by degeneration or NECROSIS followed by revascularization and reossification. Osteochondrosis often occurs in children causing varying degrees of discomfort or pain. There are many eponymic types for specific affected areas, such as tarsal navicular (Kohler disease) and tibial tuberosity (Osgood-Schlatter disease).
Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).
A strain of Rattus norvegicus used as a normotensive control for the spontaneous hypertensive rats (SHR).
The fleshy or dry ripened ovary of a plant, enclosing the seed or seeds.
The measurement of an organ in volume, mass, or heaviness.
The white liquid secreted by the mammary glands. It contains proteins, sugar, lipids, vitamins, and minerals.
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
Statistical models in which the value of a parameter for a given value of a factor is assumed to be equal to a + bx, where a and b are constants. The models predict a linear regression.
The complete summaries of the frequencies of the values or categories of a measurement made on a group of items, a population, or other collection of data. The distribution tells either how many or what proportion of the group was found to have each value (or each range of values) out of all the possible values that the quantitative measure can have.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
Persons or animals having at least one parent in common. (American College Dictionary, 3d ed)
The detection of RESTRICTION FRAGMENT LENGTH POLYMORPHISMS by selective PCR amplification of restriction fragments derived from genomic DNA followed by electrophoretic analysis of the amplified restriction fragments.
The initial stages of the growth of SEEDS into a SEEDLINGS. The embryonic shoot (plumule) and embryonic PLANT ROOTS (radicle) emerge and grow upwards and downwards respectively. Food reserves for germination come from endosperm tissue within the seed and/or from the seed leaves (COTYLEDON). (Concise Dictionary of Biology, 1990)
The capacity of a normal organism to remain unaffected by microorganisms and their toxins. It results from the presence of naturally occurring ANTI-INFECTIVE AGENTS, constitutional factors such as BODY TEMPERATURE and immediate acting immune cells such as NATURAL KILLER CELLS.
The percent frequency with which a dominant or homozygous recessive gene or gene combination manifests itself in the phenotype of the carriers. (From Glossary of Genetics, 5th ed)
The combined effects of genotypes and environmental factors together on phenotypic characteristics.
Coloration or discoloration of a part by a pigment.
A plant species of the genus SOLANUM, family SOLANACEAE. The fruit is a large, egg-shaped berry, varying in color from dark purple to red, yellowish, or white. The leaves are large and ovate. The flowers are pendant, violet, and two inches across.
One of the two pairs of human chromosomes in the group B class (CHROMOSOMES, HUMAN, 4-5).
The total number of individuals inhabiting a particular region or area.
A plant species of the genus PINUS which is the subject of genetic study.
Very young plant after GERMINATION of SEEDS.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
New immature growth of a plant including stem, leaves, tips of branches, and SEEDLINGS.
A specific pair GROUP C CHROMSOMES of the human chromosome classification.
Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.
Gradual increase in the number, the size, and the complexity of cells of an individual. Growth generally results in increase in ORGAN WEIGHT; BODY WEIGHT; and BODY HEIGHT.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
The relationships of groups of organisms as reflected by their genetic makeup.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
The use of statistical and mathematical methods to analyze biological observations and phenomena.
The functional hereditary units of INSECTS.
Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is currently defined as when SYSTOLIC PRESSURE is consistently greater than 140 mm Hg or when DIASTOLIC PRESSURE is consistently 90 mm Hg or more.
Parts of plants that usually grow vertically upwards towards the light and support the leaves, buds, and reproductive structures. (From Concise Dictionary of Biology, 1990)
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
A specific pair of GROUP B CHROMOSOMES of the human chromosome classification.
The inherent or induced capacity of plants to withstand or ward off biological attack by pathogens.
A technique for growing plants in culture solutions rather than in soil. The roots are immersed in an aerated solution containing the correct proportions of essential mineral salts. (From Concise Dictionary of Biology, 1990)
Seeds from grasses (POACEAE) which are important in the diet.

Quantitative trait loci for component physiological traits determining salt tolerance in rice. (1/4986)

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.  (+info)

Complex trait analysis of the mouse striatum: independent QTLs modulate volume and neuron number. (2/4986)

BACKGROUND: The striatum plays a pivotal role in modulating motor activity and higher cognitive function. We analyzed variation in striatal volume and neuron number in mice and initiated a complex trait analysis to discover polymorphic genes that modulate the structure of the basal ganglia. RESULTS: Brain weight, brain and striatal volume, neuron-packing density and number were estimated bilaterally using unbiased stereological procedures in five inbred strains (A/J, C57BL/6J, DBA/2J, BALB/cJ, and BXD5) and an F2 intercross between A/J and BXD5. Striatal volume ranged from 20 to 37 mm3. Neuron-packing density ranged from approximately 50,000 to 100,000 neurons/mm3, and the striatal neuron population ranged from 1.4 to 2.5 million. Inbred animals with larger brains had larger striata but lower neuron-packing density resulting in a narrow range of average neuron populations. In contrast, there was a strong positive correlation between volume and neuron number among intercross progeny. We mapped two quantitative trait loci (QTLs) with selective effects on striatal architecture. Bsc10a maps to the central region of Chr 10 (LRS of 17.5 near D10Mit186) and has intense effects on striatal volume and moderate effects on brain volume. Stnn19a maps to distal Chr 19 (LRS of 15 at D19Mit123) and is associated with differences of up to 400,000 neurons among animals. CONCLUSION: We have discovered remarkable numerical and volumetric variation in the mouse striatum, and we have been able to map two QTLs that modulate independent anatomic parameters.  (+info)

Genotyping in the MHC locus: potential for defining predictive markers in sarcoidosis. (3/4986)

In sarcoidosis, host genetic factors are discussed as contributing to disease susceptibility and course. Since tumor necrosis factor (TNF)-alpha is a central mediator of granuloma formation and since elevated TNF-alpha levels are found during active phases of sarcoidosis, genetic polymorphisms correlating with influences on TNF-alpha levels are of special interest. The complete sequencing of the MHC region and the increase in the number of identified gene polymorphisms in this locus associated with TNF-alpha production offer the opportunity of detecting new genes associated with sarcoidosis and perhaps of defining disease-associated haplotypes that bear the potential of serving as predictive markers for this disease.  (+info)

Analyses of differential gene expression in genetic hypertensive rats by microarray. (4/4986)

We identified genes that were differentially expressed between spontaneously hypertensive rats (SHR) and Wistar-Kyoto rats (WKY) using cDNA microarray analysis, and analyzed the correlation between these genes and hypertension. Twenty four genes were found to be up-regulated and 20 were down-regulated in SHR. We selected 11 genes (6 up-regulated genes: SAH, Hsp70, MCT1, RBP, IDI1, Prion; and 5 down-regulated genes: Thrombin, Dyn, SOD3, Ela1, Gst Y(b)) and subjected them to an F2 cosegregation analysis. One hundred five F2 rats were obtained from the same strains used for microarray analysis, and blood pressure was measured directly with a catheter implanted in the femoral artery. The genotypes of monocarboxylate transporter 1 and glutathione S-transferase Y(b) subunit significantly affected diastolic blood pressure in F2 rats, and these two genes are located near each other on chromosome 2. However, quantitative trait loci (QTL) analysis in this region revealed that the QTL for diastolic blood pressure were from these two genes. Antihypertensive treatment with either enalapril or hydralazine only affected the expression level of Hsp70, which was up-regulated by hydralazine, probably through compensatory sympathetic activation. We were unable to associate the other 10 genes with hypertension in SHR. Based on these results, the identification of differentially expressed genes may not be an efficient method for selecting candidate genes for hypertension in the SHR-WKY system.  (+info)

Identification of genetic loci controlling bacterial clearance in experimental Salmonella enteritidis infection: an unexpected role of Nramp1 (Slc11a1) in the persistence of infection in mice. (5/4986)

The Gram-negative bacteria, Salmonella, cause a broad spectrum of clinical diseases in both animals and humans ranging from asymptomatic carriage to life-threatening sepsis. We have developed a model to study the contribution of genetic factors to the susceptibility of 129sv and C57BL/6J inbred mice to Salmonella enteritidis during the late phase of infection. C57BL/6J mice were able to eliminate completely sublethal inoculums of S. enteritidis from their reticuloendothelial system, whereas 129sv mice could not even after 60 days post inoculation. A genome scan performed on 302 (C57BL/6J x 129sv) F2 progeny identified three dominant loci (designated Ses1 to Ses3) that are associated with disease susceptibility in 129sv mice. Two highly significant linkages were identified on chromosomes 1 (Ses1) and 7 (Ses2) with respective LOD scores of 9.9 (P = 1.4 x 10(-11)) at D1Mcg5 and 4.0 (P = 1.9 x 10(-5)) at D7Mit62. One highly suggestive QTL was located on chromosomes15 (Ses3) with a LOD score 3.4 (P = 1.2 x 10(-4)). The estimated effects of Ses1, Ses2 and Ses3 on the bacterial clearance were greater in females. Using a model of three loci, with interaction between Ses1 and Ses2 and sex as a covariate, the three QTLs explained 32% of the phenotypic variance. The candidacy of Nramp1 as the gene for Ses1 was evaluated using mice carrying a null allele at Nramp1 (129sv-Nramp1(tm1Mcg)). These mice have a significantly lower spleen bacterial load compared to the wild-type 129sv mice, strongly suggesting the involvement of Nramp1 in controlling S. enteritidis clearance during the late phase of infection.  (+info)

Plant defense genes associated with quantitative resistance to potato late blight in Solanum phureja x dihaploid S. tuberosum hybrids. (6/4986)

Markers corresponding to 27 plant defense genes were tested for linkage disequilibrium with quantitative resistance to late blight in a diploid potato population that had been used for mapping quantitative trait loci (QTLs) for late blight resistance. Markers were detected by using (i) hybridization probes for plant defense genes, (ii) primer pairs amplifying conserved domains of resistance (R) genes, (iii) primers for defense genes and genes encoding transcriptional regulatory factors, and (iv) primers allowing amplification of sequences flanking plant defense genes by the ligation-mediated polymerase chain reaction. Markers were initially screened by using the most resistant and susceptible individuals of the population, and those markers showing different allele frequencies between the two groups were mapped. Among the 308 segregating bands detected, 24 loci (8%) corresponding to six defense gene families were associated with resistance at chi2 > or = 13, the threshold established using the permutation test at P = 0.05. Loci corresponding to genes related to the phenylpropanoid pathway (phenylalanine ammonium lyase [PAL], chalcone isomerase [CHI], and chalcone synthase [CHS]), loci related to WRKY regulatory genes, and other -defense genes (osmotin and a Phytophthora infestans-induced cytochrome P450) were significantly associated with quantitative disease resistance. A subset of markers was tested on the mapping population of 94 individuals. Ten defense-related markers were clustered at a QTL on chromosome III, and three defense-related markers were located at a broad QTL on chromosome XII. The association of candidate genes with QTLs is a step toward understanding the molecular basis of quantitative resistance to an important plant disease.  (+info)

The genetic basis of the interspecific differences in wing size in Nasonia (Hymenoptera; Pteromalidae): major quantitative trait loci and epistasis. (7/4986)

There is a 2.5-fold difference in male wing size between two haplodiploid insect species, Nasonia vitripennis and N. giraulti. The haploidy of males facilitated a full genomic screen for quantitative trait loci (QTL) affecting wing size and the detection of epistatic interactions. A QTL analysis of the interspecific wing-size difference revealed QTL with major effects and epistatic interactions among loci affecting the trait. We analyzed 178 hybrid males and initially found two major QTL for wing length, one for wing width, three for a normalized wing-size variable, and five for wing seta density. One QTL for wing width explains 38.1% of the phenotypic variance, and the same QTL explains 22% of the phenotypic variance in normalized wing size. This corresponds to a region previously introgressed from N. giraulti into N. vitripennis that accounts for 44% of the normalized wing-size difference between the species. Significant epistatic interactions were also found that affect wing size and density of setae on the wing. Screening for pairwise epistatic interactions between loci on different linkage groups revealed four additional loci for wing length and four loci for normalized wing size that were not detected in the original QTL analysis. We propose that the evolution of smaller wings in N. vitripennis males is primarily the result of major mutations at few genomic regions and involves epistatic interactions among some loci.  (+info)

Nonequivalent Loci and the distribution of mutant effects. (8/4986)

It has been observed repeatedly that the distribution of new mutations of a quantitative trait has a kurtosis (a statistical measure of the distribution's shape) that is systematically larger than that of a normal distribution. Here we suggest that rather than being a property of individual loci that control the trait, the enhanced kurtosis is highly likely to be an emergent property that arises directly from the loci being mutationally nonequivalent. We present a method of incorporating nonequivalent loci into quantitative genetic modeling and give an approximate relation between the kurtosis of the mutant distribution and the degree of mutational nonequivalence of loci. We go on to ask whether incorporating the experimentally observed kurtosis through nonequivalent loci, rather than at locus level, affects any biologically important conclusions of quantitative genetic modeling. Concentrating on the maintenance of quantitative genetic variation by mutation-selection balance, we conclude that typically nonequivalent loci yield a genetic variance that is of order 10% smaller than that obtained from the previous approaches. For large populations, when the kurtosis is large, the genetic variance may be <50% of the result of equivalent loci, with Gaussian distributions of mutant effects.  (+info)

