Quantitative Trait Loci: Genetic loci associated with a QUANTITATIVE TRAIT.Quantitative Trait, Heritable: A characteristic showing quantitative inheritance such as SKIN PIGMENTATION in humans. (From A Dictionary of Genetics, 4th ed)Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Crosses, Genetic: 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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Chromosomes, Mammalian: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Models, Genetic: 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.Epistasis, Genetic: 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, Congenic: 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.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Inbreeding: The mating of plants or non-human animals which are closely related genetically.Lod Score: The total relative probability, expressed on a logarithmic scale, that a linkage relationship exists among selected loci. Lod is an acronym for "logarithmic odds."Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Genetic Variation: Genotypic differences observed among individuals in a population.Microsatellite Repeats: 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).Breeding: The production of offspring by selective mating or HYBRIDIZATION, GENETIC in animals or plants.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Linkage Disequilibrium: 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.Multifactorial Inheritance: 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.Genome-Wide Association Study: 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.Mice, Congenic: Mouse strains constructed to possess identical genotypes except for a difference at a single gene locus.Genes, Plant: The functional hereditary units of PLANTS.Oryza sativa: 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.Physical Chromosome Mapping: 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)Chromosomes: 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)Genetic Loci: 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.Likelihood Functions: 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.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.Mice, Inbred Strains: 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.Bayes Theorem: 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.Seeds: 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.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Genetics, 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.Species Specificity: 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.Disease Resistance: 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, Outbred Strains: Animals that are generated from breeding two genetically dissimilar strains of the same species.Genetic Pleiotropy: A phenomenon in which multiple and diverse phenotypic outcomes are influenced by a single gene (or single gene product.)Haplotypes: 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.Pedigree: 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.Genetic Association Studies: 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.Plant Diseases: Diseases of plants.Models, Statistical: 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.Mice, Inbred DBAHordeum: A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.Polymorphism, Genetic: 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.Flowers: The reproductive organs of plants.Hybrid Vigor: The adaptive superiority of the heterozygous GENOTYPE with respect to one or more characters in comparison with the corresponding HOMOZYGOTE.Flowering Tops: Tops of plants when in flower, including the stems, leaves and blooms.Crops, Agricultural: Cultivated plants or agricultural produce such as grain, vegetables, or fruit. (From American Heritage Dictionary, 1982)Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Genome, Human: 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.Gene Frequency: The proportion of one particular in the total of all ALLELES for one genetic locus in a breeding POPULATION.Monte Carlo Method: 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, Inbred Strains: 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)Mice, Inbred C57BLGene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Recombination, Genetic: 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.Brassica napus: A plant species of the family BRASSICACEAE best known for the edible roots.Triticum: 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.Arabidopsis: 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.Meat: 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.Environment: The external elements and conditions which surround, influence, and affect the life and development of an organism or population.Mimulus: A plant genus of the family Phrymaceae. Members contain 6-geranylflavanones and mimulone.Plant Leaves: 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)Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Body Weight: The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Glucosinolates: 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.Sus scrofa: A species of SWINE, in the family Suidae, comprising a number of subspecies including the domestic pig Sus scrofa domestica.Heredity: The transmission of traits encoded in GENES from parent to offspring.Brassica rapa: A plant species cultivated for the seed used as animal feed and as a source of canola cooking oil.Solanum: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Nuclear Family: A family composed of spouses and their children.Rats, Inbred BNSynteny: 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.Rats, Inbred Dahl: 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.Molecular Sequence Data: 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.Haploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.Lycopersicon esculentum: A plant species of the family SOLANACEAE, native of South America, widely cultivated for their edible, fleshy, usually red fruit.Hip Dysplasia, Canine: A hereditary disease of the hip joints in dogs. Signs of the disease may be evident any time after 4 weeks of age.Cattle: 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.Data Interpretation, Statistical: Application of statistical procedures to analyze specific observed or assumed facts from a particular study.Radiation Hybrid Mapping: 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.Markov Chains: 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.Sorghum: 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.Ecotype: 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, Genetic: Databases devoted to knowledge about specific genes and gene products.