The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by analyzing gene expression traits one at a time. As thousands of expression traits are typically analyzed, this can reduce power because of the need to correct for the number of hypothesis tests performed. In addition, gene expression traits exhibit a complex correlation structure, which is ignored when analyzing traits individually. To address these issues, we applied two different multivariate dimension reduction techniques, the Singular Value Decomposition (SVD) and Independent Component Analysis (ICA) to gene expression traits derived from a cross between two strains of Saccharomyces cerevisiae. Both methods decompose the data into a set of meta-traits, which are linear combinations of all the expression traits. The meta-traits were enriched for several Gene Ontology categories including metabolic
Transcript abundance from cRNA hybridizations to Affymetrix microarrays can be used for simultaneous marker development and genome-wide gene expression quantitative trait locus (eQTL) analysis of crops. We have previously shown that it is easily possible to use Affymetrix expression arrays to profil …
Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. ...
The transcriptome connects genome to the gene function and ultimate phenome in biology. Sofar, transcriptomic approach was not used in peanut for performing trait mapping in bi-parentalpopulations. In this research, we sequenced the whole transcriptome in immature seeds in apeanut recombinant inbred line (RIL) population and explored thoroughly the landscape oftranscriptomic variations and its genetic basis. The comprehensive analysis identified total49 691 genes in RIL population, of which 92 genes followed a paramutation-like expressionpattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and15 837 distant eQTLs contributing to the whole-genome transcriptomic variation in peanut.There were 94 eQTL hot spot regions detected across the genome with the dominance of distanteQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putativecandidate gene and developed a linked marker InDel02 underlying a major QTL responsible forpurple ...
Expression quantitative trait loci (eQTL) analysis is a powerful method to detect correlations between gene expression and genomic variants and is widely used to interpret the biological mechanism underlying identified genome wide association studies (GWAS) risk loci. Numerous eQTL studies have been performed on different cell types and tissues of which the majority has been based on microarray technology. We present here an eQTL analysis based on cap analysis gene expression sequencing (CAGEseq) data created from human postmortem frontal lobe tissue combined with genotypes obtained through genotyping arrays, exome sequencing, and CAGEseq. Using CAGEseq as an expression profiling technique combined with these different genotyping techniques allows measurement of the molecular effect of variants on individual transcription start sites and increases the resolution of eQTL analysis by also including the non-annotated parts of the genome. We identified 2410 eQTLs and show that non-coding transcripts are
TY - JOUR. T1 - A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare. AU - Hori, Kiyosumi. AU - Yamamoto, Toshio. AU - Ebana, Kaworu. AU - Takeuchi, Yoshinobu. AU - Yano, Masahiro. PY - 2009/10/5. Y1 - 2009/10/5. N2 - To identify quantitative trait loci (QTLs) associated with culm length in Japanese japonica rice varieties, we conducted QTL analyses using a set of reciprocal backcrossed inbred lines (BILs) from crosses between Nipponbare and Koshihikari. We detected five QTLs in the two BILs that are involved in the culm-length difference between Nipponbare and Koshihikari. A QTL located on the short arm of chromosome 1, qCL1, was commonly detected near the simple sequence repeat (SSR) marker RM8068 in both BILs in three growing seasons. The Nipponbare allele of qCL1 shortened from 1.9 to 3.0 cm of culm length. Substitution lines (SLs) of Koshihikari in which the QTL was replaced with the Nipponbare allele exhibited decreased lengths of ...
The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and other quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. In the eQTL analysis, we utilize a recently proposed hierarchical multiple testing strategy which controls error rates regarding the discovery of functional variants. Our results ...
Background: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2. Results: We detected over 19,000 independent lead cis-eQTLs and over 6000 independent lead trans-eQTLs, targeting over 10,000 gene targets (eGenes), with a false discovery rate (FDR) , 5%. Of previously published significant GWAS SNPs, 48% are identified to be significant eQTLs in our study. Some trans-eQTLs point toward novel mechanistic explanations for the association of the SNP with the GWAS-related phenotype. We ...
Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are
The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes a method for breeding soybean plants containing quantitative trait loci that are associated with resistance to Asian Soybean Rust (ASR), a fungal disease associated with Phakopsora spp. The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program for resistance to ASR.
Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a ...
Abstract: Detecting genetic loci responsible for variation in quantitative traits is a problem of great importance to biologists. The location on a genetic map responsible for a quantitative trait is referred to as Quantitative Trait Loci, or QTL. This thesis uses a Bayesian Hierarchical Regression model which incorporates variability both within and between lines to detect the QTL. This method is applied to a simulated data set using the line information from Bay-0 × Shahdara population to find the activation probability of each genetic segment via the Gibbs sampler and Monte Carlo integration techniques. Using the activation probability, which indicates the influence of each segment within all the models, the QTL is detected. The results show that it is an effective way to detect QTL.. Bayesian hierarchical regression model to detect quantitative trait loci ...
OBJECTIVES: In sib pair studies, quantitative trait loci (QTL) identification may be adversely affected by non-normality in the phenotypic distribution, particularly when subjects falling in the tails of the distribution bias the trait mean or varian
IN the mapping of quantitative trait loci (QTL) in an experimental cross, selective genotyping (in which only the individuals at the extremes of the phenotype distribution are genotyped) can provide nearly equivalent power to complete genotyping at a reduced cost (Lander and Botstein 1989; Darvasi and Soller 1992).. Interval mapping with selectively genotyped data is best performed with consideration of all individuals, even those that were not genotyped (Lander and Botstein 1989). Consideration of only the genotyped individuals results in a biased estimate of the QTL effect. Haley-Knott regression (Haley and Knott 1992) generally provides a good approximation to standard interval mapping, but should be avoided in the case of selective genotyping, as it tends to produce inflated evidence for linkage (Feenstra et al. 2006).. Despite the common use of selective genotyping for QTL mapping and the extensive literature on significance thresholds for QTL mapping, we are not aware of any discussion of ...
Genome-wide studies of gene expression have successfully identified genetic variants that contribute to the variation of gene expression within populations [1-11]. The objective of genome-wide association studies (GWAS) is to map genotypic variation to phenotypic variation. Jansen and Nap [12] proposed extending the GWAS paradigm to deal with quantitative endophenotypes, e.g. RNA, protein and metabolite abundance in a cell. To date, consideration of RNA abundance has received most attention in the literature [1-11]. Those variants that affect gene expression are referred to as expression quantitative trait loci (eQTLs) of which thousands have been reported [1-11]. Most studies have focused on single nucleotide polymorphisms (SNPs).. The literature reports two classes of eQTL, cis-acting SNPs and trans-acting SNPs. Cis-acting SNPs lie within a gene or near the transcription start or stop site of a gene and correlate with the expression of that gene. In contrast, trans-acting SNPs can lie anywhere ...
TY - JOUR. T1 - A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. AU - Manichaikul, Ani. AU - Moon, Jee Young. AU - Sen, Śaunak. AU - Yandell, Brian S.. AU - Broman, Karl W.. PY - 2009/3. Y1 - 2009/3. N2 - The identification of quantitative trait loci (QTL) and their interactions is a crucial step toward the discovery of genes responsible for variation in experimental crosses. The problem is best viewed as one of model selection, and the most important aspect of the problem is the comparison of models of different sizes. We present a penalized likelihood approach, with penalties on QTL and pairwise interactions chosen to control false positive rates. This extends the work ofBroman and Speed to allow for pairwise interactions among QTL. A conservative version of our penalized LOD score provides strict control over the rate of extraneous QTL and interactions; a more liberal criterion is more lenient on interactions but seeks ...
TY - JOUR. T1 - Identification of quantitative trait locus for abscisic acid responsiveness on chromosome 5A and association with dehydration tolerance in common wheat seedlings. AU - Iehisa, Julio C.M.. AU - Matsuura, Takakazu. AU - Mori, Izumi C.. AU - Takumi, Shigeo. PY - 2014/1/1. Y1 - 2014/1/1. N2 - The phytohormone abscisic acid (ABA) plays important roles in response to environmental stress as well as in seed maturation and dormancy. In common wheat, quantitative trait loci (QTLs) for ABA responsiveness at the seedling stage have been reported on chromosomes 1B, 2A, 3A, 6D and 7B. In this study, we identified a novel QTL for ABA responsiveness on chromosome 5A using an F2 population derived from a cross between the common wheat cultivar Chinese Spring (CS) and a chromosome substitution line of CS with chromosome 5A of cultivar Hope (Hope5A). This QTL was found in a similar chromosomal region to previously reported QTLs for drought tolerance and seed dormancy. Physiological ...
Soybean [Glycine max (L.) Merr.] is an important oilseed crop which produces about 30 %of the worlds edible vegetable oil. The quality of soybean oil is determined by its fatty acid composition. Soybean oil high in oleic and low in linolenic fatty acids is desirable for human consumption and other uses. The objectives of this study were to identify quantitative trait loci (QTLs) for unsaturated fatty acids and to evaluate the genetic effects of single QTL and QTL combinations in soybean. A population of recombinant inbred lines derived from the cross of SD02-4-59 X A02-381100 was evaluated for fatty acid content in seven environments. In total, 516 polymorphic single nucleotide polymorphism markers, 477 polymorphic simple sequence repeat markers and three GmFAD3 geneswere used to genotype the mapping population. By using the composite interval mapping and/or the interval mapping method, a total of 15 QTLs for the three unsaturated fatty acids were detected in more than two environments. Two QTLs for
Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five disease resistance QTL that colocalized with defense response genes were accumulated by marker-aided selection to develop blast-resistant varieties. One advanced backcross line carrying the major-effect QTL on chromosome (chr) 8, which included a cluster of 12 germin-like protein (OsGLP) gene members, exhibited resistance to rice (Oryza sativa) blast disease over 14 cropping seasons. To determine if OsGLP members contribute to resistance and if the resistance was broad spectrum, a highly conserved portion of the OsGLP coding region was used as an RNA interference trigger to silence a few to all expressed chr 8 OsGLP family members. Challenge with two different fungal pathogens (causal agents of rice blast and sheath ...
The accumulation of intracellular fat depots is a polygenic trait. Therefore, the extent of lipid storage in the individuals of a species covers a broad range and is determined by many genetic factors. Quantitative trait loci analysis can be used to identify those genetic differences between two strains of the same species that are responsible for the differences in a given phenotype. We used this method and complementary approaches to identify genes in the yeast Saccharomyces cerevisiae that are involved in neutral lipid storage. We selected two yeast strains, the laboratory strain BY4741 and the wine yeast AWRI1631, with a more than two-fold difference in neutral lipid content. After crossing, sporulation and germination, we used fluorescence activated cell sorting to isolate a subpopulation of cells with the highest neutral lipid content from the pool of segregants. Whole genome sequencing of this subpopulation and of the unsorted pool of segregants implicated several loci that are involved in lipid
Deerhake, Marion Elizabeth, Quantitative trait loci analysis of blood pressure in an eight intercross mouse study (2008). Summer and Academic Year Student Reports. 2234 ...
TY - JOUR. T1 - Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene. AU - Al Abri, Mohammed A.. AU - Posbergh, Christian. AU - Palermo, Katelyn. AU - Sutter, Nathan B.. AU - Eberth, John. AU - Hoffman, Gabriel E.. AU - Brooks, Samantha A.. PY - 2016/10/19. Y1 - 2016/10/19. N2 - Withers height is an important economic trait for the American Miniature Horses (AMHs) as the breeders primary objective is to produce small and proportionate animals. Identification of Quantitative Trait Loci (QTLs) affecting height in this breed will result in a better understanding of the genetic architecture and biological pathways contributing to skeletal development. In earlier work, we genotyped 48 horses from 16 different breeds that represent extremes in body size, using the Equine SNP50 bead chip (Illumina Inc). In this study, we applied a dominant model Genome-wide association study (GWAS), a genome-wide fixation index (FST) estimation, as well as a ...
MalaCards based summary : Bone Mineral Density Quantitative Trait Locus 12, is also known as bone mineral density qtl 12, osteoporosis. An important gene associated with Bone Mineral Density Quantitative Trait Locus 12 is UGT2B17 (UDP Glucuronosyltransferase Family 2 Member B17). Affiliated tissues include bone ...
MalaCards based summary : Bone Mineral Density Quantitative Trait Locus 11, also known as bmnd11, is related to osteoporosis. An important gene associated with Bone Mineral Density Quantitative Trait Locus 11 is BMND11 (Bone Mineral Density QTL 11). Affiliated tissues include bone ...
A four-stage approach was used to analyse epistasis based on the pre-corrected phenotypes where SNP genotypes were fitted as fixed factors: 1) single SNP regression to identify qSNPs (see above); 2) detect qSNP × qSNP pairs [9]; 3) detect qSNP × non-qSNP pairs; 4) detect non-qSNP × non-qSNP pairs. Nested tests were used to identify significant epistatic pairs; the first test compares the full model (y = μ+SNP1+SNP2+SNP1 *SNP2+e) with the NULL model (y = μ+e); the second test compares the full model with the two-SNP model (y = μ+SNP1+SNP2+e) (i.e. epistasis test). Only pairs that were significant for the first test enter the epistasis test. When either SNP1 or SNP2 is a qSNP, the first test is changed to ensure the full model is better than the single SNP model (y = μ+qSNP +e) before the epistasis test. When both SNP1 and SNP2 are qSNPs, only the epistasis test is needed. To avoid spurious interactions between closely located SNPs an arbitrary minimum distance of 10 cM was applied to any ...
TY - JOUR. T1 - Identification of porcine Lhx3 and SF1 as candidate genes for QTL affecting growth and reproduction traits in swine. AU - Smith, T. P.L.. AU - Showalter, A. D.. AU - Sloop, K. W.. AU - Rohrer, G. A.. AU - Fahrenkrug, S. C.. AU - Meier, B. C.. AU - Rhodes, S. J.. PY - 2001. Y1 - 2001. N2 - The distal portion of the long arm of porcine chromosome 1 has been shown to harbour several quantitative trait loci affecting growth and reproductive traits in swine. In order to identify potential candidate genes that might underlie these effects, a comparative mapping analysis was undertaken to define the extent of orthologous segments of human chromosome 9. A microsatellite associated with heat shock protein (HSP) A5 was used to define the proximal boundary of the quantitative trait loci (QTL) region, which suggests the human orthologue of the gene(s) responsible for the observed effects lies between HSPA5 and the q arm telomere of human chromosome 9. Examination of this region revealed two ...
Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the mineral content of bovine longissimus dorsi muscle can contribute to the identification of genes that control mineral balance, transportation, absorption and excretion and that could be associated to metabolic disorders. We applied a genome-wide association strategy and genotyped 373 Nelore steers from 34 half-sib families with the Illumina BovineHD BeadChip. Genome-wide association analysis was performed for mineral content of longissimus dorsi muscle using a Bayesian approach implemented in the GenSel software. Muscle mineral content in Bos indicus cattle was moderately heritable, with estimates ranging from 0.29 to 0.36. Our results suggest that variation in mineral content is influenced by numerous small-effect QTL (quantitative trait loci) but a large-effect QTL that explained 6.5% of the
Three quantitative trait loci (QTL) located on chromosome 1H, single QTL located on chromosomes 1H, 2H, 4H, 5H and 7H, were identified to be responsible for salinity tolerance under different environments. Waterlogging stress, daylight length and temperature showed significant effects on barley salinity tolerance. The QTL for salinity tolerance mapped on chromosomes 4H and 7H, QSlwd.YG.4H, QSlwd.YG.7H and QSlww.YG.7H were only identified in winter trials, while the QTL on chromosome 2H QSlsd.YG.2H and QSlsw.YG.2H were only detected in summer trials. Genes associated with flowering time were found to pose significant effects on the salinity QTL mapped on chromosomes 2H and 5H in summer trials. Given the fact that the QTL for salinity tolerance QSlsd.YG.1H and QSlww.YG.1H-1 reported here have never been considered in the literature, this warrants further investigation and evaluation for suitability to be used in breeding programs.. ...
Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content (GPC); test weight (TW); single kernel characterization system (SKCS)-estimated kernel weight (SKW); kernel diameter (KD); kernel hardness measured by near-infrared reflectance spectroscopy (NIRS) hardness index (NHI); and SKCS-hardness index (SHI), a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers was developed using recombinant inbred lines (RILs) derived from Ning7840 x Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes, excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic ...
Serum lactate dehydrogenase (LDH) is used in diagnosing many diseases and is significantly determined by genetic factors. Three genes coding for LDH isoenzymes were mapped to chromosome 11q15 and 12p12. We used 330 Framingham Heart Study largest families for microsatellite linkage scan and 100K SNPs association scan to determine quantitative trait loci of LDH level. We estimated the heritability at 41%. Our genome-wide linkage analysis yielded several chromosomal regions, other than 11q and 12p, with LOD scores between 1 and 2.5. None of the 100K SNPs with a P-value ,10^-4 in our genome-wide association study was close to the chromosomal regions where the LDH genes reside. Our study demonstrated a strong genetic effect on the variation of LDH levels. There may not be a single gene with a large effect, instead may be several genes with small effects in controlling the variation of serum LDH. Those genes may be located on chromosomal regions that differ from where the genes encoding LDH isoenzymes ...
Breeding chickens for heat tolerance is desirable. The F18 and F19 generations of a broiler by Fayoumi advanced intercross line (AIL) was used to facilitate fine mapping of QTL. Three major phenotype collection phases were: pre-heat, acute heat, and chronic heat, with birds being exposed to daily heat cycles from 22 to 28 days of age. Body temperature was measured at all three phases; body weight at pre-heat and chronic heat phases. Breast muscle yield (as percentage of body weight) was measured after necropsy at d 28. Feed digestibility was assayed from ileal content collected at d 28. Birds were genotyped using a 600K Affymetrix chicken SNP array. Using GenSel significant QTL were found for each of the measured traits, indicating the feasibility of improving performance under hot conditions by genomic selection. This is the first GWAS using this novel AIL of chickens under heat stress.. ...
Low soil P availability is a primary constraint to common bean (Phaseolus vulgaris L.) production in Latin America and Africa. Substantial genotypic variation in bean adaptation to low phosphorus (LP) availability has been linked with root traits that enhance the efficiency of soil foraging. The objectives of this study were to identify quantitative trait loci (QTLs) for P accumulation and associated root architectural traits, to facilitate genetic improvement and to reveal physiological relationships. Eighty‐six F5.7 recombinant inbred lines (RILs) were developed from a cross between G19833, an Andean landrace with high total P accumulation, and DOR 364, a Mesoamerican cultivar with low total P accumulation in LP conditions. A genetic map constructed with restriction fragment length polymorphisms (RFLPs), microsatellites, and PCR‐based markers covering 1703 centimorgans (cM) total genetic distance and all eleven linkage groups (LGs) was used for QTL analysis. Seventy‐one RILs were ...
Genome editing (GE) is a method that enables specific nucleotides in the genome of an individual to be changed. To date, use of GE in livestock has focussed on simple traits that are controlled by a few quantitative trait nucleotides (QTN) with large effects. The aim of this study was to evaluate the potential of GE to improve quantitative traits that are controlled by many QTN, referred to here as promotion of alleles by genome editing (PAGE). Multiple scenarios were simulated to test alternative PAGE strategies for a quantitative trait. They differed in (i) the number of edits per sire (0 to 100), (ii) the number of edits per generation (0 to 500), and (iii) the extent of use of PAGE (i.e. editing all sires or only a proportion of them). The base line scenario involved selecting individuals on true breeding values (i.e., genomic selection only (GS only)-genomic selection with perfect accuracy) for several generations. Alternative scenarios complemented this base line scenario with PAGE (GS + PAGE).
Differences in floral morphologies affect pollination behaviour in many flowering plants. In the genus Oryza, several differences in the size of floral organs are known. In this study, we focused on the differences in the size of floral organs between common cultivated rice, Oryza sativa L. and its wild ancestor, O. rufipogon. We compared floral morphologies between cultivated rice O. sativa cv. Nipponbare and O. rufipogon W630. We first evaluated temporal changes in filament and anther lengths. W630 had longer filaments with rapid elongation within 15 min after spikelet opening. W630 also had longer anthers than Nipponbare, and size of anther was consistent throughout all time examined. We also analysed other six floral traits, and found that W630 had higher stigma and style length, as well as lemma and palea length, but lower lemma and palea width. Quantitative trait locus (QTL) analysis was performed to identify the loci controlling these floral traits, using backcross recombinant inbred
The whitebacked planthopper (WBPH), Sogatella furcifera Horváth, is a serious rice pest in Asia. Ovicidal resistance is a natural rice defense mechanism against WBPH and is characterized by the formation of watery lesions (WLs) and increased egg mortality (EM) at the WBPH oviposition sites. This study aimed to understand the genetic and molecular basis of rice ovicidal resistance to WBPH by combining genetic and genomic analyses. First, the ovicidal trait in doubled haploid rice lines derived from a WBPH-resistant cultivar (CJ06) and a WBPH-susceptible cultivar (TN1) were phenotyped based on the necrotic symptoms of the leaf sheaths and EM. Using a constructed molecular linkage map, 19 quantitative trait loci (QTLs) associated with WLs and EM were identified on eight chromosomes. Of them, qWL6 was determined to be a major QTL for WL. Based on chromosome segment substitution lines and a residual heterozygous population, a high-resolution linkage analysis further defined the qWL6 locus to a 122-kb region
Detecting both the majors genes that control the phenotypic mean and those controlling phenotypic variance has been raised in quantitative trait loci analysis. In order to mapping both kinds of genes, we applied the idea of the classic Haley-Knott regression to double generalized linear models. We performed both kinds of quantitative trait loci detection for a Red Jungle Fowl x White Leghorn F2 intercross using double generalized linear models. It is shown that double generalized linear model is a proper and efficient approach for localizing variance-controlling genes. We compared two models with or without fixed sex effect and prefer including the sex effect in order to reduce the residual variances. We found that different genes might take effect on the body weight at different time as the chicken grows.. ...
The genetics of sexual isolation, behavioral differences between species that prevent mating, is understood poorly. Pheromonal differences between species can influence sexual isolation in many animals and in some cases a single locus can cause large functional changes in pheromonal mating signals. Drosophila cuticular hydrocarbons (CHCs) can function as pheromones and consequently affect mate recognition. In a previous study of the two major CHCs in females that affect mating discrimination between Drosophila simulans and D. sechellia, quantitative trait loci (QTL) were identified on the X and third chromosome, and a few candidate genes were potentially implicated. Here we specifically test candidate genes for CHC biosynthesis and determine the genetic architecture of four additional CHCs that differ in abundance between D. simulans and D. sechellia females. The same QTL, and new ones, were found for additional CHCs. By examining all these CHCs and exploring their covariance, we were able to ascribe
Di Nicolantonio, R., Kostka, V., Kwitek, A., Jacob, H., Thomas, W.G. and Harrap, S.B. 2006, Fine mapping of Lvm1: a quantitative trait locus controlling heart size independently of blood pressure, Pulmonary pharmacology & therapeutics, vol. 19, no. 1, pp. 70-73, doi: 10.1016/j.pupt.2005.02.010. ...
Coffee Berry Disease (CBD) is a major constraint that limits Coffea arabica production, whose resistance is governed by three genes, T, R that are dominant and recessive k in varieties Hibrido de Timor (HDT), Rume Sudan (RS) and K7 respectively. This study identified the genomic region occupied by R-gene using F2 genotypes from varieties RS and SL28; and Single Nucleotide Polymorphic (SNP) markers obtained through Genotyping by Sequencing. Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. The Linkage map spread over 5525.39 cM across eleven coffee chromosomes (Chr). The QTL was analyzed by both Interval Mapping (IM) and Inclusive Composite Interval Mapping (ICIM) using SNP markers and CBD resistance mean scores of the F2 genotypes and their parents. Three QTLs, qCBD 1-1 in Chr 1, qCBD 2-1 and qCBD 2-2 in Chr 2 were significantly associated with CBD resistance, detected by both IM and ICIM at LOD ≥ 2.5 (P≤0.05).  Two
Quantitative resistance of Salix to Melampsora larici--epitea leaf rust was studied in 2 Salix mapping populations. One population was a backcross between a S, schwerinii x S. viminalis hybrid and S. viminalis, and the other was all F-2 population between S. viminalis and S. dasyclados. A leaf disc bioassay was used to study the components of quantitative resistance (latent period, uredinia number, and uredinia size) to 3 isolates of the leaf rust. The analysis of quantitative trait loci (QTLs) revealed 9 genomic regions in the backcross population and 7 genomic regions in the F-2 population that were important for rust resistance, with QTLs explaining 8-26% of the phenotypic variation. An important genomic region was identified for the backcross population in linkage group 2, where QTLs were identified for all resistance components for 2 of the rust isolates. Four of the QTLs had overlapping mapping intervals, demonstrating a common genetic background for latent period, uredinia diameter, and ...
TY - JOUR. T1 - A polymerase chain reaction-based linkage map of broccoli and identification of quantitative trait loci associated with harvest date and head weight. AU - Brown, Allan F.. AU - Jeffery, Elizabeth H.. AU - Juvik, John A.. N1 - Copyright: Copyright 2020 Elsevier B.V., All rights reserved.. PY - 2007/7. Y1 - 2007/7. N2 - A set of 216 polymerase chain reaction-based molecular markers was screened for polymorphisms using two morphologically dissimilar broccoli (Brassica oleracea L. ssp. italica Plenck) lines, VI-158 and Brocolette Neri E. Cespuglio. Fifty-nine of these simple sequence repeat (SSR) and sequence-related amplified polymorphic (SRAP) primer pairs generated 69 polymorphisms that were used to construct a linkage map of broccoli from a population of 162 F2:3 families derived from the cross between these two lines. Ten linkage groups were generated that spanned a distance of 468 cM with an average interval width of 9.4 cM. The map was used to identify quantitative trait ...
Limb bone lengths and bone mineral density (BMD) have been used to assess the bone growth and the risk of bone fractures in pigs, respectively. It has been suggested that limb bone lengths and BMD are under genetic control. However, the knowledge about the genetic basis of the limb bone lengths and mineralisatinon is limited in pigs. The aim of this study was to identify quantitative trait loci (QTL) affecting limb bone lengths and BMD of the distal femur in a White Duroc × Erhualian resource population. Limb bone lengths and femoral bone mineral density (fBMD) were measured in a total of 1021 and 116 F2 animals, respectively. There were strong positive correlations among the lengths of limb bones and medium positive correlations between the lengths of limb bones and fBMD. A whole-genome scan involving 183 microsatellite markers across the pig genome revealed 35 QTL for the limb bone lengths and 2 for femoral BMD. The most significant QTL for the lengths of five limb bones were mapped on two
TY - JOUR. T1 - Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA. AU - Terpstra, I.R.. AU - Snoek, L.B.. AU - Keurentjes, J.J.B.. AU - Peeters, A.J.M.. AU - van den Ackerveken, G.. PY - 2010. Y1 - 2010. N2 - Gene expression differences between individuals within a species can be largely explained by differences in genetic background. The effect of genetic variants (alleles) of genes on expression can be studied in a multifactorial way by application of genetical genomics or expression quantitative trait locus (eQTL) mapping. In this paper we present a strategy to construct regulatory networks by application of genetical genomics in combination with transcript profiling of mutants that are disrupted in single genes. We describe the network identification downstream of the receptor-like kinase ERECTA in Arabidopsis (Arabidopsis thaliana). Extending genetical genomics on the Landsberg erecta/Cape Verde islands (Ler/Cvi) ...
In previous work, we identified genetic correlations between cAMP accumulation in the cerebellum and sensitivity to the incoordinating effects of ethanol. A genetic correlation suggests that common genes underlie the phenotypes investigated. One method for provisionally identifying genes involved in a given phenotypic measure is quantitative trait locus (QTL) analysis. Using a panel of 30 BXD recombinant inbred strains of mice and the progenitors (DBA/2J and C57BL/6J), and the dowel test for ataxia, we measured the blood ethanol concentrations at the time an animal first fell from the dowel and acute functional tolerance (AFT), and investigated cAMP signaling in the cerebellum. Cyclic AMP accumulation was measured in whole-cell preparations of cerebellar minces from individual mice under basal or stimulated conditions. We conducted a genome-wide QTL analysis of the behavioral and biochemical measures with >2000 genetic markers to identify significant associations. Western blot and comparative ...
TY - JOUR. T1 - Quantitative trait loci and molecular markers associated with wheat allelopathy. AU - Wu, Hanwen. AU - Pratley, James. AU - Ma, W. AU - Haig, Terrence. N1 - Imported on 12 Apr 2017 - DigiTool details were: Journal title (773t) = Theoretical and Applied Genetics: international journal of plant breeding research. ISSNs: 0040-5752; PY - 2003. Y1 - 2003. N2 - Wheat (Triticum aestivum L.) has been examined for allelopathic potential against annual ryegrass (Lolium rigidum). The bioassay technique, equal-compartment-agar-method, was employed to evaluate seedling allelopathy in a doubled-haploid (DH) population derived from cv Sunco (weakly allelopathic) and cv Tasman (strongly allelopathic). A significant difference in allelopathic activity was found among the DH lines, which inhibited the root length of ryegrass across a range from 23.7 to 88.3%. The phenotypic data showed that wheat allelopathic activity was distributed normally within this DH population and a substantial ...
In dairy cattle, quantitative trait nucleotides (QTNs) underlying quantitative trait loci (QTL) for milk production traits have been identified in bovine DGAT1, GHR and ABCG2 genes. The SPP1 gene has also been proposed to be a regulator of lactation. In sheep, QTL underlying milk production traits h …
3C technologies have enabled studies of the dynamics of high-order chromatin structures and long-range chromatin interactions (26-30). However, how these long-range interactions contribute to biological processes and human diseases is not well understood. Our research has focused on an enhancer containing the PCa risk-associated rs55958994 SNP, integrating higher-order chromatin structure data, gene expression profiling, and functional assays. Our results suggest that the rs55958994-containing enhancer regulates PCa progression through long-range interactions with multiple genes. Among these genes, ITGA5, CDH23, and CNTN1 were verified to be both regulated by the rs55958994-containing enhancer and associated with PCa progression; deletion of the enhancer region in PCa cells induced down-regulation of these target genes and led to defects in tumor initiation and migration and loss of CSCs.. Previous eQTL (expression quantitative trait locus) analyses suggested that rs55958994 is linked to KRT8 ...
Shirali M., Miraei‐Ashtiani S.R., Pakdel A., Haley C., Navarro P. and Pong‐Wong R, 2015, A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic Breeding Values under Different Quantitative Trait Locus (QTL) Model Assumptions, Iranian Journal of Applied Animal Science, 5(1), 41-46 Shirali M., Miraei‐Ashtiani S.R., Pakdel A., Haley C., Navarro P. and Pong‐Wong R, 2015, A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic Breeding Values under Different Quantitative Trait Locus (QTL) Model Assumptions, Iranian Journal of Applied Animal Science, 5(1), 41-46
BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is associated with obesity and the metabolic syndrome and affects over one third of American adults. A subset of NAFLD patients develop advanced disease associated with liver injury, scar tissue (fibrosis), and cirrhosis, increasing risk for liver-related mortality, including primary liver cancer. Several genes have been associated with NAFLD, but determination of their function in the disease process has been difficult. We hypothesized that expression quantitative trait loci (eQTL) analysis would improve the identification of causally related genetic variants by integrating single nucleotide polymorphisms (SNPs) with gene expression. METHODS: Patients with biopsy-proven NAFLD were selected based on fibrosis stage (mild NAFLD: stage F0-F1 vs. advanced NAFLD: stage F3-F4). Genomic data, including genotype (Cardiometabolic SNP array, Illumina), methylation (Human Methylation450 BeadChip, Illumina) and expression (Human U133 Plus 2.0 GeneChip, ...
ILs and advanced backcross QTL approaches are now well-established tools for dissecting the genetic basis of complex polygenic traits in plant populations. In this study, S. pennellii ILs were used to identify a fruit firmness QTL located to an 8.6-Mb region on tomato chromosome 2. A prior study had identified a firmness QTL, fir2.1 in Solanum pimpinellifolium (Doganlar et al., 2002), mapping within this region. Conservation of QTLs within the Solanaceace family has been demonstrated for a number of traits including fruit size, shape, and weight (Saliba-Colombani et al., 2001; Frary et al., 2004). However, QTL fir2.1 in S. pimpinellifolium has not been further resolved by fine-mapping. In this work, we have used a composite mapping population of M82 × IL 2-3 F2 and M82 × IL 2-4 F3 to resolve the S. pennellii firmness QTL on chromosome 2 and report that at least several major firmness effects occur within a mapping interval of approximately 8.6 Mb, delineated by markers CT255 and TG527. Other ...
CONTEXT: Recently, a quantitative trait locus for stature was reported on chromosome 3p26 in patients with type 2 diabetes. OBJECTIVE: Given that ghrelin is a peptide involved in GH release and located on 3p26, we hypothesized that variation within its gene (GHRL) may be responsible for the quantitative trait locus on 3p26. DESIGN: The evidence for linkage around GHRL was refined with the genotyping of an additional four microsatellites (D3S4545, D3S1537, D3S1597, and D3S3611), giving a total of 27 markers, followed by multipoint variance components linkage analysis. Probands from the linkage families were typed for five common single nucleotide polymorphisms (SNPs) within GHRL and tested for association with adult stature using haplotype trend regression. RESULTS: The maximum multipoint evidence for linkage between adult stature and the 27 microsatellites yielded an LOD score of 2.58 (P = 0.0003) between D3S1297 and D3S1304. Five common (frequency of | or =5%) SNPs were typed in the probands [two