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.Swine: 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).Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Chromosomes, Human, Pair 1: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.Chromosomes, Human, Pair 2: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.Genes, Dominant: Genes that influence the PHENOTYPE both in the homozygous and the heterozygous state.Droughts: Prolonged dry periods in natural climate cycle. They are slow-onset phenomena caused by rainfall deficit combined with other predisposing factors.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Analysis of Variance: A statistical technique that isolates and assesses the contributions of categorical independent variables to variation in the mean of a continuous dependent variable.Mice, Inbred C3HHeterozygote: An individual having different alleles at one or more loci regarding a specific character.Eucalyptus: 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.Regression Analysis: 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.Homozygote: An individual in which both alleles at a given locus are identical.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Computational Biology: 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.Least-Squares Analysis: 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.Oligonucleotide Array Sequence Analysis: 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.Reproduction: The total process by which organisms produce offspring. (Stedman, 25th ed)Body Size: The physical measurements of a body.Soybeans: An annual legume. The SEEDS of this plant are edible and used to produce a variety of SOY FOODS.Polymorphism, Restriction Fragment Length: 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.Mutation: 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.Ascomycota: 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.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Genetics, Behavioral: 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.Pennisetum: 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.Genomic Imprinting: 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)Helianthus: 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.Chromosomes, Human: 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.Rats, Inbred SHR: A strain of Rattus norvegicus with elevated blood pressure used as a model for studying hypertension and stroke.Sex Characteristics: 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.Osteochondrosis: 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).Genotyping Techniques: Methods used to determine individuals' specific ALLELES or SNPS (single nucleotide polymorphisms).Rats, Inbred WKY: A strain of Rattus norvegicus used as a normotensive control for the spontaneous hypertensive rats (SHR).Fruit: The fleshy or dry ripened ovary of a plant, enclosing the seed or seeds.Organ Size: The measurement of an organ in volume, mass, or heaviness.Milk: The white liquid secreted by the mammary glands. It contains proteins, sugar, lipids, vitamins, and minerals.X Chromosome: 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.Linear Models: 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.Statistical Distributions: 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.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Gene Expression Regulation: 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.Siblings: Persons or animals having at least one parent in common. (American College Dictionary, 3d ed)Amplified Fragment Length Polymorphism Analysis: 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.Germination: 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)Immunity, Innate: 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.Penetrance: 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)Gene-Environment Interaction: The combined effects of genotypes and environmental factors together on phenotypic characteristics.Pigmentation: Coloration or discoloration of a part by a pigment.Solanum melongena: 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.Chromosomes, Human, Pair 5: One of the two pairs of human chromosomes in the group B class (CHROMOSOMES, HUMAN, 4-5).Population: The total number of individuals inhabiting a particular region or area.Pinus taeda: A plant species of the genus PINUS which is the subject of genetic study.Seedling: Very young plant after GERMINATION of SEEDS.Chromosomes, Artificial, Bacterial: 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, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.Plant Shoots: New immature growth of a plant including stem, leaves, tips of branches, and SEEDLINGS.Chromosomes, Human, Pair 6: A specific pair GROUP C CHROMSOMES of the human chromosome classification.Disease Models, Animal: 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.Growth: 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.Genetic Complementation Test: 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.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Chromosomes, Human, Pair 7: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Gene Regulatory Networks: 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.Biometry: The use of statistical and mathematical methods to analyze biological observations and phenomena.Genes, Insect: The functional hereditary units of INSECTS.Blood Pressure: PRESSURE of the BLOOD on the ARTERIES and other BLOOD VESSELS.Hypertension: 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.Mice, Inbred APlant Stems: 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)Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.Chromosomes, Human, Pair 4: A specific pair of GROUP B CHROMOSOMES of the human chromosome classification.Plant Immunity: The inherent or induced capacity of plants to withstand or ward off biological attack by pathogens.Hydroponics: 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)Cereals: Seeds from grasses (POACEAE) which are important in the diet.