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作 者:Kun Li, Hongwu Wang, Xiaojiao Hu, Feiqian Ma, Yujin Wu, Qi Wang, Zhifang Liu, and Changling Huang. 影响因子: 4.298. 刊物名称: Frontiers in plant science. 出版年份: 2017. 卷: 8 期:24 August 页码: 1472. 文章摘要 : The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came ...
Abundant contribution of short tandem repeats to gene expression variation in humans Melissa Gymrek , Thomas Willems , Haoyang Zeng , Barak Markus , Mark J Daly , Alkes L Price , Jonathan Pritchard , Yaniv Erlich doi: Expression quantitative trait loci (eQTLs) are a key tool to dissect cellular processes mediating complex diseases.…
Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the
Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent ...
Schizophrenia is a complex, highly heritable and heterogeneous disease with estimated heritability ranging up to 80%. It affects approximately 0.5-1% of the world population. During the past decade, numerous schizophrenia-associated variants and loci in world-wide populations have been identified, but most of the risk single-nucleotide polymorphisms (SNPs) or variants identified by GWASs were located in intergenic, intronic or other non-coding regions. To identify the causal genes at the reported risk loci and to elucidate how these risk genes influence the pathogenesis of schizophrenia remains a daunting task. Previous studies showed that most complex disease-associated variants confer risk for the illnesses by acting as eQTL to influence gene expression in cis or in trans. By integrating a large-scale schizophrenia GWAS data and brain prefrontal cortex expression quantitative trait loci (eQTL) data, a team of scientists from the Kunming Institute of Zoology (KIZ) of the Chinese Academy of ...
Brassica napus L. is a widely cultivated oil crop and provides important resources of edible vegetable oil, and its quality is determined by fatty acid composition and content. To explain the genetic basis and identify more minor loci for fatty acid content, the multi-locus random-SNP-effect mixed linear model (mrMLM) was used to identify genomic regions associated with fatty acid content in a genetically diverse population of 435 rapeseed accessions, including 77 winter-type, 55 spring-type, and 303 semi-winter-type accessions grown in different environments. A total of 149 quantitative trait nucleotides (QTNs) were found to be associated with fatty acid content and composition, including 34 QTNs that overlapped with the previously reported loci, and 115 novel QTNs. Of these, 35 novel QTNs, located on chromosome A01, A02, A03, A05, A06, A09, A10, and C02, respectively, were repeatedly detected across different environments. Subsequently, we annotated 95 putative candidate genes by BlastP ...
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A genome-wide association study (GWAS) was conducted to identify expression quantitative trait loci (eQTLs) for the genes involved in phosphatidylinositol-3-kinase/v-akt murine thymoma viral oncogene homolog (PI3K/AKT) pathway.Data on mRNA expression of 341 genes in lymphoblastoid cell lines of 373 Europeans recruited by the 1000 Genomes Project using Illumina HiSeq2000 were utilized. We used their genotypes at 5,941,815 nucleotide variants obtained by Genome Analyzer II and SOLiD.The association analysis revealed 4166 nucleotide variants associated with expression of 85 genes (P < 5 × 10). A total of 73 eQTLs were identified as association signals for the expression of multiple genes. They included 9 eQTLs for both of the genes encoding collagen type I alpha 1 (COL1A1) and integrin alpha 11 (ITGA11), which synthesize a major complex of plasma membrane. They also included eQTLs for type IV collagen molecules; 13 eQTLs for both collagen type IV alpha 1 (COL4A1) and collagen type IV alpha 2 ...
Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P,0.001) and apoptosis (P,0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F₁individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F₂ hybrids. Quantitative trait loci analysis of 287 F₂ fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P,0.001) with overdominance effect. ...
Individual kernel weight is an important trait for maize yield determination. We have identified genomic regions controlling this trait by using the B73xMo17 population; however, the effect of genetic background on control of this complex trait and its physiological components is not yet known. The objective of this study was to understand how genetic background affected our previous results. Two nested stable recombinant inbred line populations (N209xMo17 and R18xMo17) were designed for this purpose. A total of 408 recombinant inbred lines were genotyped and phenotyped at two environments for kernel weight and five other traits related to kernel growth and development. All traits showed very high and significant (P , 0.001) phenotypic variability and medium-to-high heritability (0.60−0.90). When N209xMo17 and R18xMo17 were analyzed separately, a total of 23 environmentally stable quantitative trait loci (QTL) and five epistatic interactions were detected for N209xMo17. For R18xMo17, 59 ...
TY - JOUR. T1 - Exploring hepsin functional genetic variation association with disease specific protein expression in bipolar disorder. T2 - Applications of a proteomic informed genomic approach. AU - Nassan, Malik. AU - Jia, Yun Fang. AU - Jenkins, Greg. AU - Colby, Colin. AU - Feeder, Scott. AU - Choi, Doo Sup. AU - Veldic, Marin D. AU - McElroy, Susan L.. AU - Bond, David J.. AU - Weinshilboum, Richard M. AU - Biernacka, Joanna M. AU - Frye, Mark A. PY - 2017/12/1. Y1 - 2017/12/1. N2 - In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five ...
Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through ...
|i|SLC30A8|/i| encodes zinc transporter 8 which is involved in packaging and release of insulin. Evidence for the association of|i| SLC30A8|/i| variants with type 2 diabetes (T2D) is inconclusive. We interrogated single nucleotide polymorphisms (SNPs) around|i| SLC30A8|/i| for association with T2D in high-risk, pedigreed individuals from extended Mexican American families. This study of 118 SNPs within 50 kb of the|i| SLC30A8|/i| locus tested the association with eight T2D-related traits at four levels: (i) each SNP using measured genotype approach (MGA); (ii) interaction of SNPs with age and sex; (iii) combinations of SNPs using Bayesian Quantitative Trait Nucleotide (BQTN) analyses; and (iv) entire gene locus using the gene burden test. Only one SNP (rs7817754) was significantly associated with incident T2D but a summary statistic based on all T2D-related traits identified 11 novel SNPs. Three SNPs and one SNP were weakly but interactively associated with age and sex, respectively. BQTN analyses could
Beamer WG, Shultz KL, Churchill GA, Frankel WN, Baylink DJ, Rosen CJ, Donahue LR. Quantitative trait loci for bone density in C57BL/6J and CAST/EiJ inbred mice. Mamm Genome. 1999 Nov;10(11):1043-9. PubMed 10556421 Ackert-Bicknell CL, Karasik D, Li Q, Smith RV, Hsu YH, Churchill GA, Paigen BJ, Tsaih SW. Mouse BMD quantitative trait loci show improved concordance with human genome-wide association loci when recalculated on a new, common mouse genetic map. J Bone Miner Res. 2010 Aug;25(8):1808-20. PubMed 20200990 ...
Mediators of Inflammation is a peer-reviewed, Open Access journal that publishes original research and review articles on all types of inflammatory mediators, including cytokines, histamine, bradykinin, prostaglandins, leukotrienes, PAF, biological response modifiers and the family of cell adhesion-promoting molecules.
Increasingly, baseline peripheral blood cell counts are implicated as risk factors for common complex diseases. While genetic influences on these hematologic parameters are firmly established, the gen
Non-insulin-dependent diabetes mellitus (NIDDM) is a prototypical multifactorial disease. Genetic predisposition and obesity are major risk factors for NIDDM development and the interactions between these factors are likely to be important in the eti
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints ...
The study was conducted to investigate genetic variability among 113 aromatic and fine local rice genotypes of which five were exotic in origin. The test genotypes were evaluated for 19 growth traits, yield components, and yield. All the quantitative traits varied significantly among the test genotypes. High heritability along with high genetic advance was observed for flag leaf area, secondary branches per panicle, filled grains per panicle, grain length, grain breadth, grain length breadth ratio, and 1000 grain weight. Such findings suggested preponderance of additive gene action in gene expression for these characters. Grain yield was significantly and positively correlated with days to flowering, days to maturity, panicle length, filled grains per panicle, and 1000 grain weight. According to D2 cluster analysis, 113 test genotypes formed 10 clusters. Selection of parents from the clusters V and X followed by hybridization would possibly result in desirable heterosis for the development of ...
A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematically prioritize both variants and genes that confer susceptibility to mental diseases in personal genomes of individual patients and to facilitate the development of personalized treatment or therapeutic approaches. Leveraging deep neural network on the TensorFlow framework, we developed a computational tool, integrated Mental-disorder GEnome Score (iMEGES), for analyzing whole genome/exome sequencing data on personal genomes. iMEGES takes as input genetic mutations and phenotypic information from a patient with mental disorders, and outputs the rank of whole genome susceptibility variants and the prioritized disease-specific genes for mental disorders by integrating contributions from coding and non-coding variants, structural variants (SVs), known brain expression quantitative trait loci (eQTLs),
In a first-of-its-kind study, NC State researchers applied a new approach to examine how members of two different species - a plant and a pathogen, for example, or a bacterium and a human - interact at the molecular level, and whether slight genetic changes in one species could affect gene expression in the other.. In a paper published in the journal Genetics, NC State plant pathologists, biologists and statisticians use a genetic mapping method - expression quantitative trait locus, or eQTL, mapping - applied in a novel way to describe these interactions, opening the door for further work on these complex relationships.. Were really trying to get to the genetics behind the interactions between two different organisms, said David McK. Bird, a NC State plant pathology professor and co-corresponding author of the paper. Genetics gives us causality more than just correlation.. We used an interactive system to see if DNA changes in one species would affect the characteristics in another ...
Alzheimers disease (AD) is the most common neurodegenerative disease in the elderly and the leading cause of dementia in humans. Evidence shows that cellular trafficking and recycling machineries are associated with AD risk. A recent study found that the coat protein complex I (COPI)-dependent trafficking in vivo could significantly reduce amyloid plaques in the cortex and hippocampus of neurological in the AD mouse models and identified 12 single-nucleotide polymorphisms in COPI genes to be significantly associated with increased AD risk using 6,795 samples. Here, we used a large-scale GWAS dataset to investigate the potential association between the COPI genes and AD susceptibility by both SNP and gene-based tests. The results showed that only rs9898218 was associated with AD risk with P = 0.017. We further conducted an expression quantitative trait loci (eQTLs) analysis and found that rs9898218 G allele was associated with increased COPZ2 expression in cerebellar cortex with P = 0.0184. Importantly,
Differential HLA-C levels influence several human diseases, but the mechanisms responsible are incompletely characterized. Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals from the 1000 Genomes dataset.. We tested 68,726 SNPs within the MHC for association with HLA-C level. The HLA-C promoter region variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant association with HLA-C levels (p = 4.2 x 10-66). This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 x 10-20) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p < 10-15).. rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher ...
BACKGROUND: Complex etiology and pathogenesis of pathophysiological components of the cardio-metabolic syndrome have been demonstrated in humans and animal models. METHODOLOGY/PRINCIPAL FINDINGS: We have generated extensive physiological, genetic and genome-wide gene expression profiles in a congenic strain of the spontaneously diabetic Goto-Kakizaki (GK) rat containing a large region (110 cM, 170 Mb) of rat chromosome 1 (RNO1), which covers diabetes and obesity quantitative trait loci (QTL), introgressed onto the genetic background of the normoglycaemic Brown Norway (BN) strain. This novel disease model, which by the length of the congenic region closely mirrors the situation of a chromosome substitution strain, exhibits a wide range of abnormalities directly relevant to components of the cardio-metabolic syndrome and diabetes complications, including hyperglycaemia, hyperinsulinaemia, enhanced insulin secretion both in vivo and in vitro, insulin resistance, hypertriglyceridemia and altered pancreatic
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available,
We will work to validate, dissect and characterize a QTL for kernel weight (KW) located on chromosome 6A. The QTL was identified in a RIL population derived the cross SS-MPV 57 x Massey when grown at Raleigh, NC for three years. The QTL has an additive effect of 1.75 mg. In this population, the KW QTL coincides with plant height QTL having an additive effect of 3.78 cm. Heterozygous plants were identified in F5-derived RIL for development of fine-mapping populations. This QTL region is physically large and spans the centromere. Observed recombination in the HIFs has been localized towards the ends of the QTL interval.. A second population of 358 RIL from the cross SS-MPV57 x LA95135 is being used to validate the KW QTL effect. This population is also being targeted for identification of additional QTL in regions more amenable to fine-mapping and cloning.. ...
We have examined the genetics of nonhost resistance in Arabidopsis, using the bean pathogen Pseudomonas syringae pv. phaseolicola race 6 1448A to probe accessions for natural variation in basal defense. Symptoms rarely developed in leaves of Niedersenz (Nd), some yellowing and occasional necrosis developed in Columbia (Col), whereas tissue collapse was observed in Wassilewskija (Ws) after inoculation by infiltration. Analysis of F2 progeny and recombinant inbred lines (RIL) from a cross between Col and Nd revealed a pattern of continuous symptom increase, indicating the operation of quantitative determinants of resistance. By mapping quantitative trait loci (QTL), significant linkage was determined for resistance (low symptom score) to markers on chromosome 4. Segregation in the F2 cross from Nd × Ws indicated the operation of two dominant genes for resistance, one of which was FLS2 encoding the flagellin receptor. The requirement for FLS2 to confer resistance was confirmed by transgenic ...
This timely text presents a comprehensive guide to genetic association, a new and rapidly expanding field that aims to elucidate how our genetic code (genotypes) influences the traits we possess (phenotypes). The book provides a detailed review of methods of gene mapping used in association with experimental crosses, as well as genome-wide association studies. Emphasis is placed on model selection procedures for analyzing data from large-scale genome scans based on specifically designed modifications of the Bayesian information criterion. Topics and features: Presents a thorough introduction to the theoretical background to studies of genetic association (both genetic and statistical) Reviews the latest advances in the field, highlighting the advantages and shortcomings of the currently most commonly used methods Illustrates the properties of methods for mapping quantitative trait loci using computer simulations and the analysis of real data Discusses open challenges that remain to be solved in ...
Quantitative trait loci[edit]. A quantitative trait locus (QTL) refers to a suite of genes that controls a quantitative trait. ... A quantitative trait is one that is influenced by several different genes as opposed to just one or two.[39] QTLs are analyzed ... Individuals that are heterozygous at a particular locus have a higher fitness than homozygotes at that locus. Inbreeding leads ... Quantitative PCR may also be used to analyze gene expression as a result of changes in environmental conditions or different ...
DNA locus associated with variation in a quantitative trait. A quantitative trait locus (QTL) is a locus (section of DNA) that ... A quantitative trait locus (QTL) is a region of DNA which is associated with a particular phenotypic trait, which varies in ... Complex Trait Consortium (2003). "The nature and identification of quantitative trait loci:a community's view". Nature Reviews ... Retrieved from "" ...
Hoeschele I (2004-07-15). "Mapping Quantitative Trait Loci in Outbred Pedigrees". Handbook of Statistical Genetics. John Wiley ... "Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens ... "Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits". Animal Genetics ... A single locus will entirely produce one's phenotype although two alleles are inherited. This genotype class is called parental ...
... in linkage disequilibrium with a quantitative trait locus (QTL) that contributes to the trait of interest. Association mapping ... Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat ... Hoeschele, I. (2004-07-15). "Mapping Quantitative Trait Loci in Outbred Pedigrees". Handbook of Statistical Genetics. ... is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link ...
Replication timing quantitative trait loci affects DNA replication. In order to categorize a mutation as such, the "normal" ... Also, many traits are determined by hundreds of genes (or loci), so that each locus has only a minor effect. For instance, ... Araten DJ, Golde DW, Zhang RH, Thaler HT, Gargiulo L, Notaro R, Luzzatto L (September 2005). "A quantitative measurement of the ... "Locus Specific Mutation Databases". Leiden, the Netherlands: Leiden University Medical Center. Retrieved 18 October 2015. " ...
Hunt, G; Page R; Fondrk M; Dullum C (1995). "Major quantitative trait loci affecting honey bee foraging behavior". Genetics. ... Worker food preferences have been connected to genotypic variation at specific quantitative trait loci. African bees are " ... The main difference found between African and European honey bees were a few behavioral traits in the worker bees that were all ... The balancing of evolutionary costs and benefits have shaped the distribution of these genotypic traits. A bee population must ...
A quantitative trait locus (QTL) is a region of DNA which is associated with a particular phenotypic trait, which varies in ... A quantitative trait locus (QTL) is a section of DNA (the locus) which correlates with variation in a phenotype (the ... "Quantitative trait locus (QTL) analysis". Nature Education (1.1).. *^ a b c "Archived copy". Archived from the original on 3 ... Quantitative Trait Locus (QTL) Analysis @ Scitable. *Mapping Quantitative Trait Loci. *What are Quantitative Trait Loci? - ...
May 2018). "PM20D1 is a quantitative trait locus associated with Alzheimer's disease". Nature Medicine. 24 (5): 598-603. doi: ... Methylation at or near the PM20D1 locus has been correlated to body mass index. In humans, the PM20D1 locus has been associated ...
Mukeshimana, Gerardine; Butare, Louis; Cregan, Perry B.; Kelly, James D. (May 2014). "Quantitative Trait Loci Associated with ... Mukeshimana, Gerardine; Lasley, Amy L. (May 2014). "Identification of Shoot Traits Related to Drought Tolerance in Common Bean ...
Quantitative trait locus: Primates, chimp and gibbon, represented the closest group of orthologous proteins in relation to ... FAM193A QTL (quantitative trait loci) Search Result - Rat Genome Database. ... Family with sequence similarity 193 member A is a protein that in humans is encoded by the FAM193A gene located on locus p16.3 ...
Several additional loci have been identified. Also, several quantitative trait loci for BMI have been identified. Confirmed and ... January 2002). "Quantitative-Trait Loci Influencing Body-Mass Index Reside on Chromosomes 7 and 13: The National Heart, Lung, ... 18 January 2009). "Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in ... January 2009). "Six new loci associated with body mass index highlight a neuronal influence on body weight regulation". Nat. ...
Major quantitative trait loci affecting honey bee foraging behavior. Genetics 141: 1537-1545. Hunt, G. J, and R.E. Page. 1995. ... Complex social behavior derived from maternal reproductive traits. Nature 439: 76-78 [cover article]. Nelson, C.M., K.E. Ihle, ...
RAPSN Fetal hemoglobin quantitative trait locus 1; 141749; HBG1 Fetal hemoglobin quantitative trait locus 1; 141749; HBG2 FG ... POR Anxiety-related personality traits; 607834; SLC6A4 Aortic aneurysm, familial thoracic 4; 132900; MYH11 Aortic aneurysm, ...
1996). "A genome-wide search for quantitative trait loci underlying asthma". Nature. 383 (6597): 247-50. Bibcode:1996Natur.383 ...
May 2008). "A genome-wide association study identifies protein quantitative trait loci (pQTLs)". PLOS Genetics. 4 (5): e1000072 ...
"Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype". PLOS Biology. 5 (11): e297. doi:10.1371/journal. ... This study also linked FABP7 variation to weak prepulse inhibition in mice; deficit in PPI is an endophenotypic trait observed ...
2008). Cheung VG (ed.). "A genome-wide association study identifies protein quantitative trait loci (pQTLs)". PLOS Genet. 4 (5 ...
"Congenital Sensorineural Deafness in Dalmatian Dogs Associated with Quantitative Trait Loci". PLOS ONE. 8 (12): e80642. Bibcode ... The goal of the project is to preserve and improve the Dalmatian breed by breeding parent dogs with the following traits: ... scientific way to correct genetic health problems associated with certain breed traits and still preserve the integrity of the ...
A genetic study identified two quantitative trait loci (QTL) that control hearing function. One QTL, named age-related hearing ... Drayton, M.; Noben-Trauth, K. (2006). "Mapping quantitative trait loci for hearing loss in Black Swiss mice". Hearing Research ... The locus extends over about 8 kbp and contains the six coding exons that give rise to an open reading frame of 639 nucleotides ... A genetic locus conferring susceptibility was identified (juvenile audiogenic monogenic seizures1, jams1) on chromosome 10. A ...
1996). "A genome-wide search for quantitative trait loci underlying asthma". Nature. 383 (6597): 247-50. doi:10.1038/383247a0. ...
Branham, Sandra E.; Stansell, Zachary J.; Couillard, David M.; Farnham, Mark W. (1 March 2017). "Quantitative trait loci ... ISBN 978-0-85199-395-9. Stansell, Zachary; Farnham, Mark; Björkman, Thomas (2019). "Complex Horticultural Quality Traits in ...
"Mapping quantitative trait loci using linkage disequilibrium: marker- versus trait-based methods". Behavior Genetics. 35 (2): ... Gene maps or Qualitative Trait Loci (QTL) maps can be produced using two separate methods. One way uses the frequency of marker ... In genetics, complete linkage is defined as the state in which two loci are so close together that alleles of these loci are ... Learning about linkage of traits in sugar cane has led to more productive and lucrative growth of the crop. Sugar cane is a ...
... most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes). Recent findings have ... Butlin, Roger K.; Tregenza, Tom (February 28, 1998). "Levels of genetic polymorphism: marker loci versus quantitative traits". ... marker loci versus quantitative traits". Philosophical Transactions of the Royal Society B. 355 (1404): 1865. doi:10.1098/rstb. ... Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits ...
Mendelian error Quantitative trait locus SNP genotyping "Genotyping definition". NIH. 2011-09-21. Retrieved 2011-09-21. " ...
Quantitative trait locus which relates gene expression to genotypes. Genetic analysis of gene expression. Characterization of ... Genetics of alcohol-associated traits in monkeys. A dedicated section (Pilot projects) launches 2 to 4 projects annually. ...
Cardon LR, Smith SD, Fulker DW, Kimberling WJ, Pennington BF, DeFries JC (October 1994). "Quantitative trait locus for reading ... "Quantitative-trait locus for specific language and reading deficits on chromosome 6p". American Journal of Human Genetics. 64 ( ... Londin ER, Meng H, Gruen JR (June 2003). "A transcription map of the 6p22.3 reading disability locus identifying candidate ...
Genetic disorders polygenes Quantitative trait locus Duarte, Christine W.; Vaughan, Laura K.; Beasley, T. Mark; Tiwari, Hemant ... Continuous traits exhibit normal distribution in population and display a gradient of phenotypes while discontinuous traits ... "Common disorders are quantitative traits". Nature Reviews Genetics. 10 (12): 872-878. doi:10.1038/nrg2670. ISSN 1471-0056. PMID ... the individual either has the trait or does not. However, multifactorial traits may be discontinuous or continuous. ...
There is already a complete quantitative trait loci map for the juvenile traits. These plants are a few of the common examples ... Forster MA, Bonser SP (January 2009). "Heteroblastic development and the optimal partitioning of traits among contrasting ... are helpful in the study of gene expression in heteroblastic plants because none of them express obvious heteroblastic traits. ...
There were 3 quantitative trait loci that explained most of the phenotype variation. Indicators of recent selection were shown ... Their behavioural traits include guarding, herding, and hunting, and personality traits such as hypersocial behavior, boldness ... Their behavioural traits include guarding, herding, and hunting, retrieving, and scent detection. Their personality traits ... These breeds possess distinct traits related to morphology, which include body size, skull shape, tail phenotype, fur type and ...
"Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide". Science. 299 ( ... "Genetic analysis of a complex trait in the Utah Genetic Reference Project: a major locus for PTC taste ability on chromosome 7q ... and a secondary locus on chromosome 16p". Human Genetics. 112 (5-6): 567-72. doi:10.1007/s00439-003-0911-y. PMID 12624758. ...
The locus affects the expressed trait only through changing the expression of other loci. Over time, that locus would affect ... One basic model of pleiotropy's origin describes a single gene locus to the expression of a certain trait. ... one that affects the signaling trait and one that affects the receptor trait.[13] In such a case, pleiotropy would facilitate ... This may occur when the trait is beneficial for the organism's early life, but not its late life. Such "trade-offs" are ...
BMIQ5: Body mass index quantitative trait locus 5. *C16orf13/JFP2: encoding protein Chromosome 16 open reading frame 13 ... For cytogenetic banding nomenclature, see article locus. *^ a b These values (ISCN start/stop) are based on the length of bands ... Maillard, A M (25 November 2014). "The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity". ...
... epistasis started to be studied in relation to Quantitative Trait Loci (QTL) and polygenic inheritance. ... Additive A locus. Additive B locus. Dominance A locus. Dominance B locus ... Quantitative trait values after two mutations either alone (Ab and aB) or in combination (AB). Bars contained in the grey box ... Quantitative genetics focuses on genetic variance due to genetic interactions. Any two locus interactions at a particular gene ...
Mendelian trait[edit]. A Mendelian trait is one that is controlled by a single locus in an inheritance pattern. In such cases, ... When parents are homozygous for each trait (SSbb and ssBB), their children in the F1 generation are heterozygous at both loci ... the biological selection of an allele for one trait has nothing to do with the selection of an allele for any other trait. ... The presence of an allele does not mean that the trait will be expressed in the individual that possesses it. If the two ...
The consensus definition now requires a trait to be heritable for it to be considered epigenetic.[4] Misuse of the scientific ... a phenomenon in mammals where the father and mother contribute different epigenetic patterns for specific genomic loci in their ... In 2008, a consensus definition of the epigenetic trait, "stably heritable phenotype resulting from changes in a chromosome ... The ability of Sup35 to form prions may be a conserved trait. It could confer an adaptive advantage by giving cells the ability ...
Cardon LR, Abecasis GR (2003). "Using haplotype blocks to map human complex trait loci". Trends Genet. 19: 135-140. doi:10.1016 ... Quantitative amino acid analysis is typically performed using the ninhydrin reaction, followed by liquid chromatography to ... Urine organic acid analysis can be either performed using quantitative or qualitative methods, but in either case the test is ...
... limitations that can significantly increase the type-1 error rate and reduce the power to map human quantitative trait loci ( ... Gregor Mendel's Law of Independent Assortment states that every trait is inherited independently of every other trait. But ... If the loci we're analysing are very close (less than 7 cM) a double crossover is very unlikely. When distances become higher, ... The LOD score compares the likelihood of obtaining the test data if the two loci are indeed linked, to the likelihood of ...
... the environment has a bigger influence on the total variation of the trait. For example, human height is a trait with complex ... Diploid organisms with two copies of the same allele of a given gene are called homozygous at that gene locus, while organisms ... Blending of traits in the progeny is now explained by the action of multiple genes with quantitative effects. Another theory ... Often different genes can interact in a way that influences the same trait. In the Blue-eyed Mary (Omphalodes verna), for ...
For a few highly heritable traits, studies have identified loci associated with variance in that trait, for instance in some ... Quantitative studies of heritable traits throw light on the question. Developmental genetic analysis examines the effects of ... Trait B shows a high heritability since correlation of trait rises sharply with the degree of genetic similarity. Trait C shows ... additive contributions of genes and environment to the trait. As an analogy, some laypeople may think of the degree of a trait ...
Quantitative trait loci (QTL) mapping is another statistical method used to determine the chromosomal positions of a set of ... One of the most noticeable results of further research into neurogenetics is a greater knowledge of gene loci that show linkage ... Research in neurogenetics has yielded some promising results, though, in that mutations at specific gene loci have been linked ... R. W. Williams (1998) Neuroscience Meets Quantitative Genetics: Using Morphometric Data to Map Genes that Modulate CNS ...
"X-inactivation informs variance-based testing for X-linked association of a quantitative trait". BMC Genomics. 16: 241. doi: ... DNA FISH signals from Xist loci are shown in yellow color, marking both active and inactive X-chromosomes (Xa, Xi). The nucleus ...
... and fitness is precisely the target trait of natural selection. Thus, Wright's inbreeding coefficient F. for neutral loci does ... instead of linear is just that fitness is usually considered a multiplicative trait). The rate at which fitness declines as F. ... is the standard measure of inbreeding, and gives the probability that, at any given neutral locus, an individual has inherited ... due to (partially) recessive deleterious alleles that were present at low frequencies at different loci. This means that, in ...
National Agricultural Innovation Project: Identification of Quantitative Trait Loci for Milk yield, Fat and Protein Percent in ...
... one gene affecting more than one trait) and other interactions between loci and alleles within the genome.[4] Advances in ... it reflects the change in orientation towards the quantitative analysis of complete or near-complete assortment of all the ...
Lampe, Virginie (2009-05-22). "Dissertation: Fine mapping of quantitative trait loci (QTL) for osteochondrosis in Hanoverian ...
Genetic Drift in Phenotypic Evolution Using Quantitative Trait Locus Data". Genetics. 149 (4): 2099-2104. PMC 1460271. PMID ... On each graph, the x-axis variable is the type of phenotypic trait and the y-axis variable is the amount of organisms. Group A ... This analysis showed that the genetic loci correlating to directional selection was higher than expected; meaning directional ...
Positional cloning of the human quantitative trait locus underlying taste sensitivity to phenylthiocarbamide.. Science. 2003, ... Genetic analysis of a complex trait in the Utah Genetic Reference Project: a major locus for PTC taste ability on chromosome 7q ... a major locus for PTC taste ability on chromosome 7q and a secondary locus on chromosome 16p. Hum. Genet. 2003, 112 (5-6): 567- ... Drayna D, Coon H, Kim UK, Elsner T, Cromer K, Otterud B, Baird L, Peiffer AP, Leppert M. Genetic analysis of a complex trait in ...
Chen CH, Suckling J, Lennox BR, Ooi C, Bullmore ET (February 2011). "A quantitative meta-analysis of fMRI studies in bipolar ... Decreased sensitivity of regulatory α2 adrenergic receptors as well as increased cell counts in the locus ceruleus indicated ... suggesting that it is a trait marker.[66] ... failed to find any particular locus that exerts a large effect ...
a) Replication of the STR locus has proceeded without a mutation. (b) Replication of the STR locus has led to a gain of one ... linked to a trait of interest (e.g. productivity, disease resistance, stress tolerance, and quality), rather than on the trait ... 1997). "Simple sequence repeats as a source of quantitative genetic variation". Trends Genet. 13 (2): 74-78. doi:10.1016/S0168- ... using 10 loci and a sex marker. The Americans[64] increased this number to 13 loci.[65] The Australian database is called the ...
BMIQ5: Body mass index quantitative trait locus 5. *C16orf13/JFP2: encoding protein Chromosome 16 open reading frame 13 ... For cytogenetic banding nomenclature, see article locus. *^ a b These values (ISCN start/stop) are based on the length of bands ... "The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity". Molecular Psychiatry. 20 (1): 140- ...
Douglas Scott Falconer (1989). Introduction to quantitative genetics. Longman, Scientific & Technical. ISBN 978-0-470-21162-5. ... using mixed effects models implemented in software such as Genome-wide complex trait analysis (GCTA).[40][41] To do this, ... "Biological insights from 108 schizophrenia-associated genetic loci". Nature. 511 (7510): 421-7. Bibcode:2014Natur.511..421S ... although the extent of genetic influence for any particular trait can differ widely.[11][12] A decade later, in February 1970, ...
... zafê karakteristikan halo deha kompleksti derê Quantitative trait locus ya zi multiple interacting genes teref ra kontol beno.[ ... marker loci versus quantitative traits". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 353 (1366): 187-98. ...
In particular, if the trait is quantitative and univariate then both higher and lower trait levels are favoured. Disruptive ... Genetic linkage occurs when the loci of two alleles are in close proximity on a chromosome. During the formation of gametes, ... By effect on a traitEdit. Selection has different effects on traits. Stabilizing selection acts to hold a trait at a stable ... Orgel, Leslie E. (1987). "Evolution of the Genetic Apparatus: A Review". Cold Spring Harbor Symposia on Quantitative Biology. ...
a b Landy, F. J. (2010). Employment discrimination litigation: behavioral, quantitative, and legal perspectives. San Francisco ... However, they do not agree on other anxiety indicators such as frequent pauses and biting or licking of lips.[164] Trait ... A longitudinal study of the mediating effects of interviewing self-efficacy and the moderating effects of internal locus of ... Low assertiveness has been identified as the key trait related to interview anxiety. Thus, the most important indicators of ...
Fine mapping of quantitative trait loci (QTL) for osteochondrosis in Hanoverian warmblood horses" (PDF). Veterinary University ...
... see quantitative trait locus).. Natural hair colors[edit]. Natural hair color can be black, blond, brown, red, or white; all ... In males, the supposedly recessive trait is often expressed in parts of the facial hair or beard. Valverde P, Healy E, Jackson ... The possibility of which trait may appear in an offspring can be determined with a Punnett square. ... A person's genotype for a multifactorial trait can interact with the environment to produce varying phenotypes ( ...
6. Locus-locus interactions *Epistasis with other loci (e.g., overdominance). *Gene coupling with other loci (also see crossing ... If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the ... quantitative) genes was not realised until R. A. Fisher's (1918) paper, "The Correlation Between Relatives on the Supposition ... Autosomal - loci are not situated on a sex chromosome. *Gonosomal - loci are situated on a sex chromosome *X-chromosomal - loci ...
DNA locus associated with variation in a quantitative trait. A quantitative trait locus (QTL) is a locus (section of DNA) that ... A quantitative trait locus (QTL) is a region of DNA which is associated with a particular phenotypic trait, which varies in ... Complex Trait Consortium (2003). "The nature and identification of quantitative trait loci:a communitys view". Nature Reviews ... Retrieved from "" ...
Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to ...
1991 Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci. ... 1998 The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea ... 1994 Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195-1207. ... 1994 Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci. 34: 882- ...
Koyama ML, Levesley A, Koebner RMD, Flowers TJ, Yeo AR (2001) Quantitative trait loci for component physiological traits ... Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for ... Lee SY, Ahn JH, Cha YS, Yun DW, Lee MC, Ko JC, Lee KS, Eun MY (2006) Mapping of quantitative trait loci for salt tolerance at ... Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci ...