*  A Genome Search Identifies Major Quantitative Trait Loci on Human Chromosomes 3 and 4 That Influence Cholesterol Concentrations...

A quantitative trait locus (QTL) for the dichotomous trait for LDL size (pattern A or large buoyant LDLs versus pattern B or ... The 2 quantitative trait loci on chromosomes 3 and 4 are located in regions that contain the genes for apoD and the large ... In multipoint linkage analyses with quantitative trait loci for the 4 fraction sizes, only LDL-3, a fraction containing small ... A Genome Search Identifies Major Quantitative Trait Loci on Human Chromosomes 3 and 4 That Influence Cholesterol Concentrations ...

*  A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance...

Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of ... A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance ... A Germin-Like Protein Gene Family Functions as a Complex Quantitative Trait Locus Conferring Broad-Spectrum Disease Resistance ... Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. Five ...

*  Philosophical Transactions of the Royal Society B: Biological Sciences

2009 Quantitative trait loci analysis in animals, 2nd edn, p. 272. Wallingford, Oxford: CABI. ... 7. Maintenance of variation in quantitative traits. Let us turn now from considerations of how quantitative traits are ... a) Using individual quantitative trait loci. There has been extensive theoretical analysis and simulation to develop methods ... 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69, 315- ...

*  British Library EThOS: Genetics of litter size and prenatal survival in pigs

The aims of this study were to identify quantitative trait loci (QTL) affecting reproductive traits and to identify and ... A Large White - Meishan F2 population was scanned for QTL with effects on reproductive traits. This analysis revealed 13 ... Fourteen SNPs were found significantly associated with reproductive traits. The functional study of SPP1 examined the ... There is abundant evidence of genetic variation in these traits among pig breeds. ...

*  Table of Contents | Genetics

Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thaliana ... Comment on "On the Metropolis-Hastings Acceptance Probability to Add or Drop a Quantitative Trait Locus in Markov Chain Monte ... A Quantitative Trait Locus Mixture Model That Avoids Spurious LOD Score Peaks ... A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon ...

*  A clinical study of kuru patients with long incubation periods at the end of the epidemic in Papua New Guinea | Philosophical...

2000 Quantitative trait loci affecting prion incubation time in mice. Genomics. 69, 47-53. doi:10.1006/geno.2000.6320. ... 2001 Identification of multiple quantitative trait loci linked to prion disease incubation period in mice. Proc. Natl Acad. Sci ... 2001, 2002). It can be anticipated that the human homologues of such loci may play a key role in human susceptibility to prion ... In addition to the PrP gene, a small number of additional genetic loci with a major effect on incubation period have been ...

*  Program Details : University Catalogs : University of Minnesota

Mapping quantitative trait loci (QTL). Parentage testing. prereq: [Stat 3021 or equiv], [Biol 4003 or equiv] ... Fundamentals of quantitative genetics. Genetic/environmental influences on expression of quantitative traits. Approaches to ... Fundamentals of quantitative genetics. Genetic/environmental influences on expression of quantitative traits. Approaches to ... Processes that lead to change in quantitative traits. Applied/evolutionary aspects of quantitative genetic variation. prereq: [ ...

*  Analysis of the IBD5 locus and potential gene-gene interactions in Crohn's disease | Gut

Farmer MA, Sundberg JP, Bristol IJ, et al. A major quantitative trait locus on chromosome 3 controls colitis severity in IL-10- ... Quantitative trait loci in Drosophilia. Nat Rev Genet2002;2:11-20. ... A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. ... Single locus models were first tested in which only the effect of a single genetic variant on phenotype (that is, presence of ...

*  Hyun Lillehoj : USDA ARS

MAPPING QUANTITATIVE TRAIT LOCI AFFECTING DISEASE RESISTANCE TO AVIAN COCCIDIOSIS (73RD NECAB MTG, COLLEGE PARK, MD) - ... Fine mapping of quantitative trait loci (qtl) which control disease resistance to eimeria infection.. Avian Immunology Group ... Mapping quantitative trait locus associated with resistance to avian coccidiosis and growth. Poultry Science 82:9-16. ... FINE MAPPING OF QUANTITATIVE TRAIT LOCI (QTL) WHICH CONTROL DISEASE RESISTANCE TO EIMERIA INFECTION. - ...