... and phenotype for a set of quantitative traits in terms of the number, genomic positions, effects and interaction of QTLs ... Quantitative trait loci (QTL) mapping is a genome‐wide inference of the relationship between genotype at various genomic ... Keywords: quantitative tracts; quantitative trait loci; QTL mapping; linkage analysis; genetic architecture of complex trait ... Jiang C and Zeng Z‐B (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127. ...
Expression quantitative trait loci (eQTLs) are genomic loci that explain variation in expression levels of mRNAs. An expression ... Doss S, Schadt EE, Drake TA, Lusis AJ (May 2005). "Cis-acting expression quantitative trait loci in mice". Genome Research. 15 ... Epigenome-wide association study Quantitative trait locus (QTL) Rockman MV, Kruglyak L (November 2006). "Genetics of global ... Michaelson JJ, Loguercio S, Beyer A (July 2009). "Detection and interpretation of expression quantitative trait loci (eQTL)". ...
Splicing quantitative trait loci (abbreviated sQTLs or splicing QTLs) are quantitative trait loci that regulate alternative ... Wu E, Nance T, Montgomery SB (April 2014). "SplicePlot: a utility for visualizing splicing quantitative trait loci". ... "Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci". ...
Our objective was to map domestication-related quantitative trait loci (QTL) in T. dicoccoides. The studied traits include ... quantitative trait;. QTL,. QT loci;. HT,. plant height;. HD,. heading date;. GWH,. 100-grain weight;. YLD,. grain yield/plant; ... Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Junhua Peng, Yefim Ronin, Tzion Fahima ... Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat. Junhua Peng, Yefim Ronin, Tzion Fahima ...
Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of ... Song X. L. and Zhang T. Z. 2007 Identification of quantitative trait loci controlling seed physical and nutrient traits in ... 1998 Quantitative trait loci associated with agronomic and fiber traits of upland cotton. J. Cotton Sci. 4, 153-163.Google ... Alfred Q., Liu H. Y., Xu H. M., Li J. R., Wu J. G., Zhu S. J. and Shi C. H. 2012 Mapping of quantitative trait loci for oil ...
PROC QTL is a user-defined SAS procedure for mapping quantitative trait loci (QTL). It allows users to perform QTL mapping for ... continuous and discrete traits within the SAS platform. Users of PROC QTL are able to take advantage of all existing features ... PROC QTL-A SAS Procedure for Mapping Quantitative Trait Loci. Zhiqiu Hu1 and Shizhong Xu1. 1Department of Botany and Plant ... PROC QTL-A SAS Procedure for Mapping Quantitative Trait Loci,. International Journal of Plant Genomics,. vol. 2009. ,. Article ...
A quantitative trait locus (QTL) is a region of DNA which is associated with a particular phenotypic trait, which varies in ... A quantitative trait locus (QTL) is a section of DNA (the locus) which correlates with variation in a phenotype (the ... "Quantitative trait locus (QTL) analysis". Nature Education (1.1).. *^ a b c "Archived copy". Archived from the original on 3 ... Quantitative Trait Locus (QTL) Analysis @ Scitable. *Mapping Quantitative Trait Loci. *What are Quantitative Trait Loci? - ...
We mapped quantitative trait loci (QTL) for 67 traits and discovered 364 correlations between traits segregation and ... Genetic complexity and quantitative trait loci mapping of yeast morphological traits.. Nogami S1, Ohya Y, Yvert G. ... A quantitative comparison of BY and RM is shown for twelve phenotypes. The traits definition is illustrated under each boxplot ... The inset drawing illustrates the trait definition.. (C) Example of both epistasis and transgressive segregation. Trait C107_C ...
... mostly because genetic loci contributing to quantitative traits (quantitative trait loci, QTL) have only a small effect on the ... quantitative trait loci;. HS,. heterogeneous stock;. SM,. single marker;. DP,. dynamic programming. ... A method for fine mapping quantitative trait loci in outbred animal stocks. Richard Mott, Christopher J. Talbot, Maria G. Turri ... High-resolution mapping of quantitative trait loci (QTL) in animals has proved to be difficult because the large effect sizes ...
Identification of Quantitative Trait Loci for Glucose Homeostasis. Stephen S. Rich, Donald W. Bowden, Steven M. Haffner, Jill M ... Identification of Quantitative Trait Loci for Glucose Homeostasis. Stephen S. Rich, Donald W. Bowden, Steven M. Haffner, Jill M ... Identification of Quantitative Trait Loci for Glucose Homeostasis Message Subject (Your Name) has forwarded a page to you from ... QTL, quantitative trait locus. Risk of type 2 diabetes is mediated, in part, by genetic factors (1). Given that both insulin ...
Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice.. Yamaya T1, Obara M, Nakajima H, ... and Kasalath were employed to detect putative quantitative trait loci (QTLs) associated with the contents of cytosolic ... The relationships between the genetic variability of complex agronomic traits and traits for these two enzymes are discussed. ... Some of these QTLs were located in QTL regions for various biochemical and agronomic traits affected by nitrogen recycling. ...
... Am J Vet Res. 2009 Sep;70(9):1094-101. doi: ... Objective: To identify the quantitative trait loci (QTL) that contribute to hip dysplasia in dogs. ...
... investigators can easily measure thousands of phenotypes for quantitative trait loci (QTL) mapping. Microarray measurements are ... A review of statistical methods for expression quantitative trait loci mapping Mamm Genome. 2006 Jun;17(6):509-17. doi: 10.1007 ... investigators can easily measure thousands of phenotypes for quantitative trait loci (QTL) mapping. Microarray measurements are ...
Identification of Quantitative Trait Loci That Affect Aggressive Behavior in Mice. Edward S. Brodkin, Sarah A. Goforth, Angela ... Identification of Quantitative Trait Loci That Affect Aggressive Behavior in Mice. Edward S. Brodkin, Sarah A. Goforth, Angela ... Identification of Quantitative Trait Loci That Affect Aggressive Behavior in Mice. Edward S. Brodkin, Sarah A. Goforth, Angela ... Identification of Quantitative Trait Loci That Affect Aggressive Behavior in Mice Message Subject (Your Name) has forwarded a ...
... quantitative trait loci include Quantifying Abdominal Pigmentation in Drosophila melanogaster, Dissection and Flat-mounting ... Quantitative Trait Loci: Genetic loci associated with a Quantitative trait. Quantifying Abdominal Pigmentation in Drosophila ...
More specifically, the invention includes a method for breeding soybean plants containing quantitative trait loci that are ... The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease ... As used herein, "quantitative trait locus (QTL)" means a locus that controls to some degree numerically representable traits ... The assumption is that linked allele associates with the gene and/or quantitative trait locus (QTL) of interest. MAS can be ...
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Quantitative trait loci (QTL) for wheat resistance to aluminum (Al) toxicity were analyzed using simple sequence repeats (SSRs ...
Complete genome searches for quantitative trait loci controlling blood pressure and related traits in four segregating ... Chromosomal Mapping of Quantitative Trait Loci Controlling Elastin Content in Rat Aorta. Dominique Gauguier, Jacques Behmoaras ... Quantitative trait loci in genetically hypertensive rats. Possible sex specificity. Hypertension. 1996; 28: 898-906. ... Before quantitative trait loci (QTL) mapping, all phenotypes were regressed for sex and the standardized residuals were tested ...
Introduction: Expression quantitative trait loci (eQTL) analysis has helped validate genotype-trait associations identified ... Genome-wide Expression Quantitative Trait Loci: Results from the NHLBI. s SABRe CVD Initiative. R. Joehanes1,2, T. Huan1, C. ... 3,447 exon-level and 2,172 gene-level eQTLs are reported as trait-associated SNPs in the NHGRI GWAS catalog, giving functional ...
Aspectos biométricos da detecção de QTLS ("Quantitative Trait Loci") em espécies cultivadas. ... involved in the genetical control of the considered trait, according to its stability, in relation to the observed ...
... data set will also have broad utility for understanding the relationship between other genome-wide studies of complex traits. ... studies have implicated genetic variation that influences gene expression and that ultimately affect downstream complex traits ...
Cis-expression quantitative trait loci mapping reveals replicable associations with heroin addiction in OPRM1. ... We then tested the 16 putative cis-expression quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in ... Cis-expression quantitative trait loci mapping reveals replicable associations with heroin addiction in OPRM1 ... Cis-expression quantitative trait loci mapping reveals replicable associations with heroin addiction in OPRM1. Biological ...
Thirdly, we extend the one-locus GMA models to multiple loci. We discuss how the genetic variance components can be analyzed ... Thirdly, we extend the one-locus GMA models to multiple loci. We discuss how the genetic variance components can be analyzed ... we develop a one-locus GMA model for phase unknown genotypes by treating it as a special case of the phase known one-locus GMA ... we develop a one-locus GMA model for phase unknown genotypes by treating it as a special case of the phase known one-locus GMA ...
  • [1] QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs ) correlate with an observed trait. (
  • The number of QTLs which explain variation in the phenotypic trait indicates the genetic architecture of a trait. (
  • Typically, QTLs underlie continuous traits (those traits which vary continuously, e.g. height) as opposed to discrete traits (traits that have two or several character values, e.g. red hair in humans, a recessive trait, or smooth vs. wrinkled peas used by Mendel in his experiments). (
  • Consequently, many QTLs are associated with a single trait. (
  • Another use of QTLs is to identify candidate genes underlying a trait. (
  • Splicing quantitative trait loci (abbreviated sQTLs or splicing QTLs) are quantitative trait loci that regulate alternative splicing of pre-mRNA. (
  • Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. (
  • Quantitative trait loci (QTL) mapping is a genome‐wide inference of the relationship between genotype at various genomic locations and phenotype for a set of quantitative traits in terms of the number, genomic positions, effects and interaction of QTLs. (
  • Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. (
  • High-resolution mapping of quantitative trait loci (QTL) in animals has proved to be difficult because the large effect sizes detected in crosses between inbred strains are often caused by numerous linked QTLs, each of small effect. (
  • We have developed a robust method of fine mapping QTLs in genetically heterogeneous animals and suggest it is now cost effective to undertake genomewide high-resolution analysis of complex traits in parallel on the same set of mice. (
  • Studies using experimental crosses between inbred animal strains have been successful in mapping QTLs with effects on a number of different phenotypes, including behavior, but attempts to fine map QTLs in animals often have foundered on the discovery that a single QTL of large effect was in fact caused by multiple loci of small effect positioned within the same chromosomal region ( 4 ). (
  • These results provide impetus for future positional cloning of quantitative trait loci (QTLs). (
  • Some of these QTLs were located in QTL regions for various biochemical and agronomic traits affected by nitrogen recycling. (
  • Maxson, 2000 ), but no whole genome scan has been reported that has revealed statistically significant quantitative trait loci (QTLs) ( Lander and Kruglyak, 1995 ). (
  • Quantitative trait loci (QTLs) affecting sugar composition of the cell walls of maize ( Zea mays ) pericarp were mapped as an approach to the identification of genes involved in cereal wall biosynthesis. (
  • Contrary to some expectations, the QTLs underlying natural variation have turned out to be variant alleles of genes that play a central role in the trait under study, and not minor, secondary genes with an indirect role ( Millar, 2001 ). (
  • By contrast indirect markers are abundant across the genome and their linkages with QTLs have been established by evidence of empirical association of genotype with trait phenotype. (
  • There is enough evidence through linkage and substitution mapping to indicate that rat chromosome 1 harbors multiple blood pressure (BP) quantitative trait loci (QTLs). (
  • Initial steps to map such genes using linkage analysis in F 2 intercross or backcross populations, however, result in broad quantitative trait loci (QTLs) containing hundreds of genes. (
  • The QTLs for pubescence appeared to be identical to the previously detected the Pd1 and Ps loci controlling pubescence density. (
  • We found no candidate loci for flowering time QTLs, although one could be identical to the gene governing the long-juvenile trait or to the E6 loci controlling maturity. (
  • we suggested that much of the variation in retinal ganglion cell number in mice, and the striking bimodality of strain averages, are caused by one or two quantitative trait loci (QTLs). (
  • For example, single quantitative trait loci (QTLs) have been shown to account for 20-40% of the variance in the height of corn and the weight of tomatoes ( Tanksley, 1993 ). (
  • Quantitative trait loci (QTLs) for resistance to two potato virus Y (PVY) isolates and to potyvirus E have been mapped in a doubled-haploid progeny from the hybrid between the line Perennial with resistance factors against several potyviruses and the line Yolo Wonder, with 172 DNA markers. (
  • Based on their spectrum of action, we discriminated QTLs with PVY isolate-or potyvirus-specific effect and loci involved in the resistance to several distinct potyviruses. (
  • QTLs for PVY and potyvirus E resistance were detected in the vicinity of the pvr2 and pvr6 loci. (
  • Multiple regression analysis using the four most influential QTLs revealed that these loci controlled 86% of the genetic variance. (
  • We identified quantitative trait loci (QTLs) for RHL in the populations derived from these crosses. (
  • The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. (
  • 100 chromosomes (2 n = 100-130) and are genetically complex polyploid and aneuploids, identification of quantitative trait loci (QTLs) associated with sucrose content is considered the best option to improve sucrose content through molecular breeding. (
  • Fourteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. (
  • In this research, two recombinant inbreed line (RIL) populations derived from CI13227 x Suwon (104 RILs) and CI13227 x Everest (184 RILs) and one doubled haploid (DH) population derived from CI13227 x Lakin with 181 lines were used to identify quantitative trait loci (QTLs) for slow leaf rusting resistance. (
  • We performed a genome-wide scan for quantitative trait loci (QTLs) affecting proteinuria in a population of 356 backcross progeny derived from a cross between FGS/Kist and the standard normal strain, C57BL/6J. (
  • Many quantitative trait loci (QTLs) in different barley populations were discovered for resistance to Puccinia hordei and heterologous rust species. (
  • Four and two quantitative trait loci-near isogenic lines (QTL-NILs), respectively, were developed for basal resistance and nonhost resistance QTLs using SusPtrit as recurrent parent. (
  • The quantitative trait loci (QTLs) associated with arsenic (As) accumulation in rice were mapped using a doubled haploid population established by anther culture of F1 plants from a cross between a Japonica cultivar CJ06 and an Indica cultivar TN1 (Oryza sativa). (
  • Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. (
  • It was unknown whether this rigid resistance to BP changes is because of an insufficient hypertensive impact from limited alleles of quantitative trait loci (QTLs) or because of an existence of a master control superseding the combined strength of hypertensive QTL alleles. (
  • Results showed that there was no quantitative correlation between BP variations and the number of hypertensive QTL alleles, and that BP was only slightly elevated from a combined force of normotensive alleles from 7 QTLs. (
  • 1 The genetic architecture of polygenic hypertension has long been thought to be composed of individual constituents known as quantitative trait loci (QTLs) for blood pressure (BP). (
  • This is often an early step in identifying and sequencing the actual genes that cause the trait variation. (
  • A quantitative trait locus ( QTL ) is a region of DNA which is associated with a particular phenotypic trait , which varies in degree and which can be attributed to polygenic effects, i.e., the product of two or more genes , and their environment. (
  • Moreover, a single phenotypic trait is usually determined by many genes. (
  • The results showed that seed germination was a quantitative trait controlled by several genes, and strongly affected by salt stress. (
  • The discovery of genes that contribute to the expression of complex traits is one of the fundamental and essential tasks in genetic research. (
  • Considerable efforts have been made to isolate the genes responsible for quantitative genetic variation in human populations, but with little success, mostly because genetic loci contributing to quantitative traits (quantitative trait loci, QTL) have only a small effect on the phenotype ( 1 ). (
  • Association studies have been proposed as the most appropriate method for finding the genes that influence complex traits ( 2 ). (
  • One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. (
  • The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry. (
  • Furthermore, a single miRNA can potentially target hundreds of genes, and multiple miRNAs have the ability to target the same mRNA, acting as "fine tuners" of gene expression and adding rich complexity to the regulation of polygenic traits. (
  • Because they are typically inherited in a quantitative manner, they are more challenging to analyze, and isolation of the responsible genes is more difficult. (
  • Thus, the identification of genes controlling natural quantitative differences in cell wall properties might lead to the identification of critical, primary genes involved in hemicellulose biosynthesis. (
  • QUANTITATIVE TRAIT LOCI Introduction Many genes responsible for polygenic inheritance of particular characteristics are scattered around the genome. (
  • QTL detection: detection and estimation of associations of identified genes and gametes markers with economic traits iii. (
  • The same is true for quantitative traits influenced by many genes and under weak stabilizing selection. (
  • To test this idea, and to map genes linked to this variable and highly heritable quantitative trait, we have counted ganglion cells in 38 recombinant inbred strains (BXD and BXH) derived from parental strains that have high and low cell numbers. (
  • One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. (
  • We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. (
  • The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. (
  • In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. (
  • These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species. (
  • Genetics of tan spot resistance in wheat is complex, involving insensitivity to fungal-produced necrotrophic effectors (NEs), major resistance genes, and quantitative trait loci (QTL) conferring race-nonspecific and race-specific resistance. (