*  High‐Throughput Single Nucleotide Polymorphisms Genotyping Technologies

... wide association studies have successfullyidentified many novel genetic loci for various human complex diseases and ... 2008) A genome‐wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genetics 4: e1000072. ... quantitative traits. There are several important factors contributing to the feasibility of this approach; one of them is the ... Over the past three years, GWAS have been playing an important role in identifying novel genetic loci for various human complex ...

*  Library System/Howard University

Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. Stat Med., ... A novel approach for the simultaneous analysis of common and rare variants in complex traits. Bioinform Biol Insights, Vol.6 ( ... Simultaneous analysis of common and rare variants in complex traits: Application to SNPs (SCARVAsnp). Bioinformatics and ... Simultaneous analysis of common and rare variants in complex traits: Application to SNPs (SCARVAsnp). Bioinformatics and ...

*  Library System/Howard University

Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. Stat Med., ... Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. Stat Med., ... Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. Statistics ... Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. Statistics ...

*  Library System/Howard University

Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility ...

*  A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution. 2007;61(6):1403 ... Slate J. Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Molecular Ecology. ... Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and ... However one of their most important applications is in the search for Mendelian and Quantitative Trait Loci (QTL) [5,6]. Over ...

*  Library System/Howard University

Genetic association of a MAPK8 expression quantitative trait locus with pre-capillary pulmonary hypertension in sickle cell ... SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clinical Applications, Vol.7, No.5-6 (2013 ...

*  Chaofu Lu - Plant Sciences and Plant Pathology | Montana State University

Analysis of quantitative trait loci which contribute to anther culturability in rice (Oryza sativa L.). Molecular Breeding 4 (2 ... Using doubled haploid populations of rice for quantitative trait locus mapping. In G. S. Khush (eds) Rice Genetics III, 631-635 ... Comparison of molecular linkage maps and agronomic trait loci between DH and RIL populations derived from the same rice cross. ... Comparative mapping of QTLs for agronomic traits of rice across environments by using a doubled-haploid population. Theoretical ...

*  Publications of Patrick Giavalisco | Max Planck Institute of Molecular Plant Physiology

Identification and mode of inheritance of quantitative trait Loci for secondary metabolite abundance in tomato. The Plant Cell ...

*  Plus it

... allowing for more precise quantitative trait loci (QTL) localization than classical interval mapping (12). ... This locus has been designated Iddm20 by the curators of the Rat Genome Database (available at www.rgd.mcw.edu). ... The genome-wide scan positioned the Iddm20 locus in a 1-LOD interval bounded by D17Rat61 (at 19.7 Mb) and D17Rat115 (at 27.7 Mb ... In analyses of (BBDP × WF) × WF rats, we used poly I:C plus Treg depletion to map a locus on chromosome 4 (Iddm4) with ...

*  Combined GWAS and 'guilt by association'-based prioritization analysis identifies functional candidate genes for body size in...

Nine out of the 11 SNPs were located on previously identified quantitative trait loci for sheep meat, production or ... According to the infinitesimal model of Fisher [1], traits such as BS are genetically controlled by an infinite number of loci ... It is a composite quantitative trait that has been studied with high-throughput genomic methods, i.e. genome-wide association ... Traits were then adjusted for these effects based on the least square estimates of each class effect and for each trait. A ...

*  Functional network of genes modulating GAS QTL.Graphica | Open-i

By analyzing disease phenotypes in the context of mice genotypes we identified a highly significant quantitative trait locus ( ... By analyzing disease phenotypes in the context of mice genotypes we identified a highly significant quantitative trait locus ( ... analyzing disease phenotypes in the context of mice genotypes we identified a highly significant quantitative trait locus (QTL ... analyzing disease phenotypes in the context of mice genotypes we identified a highly significant quantitative trait locus (QTL ...

*  Peroxidase Profiling Reveals Genetic Linkage between Peroxidase Gene Clusters and Basal Host and Non-Host Resistance to Rusts...

Isolate specificity of quantitative trait loci for partial resistance of barley to Puccinia hordei confirmed in mapping ... Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide ... in earlier studies we identified six Prx genes to map within 1cM from markers associated with several quantitative trait loci ( ... A 1000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet. 2007; ...