  • The 2 quantitative trait loci on chromosomes 3 and 4 are located in regions that contain the genes for apoD and the large subunit of the microsomal triglyceride transfer protein, respectively. (
  • Recently, expression quantitative loci (eQTL) mapping studies, where expression levels of thousands of genes are viewed as quantitative traits, have been used to provide greater insight into the biology of gene regulation. (
  • Although identifying quantitative trait loci (QTL) for atherosclerosis susceptibility in experimental murine models has helped us better understand the pathophysiology of atherosclerosis, identifying the genes underlying these QTL has been a slow and difficult process. (
  • It is thus plausible that a large proportion of the GWAS loci detect the effect of risk variants within non-coding regulatory DNA elements, which can be located at a considerable distance from protein-coding and non-coding genes. (
  • An additional difficulty in the interpretation of GWAS results is that associated risk loci often span a considerable genomic region, containing a large number of variants distributed over multiple genes, transcripts, and regulatory elements. (
  • Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. (
  • Herein we report a linkage study of a six-generational pedigree of adult rats phenotyped for one dimension of impulsivity, namely premature responding on the five-choice serial reaction time task, combined with genome wide sequencing and transcriptome analysis to identify candidate genes associated with the expression of the impulsivity trait. (
  • Fine mapping of this locus identified a number of polymorphic candidate genes, however only one, beta haemoglobin, was differentially expressed in both the founder strain and F6 generation. (
  • Conclusions- We identified the gene underlying the chromosome 15 quantitative trait locus, and our results show that Zhx2 functions as a novel developmental regulator of key genes influencing lipoprotein metabolism. (
  • Phenotypic differences among inbred mouse strains can be exploited to identify genetic differences in the expression of genes underlying the trait under consideration. (
  • They are mainly governed by genes with relatively small, quantitative effects, located on QTL. (
  • Blood pressure (BP) is heritable and finding quantitative trait loci that influence BP is an important step in identifying genes responsible for BP regulation. (
  • Sixty-six pairs of dizygotic (DZ) twin subjects and their parents were used in a sib-pair analysis to look for linkage of selected candidate genes to the quantitative trait BP. (
  • Mapping loci important for BP regulation would facilitate identification of the functional genes that potentially cause the disorder. (
  • The renin gene itself has been identified as a QTL in the rat ( 5 ), hypertension (as a qualitative trait) has been linked to the angiotensinogen gene ( 6 , 7 ), and the angiotensin-converting enzyme (ACE) and angiotensin II type 1 receptor (AT 1 ) genes have been associated with increased cardiovascular risk ( 8 ). (
  • Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L. (
  • We previously performed quantitative trait locus (QTL) mapping of F2 rats from a cross between GHS and normocalciuric WKY rats as a first step in mapping the genes that contribute to hypercalciuria in the rat model ( 20 ). (
  • To identify a gene or genes regulating fracture risk at the femoral neck, we mapped quantitative trait loci (QTL) for femoral neck density and structure phenotypes using a 595 F2 progeny derived from the inbred F344 and LEW strains of rats. (
  • In domesticated livestock, single-nucleotide polymorphisms in imprinted genes influencing foetal growth and development have been shown to be associated with economically important production traits in cattle, sheep and pigs. (
  • With this method we mapped all three previously undetected loci [chromosome (Chr. (
  • After a genome-wide search for quantitative trait loci (QTL) influencing the aortic elastin, collagen, and cell protein contents in an F2 population derived from BN and LOU rats, we identified on chromosomes 2 and 14, 3 QTL specifically controlling elastin levels, and a further highly significant QTL on chromosome 17 linked to the level of cell proteins. (
  • A cluster of QTL for nine traits was found on chromosome 2B in the vicinity of the photoperiod response gene Ppd-B1 . (
  • The purpose of this protocol is to identify chromosome regions that contain quantitative trait loci (QTL) involved in controlling HCT levels. (
  • Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in Holstein. (
  • Linkage disequilibrium information and sire heterozygosity were used to select markers for linkage analysis on bovine chromosome 14 for milk production traits in 321 Holstein animals. (
  • A second major susceptibility QTL was identified for all the Ptr ToxC-producing isolates and located to the distal end of the chromosome 1A, which likely corresponds to the Tsc1 locus. (
  • In oligogenic analyses, the 2-locus LOD score (for chromosomes 3 and 4) increased significantly ( P =0.0012) to 6.1, but including the third locus on chromosome 6 did not significantly improve the LOD score ( P =0.064). (
  • Quantitative trait loci were detected for growth habit, heading date, plant height, and individual grain weight on chromosome 3H in a region that possibly contains the denso gene. (
  • Background- We previously mapped a quantitative trait locus on chromosome 15 in mice contributing to high-density lipoprotein cholesterol and triglyceride levels and now report the identification of the underlying gene. (
  • A statistically significant association (log-likelihood ratio = 25.0) between a locus on chromosome 9, which colocalized with the murine Cyp1a2 locus, and the plasma paraxanthine/caffeine ratio was identified. (
  • A second locus was identified on chromosome 1 (log-likelihood ratio = 9.7) for which no obvious candidate gene has been identified. (
  • A third locus was identified on chromosome 4 with a less statistically robust association (log-likelihood ratio = 3.4) to the paraxanthine/caffeine phenotype. (
  • Significant association was detected between the hypotrichosis phenotype and a locus on bovine chromosome 5 (BTA5) and homozygosity analysis localized the associated region to between 29 and 32 Mb. (
  • Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. (
  • We have previously mapped a major quantitative trait locus (QTL) controlling F cell levels in an extended Asian-Indian kindred with beta thalassemia to a 1.5-Mb interval on chromosome 6q23, but the causative gene(s) are not known. (
  • GeneNetwork hosts many large eQTL mapping data sets and provide access to fast algorithms to map single loci and epistatic interactions. (
  • Introduction: Expression quantitative trait loci (eQTL) analysis has helped validate genotype-trait associations identified through genome-wide association studies (GWAS). (
  • We then tested the 16 putative cis-expression quantitative trait loci (cis-eQTL) SNPs for association with heroin addiction in the Urban Health Study and two replication cohorts, totaling 16,729 European Americans, African Americans, and Australians of European ancestry. (
  • We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. (
  • We illustrate the value of our eQTL database in the context of a recent GWAS meta-analysis of coronary artery disease and provide a list of targeted eGenes for 21 of 58 GWAS loci. (
  • As melanoma progression is controlled by host immunity, here we present a novel approach interrogating immunoregulatory pathways using the genome-wide maps of expression quantitative trait loci (eQTL) to reveal biologically relevant germline variants modulating cutaneous melanoma outcomes. (
  • Expression quantitative trait loci (eQTL) analysis is a powerful method to detect correlations between gene expression and genomic variants and is widely used to interpret the biological mechanism underlying identified genome wide association studies (GWAS) risk loci. (
  • Correlation of transcript expression levels with genomic variants or quantitative trait loci (eQTL) analysis is a powerful tool to explore the possible biological consequences of candidate GWAS variants in the associated region and it can help to limit the number of variants to be considered as possibly causal. (
  • In order to assess whether gene expression variability could be influenced by several SNPs acting in cis, either through additive or more complex haplotype effects, a systematic genome-wide search for cis haplotype expression quantitative trait loci (eQTL) was conducted in a sample of 758 individuals, part of the Cardiogenics Transcriptomic Study, for which genome-wide monocyte expression and GWAS data were available. (
  • In-depth analysis of these 105 cis eQTL revealed that at 76 loci genetic associations were compatible with additive effects of several SNPs, while for the 29 remaining regions data could be compatible with a more complex haplotypic pattern. (
  • As 24 of the 105 cis eQTL have previously been reported to be disease-associated loci, this work highlights the need for conducting haplotype-based and 1000 G imputed cis eQTL analysis before commencing functional studies at disease-associated loci. (
  • Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and15 837 distant eQTLs contributing to the whole-genome transcriptomic variation in peanut.There were 94 eQTL hot spot regions detected across the genome with the dominance of distanteQTL. (
  • To improve this understanding, we conducted expression quantitative trait locus ( eQTL ) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. (
  • A quantitative trait locus ( QTL ) is a locus (section of DNA ) that correlates with variation of a quantitative trait in the phenotype of a population of organisms . (
  • Improving the power of sib pair quantitative trait loci detection by phenotype winsorization. (
  • Background: Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). (
  • The simulated quantitative phenotype data are estimated using the Bayesian posterior probabilities (BPPs) that a participant belongs to a clinically important trajectory curve. (
  • 2 3 4 However, these associations are not independent of other correlated traits, such as triglyceride concentration, which suggests small LDLs are a component of an atherogenic lipoprotein phenotype. (
  • LDL size phenotype is heritable 8 and most segregation analyses suggest the existence of a major locus for the trait. (
  • The search for genomic markers that are linked to quantitative traits is an important first step towards finding the gene variants responsible for the observed phenotype, and is consequential for commercial breeding purposes and for uncovering the mechanistic underpinnings of pathologies. (
  • Collectively, these three loci accounted for 63.2% of the variation observed in the F 2 population for this phenotype. (
  • Introduction to Quantitative Genetics 4th edn. (
  • Lynch M and Walsh B (1997) Genetics and Analysis of Quantitative Characters Sunderland, MA: Sinauer Associates. (
  • We now report a new software package called "PROC QTL" that was recently developed by the Quantitative Genetics Group at UC Riverside. (
  • 2003)` NEED FOR QTL STUDIES Molecular genetics analyses of quantitative traits lead to the identification of broadly two types of genetic markers ( causal mutations ) and indirect markers ( non functional genetic markers that are linked to QTL ).Causal mutations are hard to find for quantities traits and few examples are available. (
  • Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. (
  • This represents a unique and valuable approach to the study of complex networks using quantitative genetics. (
  • Understanding the molecular and genetic basis of complex quantitative traits is an important goal in genetics with wide-ranging ramifications across the scientific community. (
  • This study demonstrates the utility of quantitative genetics in the analysis of polygenic drug metabolism. (
  • Still, it would be almost thirty years until the theoretical framework for evolution of complex traits would be widely formalized. (
  • This distinguishes expression quantitative traits from most complex traits, which are not the product of the expression of a single gene. (
  • Experimental animals are useful for dissecting complex traits because of the greater degree of control they afford over genetic and environmental variables. (
  • Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. (
  • Genetic variation in complex traits is thought to be generated by large numbers of loci that usually have comparatively small effects on phenotypes ( Lande, 1981 ). (
  • Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. (
  • Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H (2009) A novel major quantitative trait locus controlling seed development at low temperature in soybean ( Glycine max ). (
  • One major quantitative trait loci (QTL), pcXII.1 , was consistently detected among the locations and explained between 12 to 38% of the phenotypic variation for Pseudoperonospora cubensis resistance. (
  • Thus, we have localized 2 major quantitative trait loci that influence variation in cholesterol concentrations of small LDL particles. (
  • Of these, 3,447 exon-level and 2,172 gene-level eQTLs are reported as trait-associated SNPs in the NHGRI GWAS catalog, giving functional support to the GWAS results of various phenotypes. (
  • Twenty-two of the significant SNPs were classified as "lonely significant markers" as no SNPs in the neighbor region show association with the trait. (
  • The carcass trait, back fat exhibited association with 209 SNPs in 46 genomic regions and yield grade displayed association with 172 SNPs in 69 genomic areas while there were four SNP associations with ribeye area, representing one genomic region. (
  • We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. (
  • Expression quantitative trait loci (eQTLs) are genomic loci that explain variation in expression levels of mRNAs. (
  • Chromosomal loci that explain variance in expression traits are called eQTLs. (
  • Almasy L and Blangero J (1998) Multipoint quantitative‐trait linkage analysis in general pedigrees. (
  • Lander ES and Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. (
  • Wang and Zeng (2006) also explored the Fisher type multi-allele two-locus model on partition of the genotypic variance in the presence of linkage disequilibrium (LD). (
  • Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L. (
  • Intermating of individuals in an F 2 population increases genetic recombination between markers, which is useful for linkage map construction and quantitative trait loci (QTL) mapping. (
  • The populations were grown in two environments to evaluate traits, and inbred lines from each population were genotyped with SSR and SNP markers for linkage map construction and QTL identification. (
  • These data provide us the opportunity to undertake linkage analyses using variance component method to map quantitative trait loci (QTL) of HCT. (
  • Overall, combining information from linkage disequilibrium, sire heterozygosity and genetic knowledge of traits enabled the characterization of additional markers with significant associations with milk production traits. (
  • In multipoint linkage analyses with quantitative trait loci for the 4 fraction sizes, only LDL-3, a fraction containing small LDL particles, gave peak multipoint log 10 odds in favor of linkage (LOD) scores that exceeded 3.0, a nominal criterion for evidence of significant linkage. (
  • 17 18 The evidence for these linkages has not been strong, with only the linkage of the dichotomous trait QTL to the LDL receptor locus 14 having a log 10 odds in favor of linkage (LOD) score that exceeded 3, a nominal criterion for significant evidence of linkage. (
  • Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. (
  • Linkage between genetic loci and morphological traits was first demonstrated almost a century ago [ 2 ] but early efforts [ 3 , 4 ] were difficult due to the sparsity of known genetic markers across the entire genome. (
  • Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane ( Saccharum spp. (
  • A linkage map available for the population was used for mapping quantitative trait loci (QTL) for grain Fe and Zn accumulation. (
  • The release of the bovine genome sequence in 2004 opened the door for the development of high density single nucleotide polymorphism (SNP) panels that can be used for linkage disequilibrium mapping of traits in cattle populations. (
  • Linkage for diastolic BP was found at the autosomal-dominant hypertension with brachydactyly locus. (
  • The linkage was most consistent for the IGF-1 gene locus and systolic BP. (
  • Linkage was also found between the IGF-1 gene locus and posterior cardiac wall thickness, septal thickness, and left ventricular mass index. (
  • A computer program MAPL97 for construction of DNA marker linkage map and quantitative trait locus (QTL) analysis which was written on Visual Basic and is available on Win95 system was developed and announced in a home page of web. (
  • In this study, we have performed a genetic analysis in an F2 cohort of 161 rats derived from BN and LOU rat strains to detect genetic loci contributing to quantitative variations of aortic elastin, collagen, and cell protein contents and to test a possible relationship between these loci and those linked to susceptibility to aortic IEL ruptures. (
  • The Tsn1 locus was a major susceptibility QTL for the race 1 and race 2 isolates, but not for the race 2 isolate with the ToxA gene deleted. (
  • The lipoprotein lipase gene locus has been identified as a susceptibility gene locus of hypertriglyceridemia ( 11 ), and may be relevant to so-called "familial dyslipidemic" hypertension ( 12 ). (
  • Smoking As a Quantitative Trait Locus 3, also known as lung cancer susceptibility 2 , is related to tobacco addiction and substance dependence . (
  • To identify genetic susceptibility loci for AD, we conducted a genome-wide study of atrophy in regions associated with neurodegeneration in this condition. (
  • 0.05, r = 0.98) correlation was observed between different macroscopic and microscopic parameters measured indicating that there is a possible association between partial resistance quantitative trait loci and nonhost resistance quantitative trait loci. (
  • Precision mapping of quantitative trait loci. (
  • Zeng Z‐B (1994) Precision mapping of quantitative trait loci. (
  • Alfred Q., Liu H. Y., Xu H. M., Li J. R., Wu J. G., Zhu S. J. and Shi C. H. 2012 Mapping of quantitative trait loci for oil content in cottonseed kernel. (
  • Mapping of quantitative trait loci for root hair length in wheat identifies loci that co-locate with loci for yield components. (
  • Mapping of Quantitative Trait Loci for Grain Iron and Zinc Concentration in Diploid A Genome Wheat. (
  • Their position is known as quantitative trait loci (QTL). (
  • Identification of Quantitative Trait Loci for Fibrin Clot Phenotypes. (
  • Pfahler, S. and Distl, O. (2012) Identification of Quantitative Trait Loci (QTL) for Canine Hip Dysplasia and Canine Elbow Dysplasia in Bernese Mountain Dogs. (
  • Identification of quantitative trait loci conferring resistance to ta" by Gayan K. Kariyawasam, Waseem Hussain et al. (