*  RFA-ES-17-009: Population-Based Model Organism Research for G x E Exploration in Complex Disease Outcomes (R01 Clinical Trial...

These unique resources have proven to be powerful tools for identifying individual quantitative trait loci (QTL) and candidate ... Discovery quantitative trait genes (QTGs) in mouse reference populations that affect toxicity or susceptibility have the ... Thus, mapping complex traits in mice was also very challenging. However, new genetically-diverse mouse resources have now been ... Mouse population models may additionally be utilized to identify quantitative biomarkers that are associated with toxicity ...

*  Plus it

Gu HF, Efendic S, Nordman S, Ostenson C-G, Brismar K, Brookes AJ, Prince JA: Quantitative trait loci near the insulin-degrading ... Quantitative trait measurements.. A 75-g oral glucose tolerance test was performed in a subset of the control Scandinavian ... Quantitative trait comparisons.. Only nondiabetic subjects were included in our analyses of diabetes-related phenotypes. Their ... Nominally significant differences in quantitative traits are consistent with statistical noise. We conclude that common genetic ...

*  Publications - Research - University of South Australia

V.L. Nguyen, B.L. Huynh, H. Wallwork and J. Stangoulis (2011) Identification of Quantitative Trait Loci for Grain Arabinoxylan ... Hardner, CM, Evans, K, Brien, C, Bliss, F & Peace, C 2016, 'Genetic architecture of apple fruit quality traits following ... Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping', Nature Communications, vol. 7, ...