  • Castle's was perhaps the first attempt made in the scientific literature to direct evolution by artificial selection of a trait with continuous underlying variation, however the practice had previously been widely employed in the development of agriculture to obtain livestock or plants with favorable features from populations that show quantitative variation in traits like body size or grain yield. (
  • Having data concerning different populations, it would be interesting to know whether QTL identified for a given trait in one population correspond to those detected in other populations, or whether QTL locations identified in one species correspond to QTL or other types of loci detected in corresponding regions of other species. (
  • However, the limited data available suggest that allozyme variability is a poor predictor of genetic variation in quantitative traits within populations. (
  • Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. (
  • Moreover, the populations used to construct the integrated map include all three watermelon subspecies, making this integrated map useful for the selection of breeding traits, identification of QTL, MAS, analysis of germplasm and commercial hybrid seed detection. (
  • We developed a genomic quantitative genetic approach to overcome this problem, allowing us to examine the function(s) of the plant circadian clock in different populations derived from natural accessions. (
  • Background: There are much heterogeneity in the genetic variation of type 2 diabetes (T2D).The purpose of this study was to investigate the association of seven novel genetic loci identified in a recent genome-wide association studies (GWAS) with T2D in Chinese Dong populations. (
  • These SNP platforms were utilized to map both monogenic and quantitative traits to finite genomic regions in beef cattle populations. (
  • Risk factors for osteoporotic hip fracture include reduced bone mineral density and poor structure of the femoral neck, both of which are heritable traits. (
  • A quantitative comparison of BY and RM is shown for twelve phenotypes. (
  • With high-throughput technologies now widely available, investigators can easily measure thousands of phenotypes for quantitative trait loci (QTL) mapping. (
  • I use additive risk allele models to test the association between rare genetic variants and the longitudinal quantitative phenotypes across the whole genome. (
  • Conditions under which the method is more effective than the one solely based on marker types and ordinary selection method based on phenotypes of a trait were tabulated. (
  • Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. (
  • It still maps only a single locus at a time, contradicting the known polygenic character of quantitative traits. (
  • Unfortunately, this effort is complicated by the fact that most phenotypic variation is quantitative and polygenic with at least binary interactions with the environment, development, and second site genetic variation. (
  • This study illustrates the natural diversity and complexity of cellular traits among natural yeast strains and provides an ideal framework for a genetical genomics dissection of multiple traits. (
  • The Chr 11 locus, neuron number control 1 ( Nnc1 ), accounts for one third of the genetic variance among BXH strains and more than half of that among BXD strains, but Nnc1 has no known effects on brain weight, eye weight, or total retinal cell number. (
  • Traditional genetic mapping studies that employ single-generation crosses have poor mapping resolution and limit discovery to loci that are polymorphic between the two parental strains. (
  • Furthermore, the potential for discovery of genetic associations is limited to loci that are polymorphic between the two parental inbred strains. (
  • Methods and Results- We first fine-mapped the locus by studying a series of congenic strains derived from the parental strains BALB/cJ and MRL/MpJ. (
  • We had previously demonstrated genetic variation of this trait among inbred mouse strains. (
  • Suto, Jun-ichi 2008-12-06 00:00:00 A quantitative trait locus (QTL) analysis was performed on the size and shape of the mandible in F2 mice between KK-A y and C57BL/6 J strains and the effect of the A y allele on the morphology of the mandible was analyzed. (
  • A quantitative trait locus (QTL) analysis was performed on the size and shape of the mandible in F2 mice between KK-A y and C57BL/6 J strains and the effect of the A y allele on the morphology of the mandible was analyzed. (
  • One genetic mechanism that has been investigated for its role in regulating these economically important traits is the silencing of gene expression via microRNAs [miRNA(s) or miR], a class of single-stranded, non-coding small RNA that post-transcriptionally regulate gene expression through sequence complementarity of an approximately 7 nt "seed" sequence with target mRNA sequences. (
  • The first objective of this study was to map quantitative trait loci (QTL)affecting economically important traits: milk production traits, health traits and fertility traits in the Finnish Ayshire population. (
  • In conclusion, several QTL affecting economically important traits of dairy cattle were detected. (
  • Sucrose content is one of the most important traits considered in sugarcane breeding. (
  • Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. (
  • Our result provided a first understanding of genetic basis of whole-genome transcriptomic variation in peanut and illustrates the potential of the transcriptome-aidapproach in dissecting important traits in non-model plants. (
  • The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars. (
  • Gu XY, Mei MT, Yan XL, Zheng SL, Lu YG (2000) Preliminary detection of quantitative trait loci for salt tolerance in rice. (
  • Nakamichi R, Ukai Y and Kishino H (2001) Detection of closely linked multiple quantitative trait loci using a genetic algorithm. (
  • It is suggested that these quantitative trait loci may be important for the subsequent detection of allelic variants for elevated BP. (
  • Such quantitative trait loci (QTL) could further the detection of allelic variants associated with elevated BP and thus be important in subsequent studies of hypertensive families or affected sib-pair analyses in hypertensive patients. (
  • 2006). Based on an InDel in the sequence we designed an allele-specific CAPS marker for the quantitative detection of maturity corrected resistance to the oomycete Phytophthora infestans. (
  • The detection of numerous loci in tetraploid breeding material associated with important agronomic traits provides valuable data which can be used to design additional markers not just for resistance against G. pallida but also for other traits, such as resistance to Phytophthora infestans, maturity, yield, and starch content. (
  • Jiang C and Zeng Z‐B (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. (
  • Kruglyak L and Lander ES (1995) Complete multipoint sib‐pair analysis of qualitative and quantitative traits. (
  • Alrefai R., Berke T. and Rocheford T. 1995 Quantitative trait locus analysis of fatty acid concentrations in maize. (
  • OBJECTIVES: In sib pair studies, quantitative trait loci (QTL) identification may be adversely affected by non-normality in the phenotypic distribution, particularly when subjects falling in the tails of the distribution bias the trait mean or variance. (
  • While genomic selection has facilitated increased progress on those traits, a better understanding of the genetic architecture controlling phenotypic expression cannot only improve selection in the long term but also enhance management interventions. (
  • QUANTITATIVE trait locus (QTL) mapping is an approach widely used for detecting and localizing genetic variants responsible for phenotypic variation. (
  • We had previously demonstrated interstrain variation in the phenotypic trait of serum paraxanthine/caffeine index among inbred mice. (
  • Through quantitative trait locus (QTL) mapping of rats that were bred from GHS female rats and normocalciuric Wistar Kyoto (WKY) male rats, loci that are linked to hypercalciuria and account for a 6 to eight-fold phenotypic difference between the GHS and WKY progenitors were mapped. (
  • A m … More ethod for effective selection of a quantitative trait which utilizes both information of DNA marker types and the phenotypic value of the quantitative trait was developed. (
  • Characterization of QTL involved in developmental and agronomic traits. (
  • The relationships between the genetic variability of complex agronomic traits and traits for these two enzymes are discussed. (
  • A total of 114 lines were then selected based on field agronomic traits and stripe rust resistance. (
  • The combination of agronomic traits and disease resistance results showed that 13 of these selected lines had favorable application prospects. (
  • This work focused on the identification and characterization of the genetic basis of important agronomic traits in the potato with main interest centered on resistance to the potato cyst nematode, Globodera pallida. (
  • Genetic complexity and quantitative trait loci mapping of yeast morphological traits. (
  • Our objective was to identify quantitative trait loci (QTL) for yield, phenology, and morphological traits in wheat ( Triticum aestivum L.) under different soil moisture conditions. (
  • Kao C‐H and Zeng Z‐B (1997) General formulae for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. (
  • 62 traits that had negative heritability (no detectable genetic variance) are not represented. (
  • Cockerham (1954 , 1963 ) extended Fisher's one-locus model to two bi-allelic QTL with a particular focus on epistatic variance components. (
  • Eleven chromosomal regions were found to be associated with quantitative resistance to PVY and potyvirus E by both analysis of variance and non-parametric tests. (
  • 5% of trait variance may require a sample size of up to 1000 animals. (
  • Satagopan JM, Yandell BS, Newton MA and Osborn TC (1996) A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. (
  • Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. (
  • a large number of species have been studied for numerous markers and traits. (
  • Jiang C and Zeng Z‐B (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. (
  • 2. The method of claim 1, wherein ASR resistance locus 14 is identifiable by one or more of the markers NS0095012, NSOl 19675, and NS0102630. (
  • 5. The method of claim 4, wherein ASR resistance locus 15 is identifiable by one or more of the markers NS0093385, NSOl 18716, and NS0127833. (
  • 8. The method of claim 7, wherein ASR resistance locus 16 is identifiable by one or both of the markers NSOl 13966 and NSOl 18536. (
  • The objective of this study was to identify genomic regions containing quantitative trait loci (QTL) controlling sucrose, raffinose, and stachyose in a set of 92 F 5:7 recombinant inbred lines (RILs) derived from a cross between the lines "MD96-5722" and "Spencer" by using 5376 Single Nucleotide Polymorphism (SNP) markers from the Illumina Infinium SoySNP6K BeadChip array. (
  • Once quantitative trait loci positions were established, allele substitution effects for all markers were evaluated using the same statistical model. (
  • Does a network approach, combining information about the linear organization of genomic markers with correlative information on these markers in a Bayesian formulation, lead to an analytic method with higher power for detecting quantitative trait loci? (
  • The mapping problem for quantitative trait loci (QTL) is, briefly stated, to find the genetic markers that correlate with measured quantitative traits. (
  • These regions are ideal targets for development of markers for use in marker assisted selection and are also excellent regions to investigate with further fine mapping and discovery of causal variants underlying the quantitative trait loci. (
  • The region on BTA6 was evaluated in an attempt to further refine the candidate locus interval by implementing haplotype analysis with the imputed SNP markers that were used the whole genome association analysis. (
  • Microsatellite markers were tested in the vicinity of the gene loci for insulin-like growth factor-1 (IGF-1), Liddle syndrome, autosomal-dominant hypertension with brachydactyly, angiotensinogen, angiotensin II type 1 receptor, angiotensin-converting enzyme, renin, and lipoprotein lipase. (
  • Two to eleven QTL for each of the six traits and 139 tightly linked markers to these QTL were identified. (
  • Ten generations of backcrosses produced N10F1 rats, which were intercrossed to produce rats that were homozygous for GHS loci in the HC1 region between markers D1Mit2 and D1Mit32. (
  • Quantitative trait loci (QTL) for wheat resistance to aluminum (Al) toxicity were analyzed using simple sequence repeats (SSRs) in a population of 192 F6 recombinant inbred lines (RILs) derived from a cross between an Al-resistant cultivar, Atlas 66 and an Al-sensitive cultivar, Chisholm. (
  • In this study, two quantitative trait loci (QTL) for adult plant resistance (APR) to stripe rust, QYr.nafu-2BL and QYr.nafu-3BS , were validated and introgressed from wheat line P9897 into three Chinese elite wheat cultivars, Chuanmai 42, Xiangmai 25, and Zhengmai 9023, through marker validation. (
  • This first QTL analysis of root hair length in wheat identifies loci that could usefully be further investigated for their role in tolerance to limiting conditions. (
  • Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat × wild emmer wheat RIL population. (
  • To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. (
  • Genotype imputation from the BovineSNP50 to the high density BovineHD platform was conducted to provide a denser marker panel to carry out whole genome association mapping and allow for more refinement of genomic regions associated with traits. (
  • There were 127 SNP associations with the meat quality trait, marbling, that represented 32 genomic regions. (
  • Association was detected with the traits birth weight, back fat, yield grade, ribeye area and marbling. (
  • As is true in all QTL mapping studies, the final steps in defining DNA variants that cause variation in traits are usually difficult and require a second round of experimentation. (
  • We mapped quantitative trait loci (QTL) for 67 traits and discovered 364 correlations between traits segregation and inheritance of gene expression levels. (
  • Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. (
  • Block Network Mapping provides an alternative data-driven approach to mapping quantitative trait loci that leverages correlations in the sampled genotypes. (
  • Cui H, Peng B, Xing Z, Xu G, Yu B, Zhang Q (2002) Molecular dissection of seedling-vigor and associated physiological traits in rice. (
  • We provide evidence for how previously identified GWAS loci for schizophrenia ( NRGN ), Parkinson's disease, and Alzheimer's disease (PARK16 and MAPT loci) could increase the risk for disease at a molecular level. (
  • These loci provide attractive starting points to improve our understanding of the molecular processes underlying disease, in particular given that Mendelian and sporadic forms often share common risk factors. (
  • Thirdly, we extend the one-locus GMA models to multiple loci. (
  • Bert P. F., Jouan I., Tourvieille L. D., Serre F., Philippon J., Nicolas P. and Vear F. 2003 Comparative genetic analysis of quantitative traits in sunflower ( Helianthus annuus L.). 2. (
  • Currently there are two types of statistical genetic models that are commonly used in genetic analysis of quantitative traits. (
  • Quantitative trait loci and diferential gene expression analyses reveal the genetic basis for negatively associated beta‑carotene and starch content in hexaploid sweetpotato (Ipomoea batatas (L.) Lam). (
  • Seed sucrose is a desirable trait for taste and flavor. (
  • When several crosses are available and studied simultaneously for the same trait, a first statement is to consider that the QTL are common to both crosses but that their alleles are different. (
  • An intriguing study surveying the transcriptome of murine brain tissues revealed over 1300 imprinted gene loci (approximately 10-fold more than previously reported) by RNA-sequencing from F1 hybrids resulting from reciprocal crosses. (
  • Improving understanding of the complex regulation of important pork production traits including meat quality, carcass composition, and growth will continue to be a priority for scientists and livestock producers alike. (
  • The imputed genotypes were used in a whole genome scan in order to discover quantitative trait loci that may be influencing growth, carcass and meat quality traits in an US Simmental-Angus population. (
  • Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. (
  • Heritability of survival to PD, analyzed as a binary trait, was estimated from genotyped individuals using a genomic relationship matrix constructed by two methods. (
  • However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. (
  • Nonetheless, both the F ∞ and the Fisher type models form basis in the analysis of quantitative traits. (
  • We performed quantitative trait loci (QTL) analysis of pubescence density and plant development stage because these factors are assumed to be the immediate cause of resistance to cutworm. (
  • Leicester Research Archive: Genome-wide haplotype analysis of cis expression quantitative trait loci in monocytes. (
  • A whole-genome association analysis was conducted using BovineSNP50 BeadChip to map the hypotrichosis locus to a chromosomal region. (
  • Furthermore, we performed a sib-pair analysis in the DZ twins, including genotypes of their parents, to look for loci related to the quantitative trait, BP. (
  • Three digenic epistatic interactions involving four loci were detected for two races of P odosphaera xanthii and one race of G. cichoracearum . (
  • Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. (
  • This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. (
  • Sillanpaa MJ and Arjas E (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. (
  • NM 11:333-337, 2014) with a Bayesian locus likelihood evaluation, leads to large improvements in area under the receiver operating characteristic and power over interval mapping with expectation maximization. (
  • 20 ]) combined with a new Bayesian approach to locus selection. (
  • We did not conduct a total genome scan in the DZ twins, but rather directed our attention to candidate gene loci. (
  • The candidate gene loci we selected included components of the renin-angiotensin system. (
  • The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program for resistance to ASR. (
  • Ashokkumar K. and Ravikesavan R. 2008 Genetic studies of combining ability estimates for seed oil, seed protein and fibre quality traits in upland cotton ( G. hirsutum L. (
  • The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. (
  • and b. generating soybean plants through marker assisted breeding wherein each of said soybean plants comprise ASR resistance locus 16 and at least one of ASR resistance loci 1-15 and each of said soybean plants exhibits at least partial resistance to ASR. (
  • In genetic association studies, we are often interested in direct comparison of the expected genotypic values at certain QTL or marker loci. (
  • Single marker regression [ 2 , 5 ] was the traditional approach to mapping quantitative trait loci. (
  • Significant associations with quantitative resistance were found for all marker types. (