Chromosome regionsGenetic linkage: Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked.Phenotype microarray: The phenotype microarray approach is a technology for high-throughput phenotyping of cells.Congenic: In genetics, two organisms that differ in only one locus and a linked segment of chromosome are defined as congenic. Similarly, organisms that are coisogenic differ in one locus only and not in the surrounding chromosome.Inbreeding depression: Inbreeding depression is the reduced biological fitness in a given population as a result of inbreeding, or breeding of related individuals. Population biological fitness refers to its ability to survive and reproduce itself.Genetic variation: right|thumbMicrosatellite: A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5-50 times. Microsatellites occur at thousands of locations in the human genome and they are notable for their high mutation rate and high diversity in the population.Plant breedingInfinite alleles model: The infinite alleles model is a mathematical model for calculating genetic mutations. The Japanese geneticist Motoo Kimura and American geneticist James F.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.List of sequenced eukaryotic genomesDisequilibrium (medicine): Disequilibrium}}Population stratification: Population stratification is the presence of a systematic difference in allele frequencies between subpopulations in a population possibly due to different ancestry, especially in the context of association studies. Population stratification is also referred to as population structure, in this context.Weedy rice: Weedy rice, also known as red rice, is a variety of rice (Oryza) that produces far fewer grains per plant than cultivated rice and is therefore considered a pest. The name "weedy rice" is used for all types and variations of rice which show some characteristic features of cultivated rice and grow as weeds in commercial rice fields.Premature chromosome condensation: Premature chromosome condensation (PCC) occurs in eukaryotic organisms when mitotic cells fuse with interphase cells. Chromatin, a substance that contains genetic material such as DNA, is normally found in a loose bundle inside a cell's nucleus.Decoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Southern corn leaf blight: Southern corn leaf blight (SCLB) is a fungal disease of maize caused by the plant pathogen Bipolaris maydis (also known as Cochliobolus heterostrophus in its teleomorph state).Hybrid inviability: Hybrid inviability is a post-zygotic barrier, which reduces a hybrid's capacity to mature into a healthy, fit adult.Hybrid inviability.Uniparental inheritance: Uniparental inheritance is a non-mendelian form of inheritance that consists of the transmission of genotypes from one parental type to all progeny. That is, all the genes in offspring will originate from only the mother or only the father.Hyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.Tomato seed oil: Tomato seed oil is a vegetable oil extracted from the seeds of tomatoes.Selection (relational algebra): In relational algebra, a selection (sometimes called a restriction to avoid confusion with SQL's use of SELECT) is a unary operation written asPanmixia: Panmixia (or panmixis) means random mating.King C and Stanfield W.Pleiotropy (drugs): In pharmacology, pleiotropy refers to a drug's actions, usually unanticipated, other than those for which the agent was specifically developed. It may include adverse effects which are detrimental ones, but is often used to denote additional beneficial effects.Pedigree chart: A pedigree chart is a diagram that shows the occurrence and appearance or phenotypes of a particular gene or organism and its ancestors from one generation to the next,pedigree chart Genealogy Glossary - About.com, a part of The New York Times Company.Fungicide use in the United States: A more accurate title for this page would be "Common plant pathogens to food crops in the United States".Inverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.Leaf rust (barley): Leaf rust is a fungal disease of barley caused by Puccinia hordei. It is also known as brown rust and it is the most important rust disease on barley.Gene polymorphismFlower box: __NOTOC__Terminal crossbreeding: Terminal crossbreeding is a breeding system used in animal production. It involves two (different) breeds of animal that have been crossbred.Plant breeders' rights: Plant breeders' rights (PBR), also known as plant variety rights (PVR), are rights granted to the breeder of a new variety of plant that give the breeder exclusive control over the propagating material (including seed, cuttings, divisions, tissue culture) and harvested material (cut flowers, fruit, foliage) of a new variety for a number of years.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Monte Carlo methods for option pricing: In mathematical finance, a Monte Carlo option model uses Monte Carlo methods Although the term 'Monte Carlo method' was coined by Stanislaw Ulam in the 1940s, some trace such methods to the 18th century French naturalist Buffon, and a question he asked about the results of dropping a needle randomly on a striped floor or table. See Buffon's needle.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Recombination (cosmology): In cosmology, recombination refers to the epoch at which charged electrons and protons first became bound to form electrically neutral hydrogen atoms.Note that the term recombination is a misnomer, considering that it represents the first time that electrically neutral hydrogen formed.Wheat middlings: Wheat middlings (also known as millfeed, wheat mill run, or wheat midds) is the middle of three grades into which flour and meal are classified: patents, middlings, and clears. Middlings are often used in animal feed.GAI (Arabidopsis thaliana gene)White meat: White meat or light meat refers to the lighter-colored meat of poultry as contrasted with dark meat. In a more general sense, white meat may also refer to any lighter-colored meat, as contrasted with red meats like beef and some types of game.Evolution in Variable EnvironmentCanna Leaf Roller: Cannas are largely free of pests, but in the USA plants sometimes fall victim the Canna Leaf Roller, which can actually be two different insects. Larva of the Brazilian skipper butterfly (Calpodes ethlius), also known as the Larger Canna Leaf Roller, cut the leaves and roll them over to live inside while pupating and eating the leaf.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.MyrosinaseSolanum chacoense: Solanum chacoense is a species of wild potato. It is native to South America, where it can be found in Brazil, Bolivia, Argentina, Peru, Uruguay, and Paraguay.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Ah, Sweet Mystery of Life: The Country Stories of Roald Dahl: Ah, Sweet Mystery of Life: The Country Stories of Roald Dahl is a 1989 short story collection by Roald Dahl. The book is a collection of seven of Dahl's stories published in various magazines and collections in the 1940s and 1950s.Coles PhillipsSun-dried tomato: Sun-dried tomatoes are ripe tomatoes that lose most of their water content after spending a majority of their drying time in the sun. These tomatoes are usually pre-treated with sulfur dioxide or salt before being placed in the sun in order to improve quality.Dog breeding: Dog breeding is the practice of mating selected dogs with the intent to maintain or produce specific qualities and characteristics. When dogs reproduce without such human intervention, their offsprings' characteristics are determined by natural selection, while "dog breeding" refers specifically to the artificial selection of dogs, in which dogs are intentionally bred by their owners.Beef cattle: Beef cattle are cattle raised for meat production (as distinguished from dairy cattle, used for milk production). The meat of adult cattle is known as beef.Vladimir Andreevich Markov: Vladimir Andreevich Markov (; May 8, 1871 – January 18, 1897) was a Russian mathematician, known for proving the Markov brothers' inequality with his older brother Andrey Markov. He died of tuberculosis at the age of 25.Sweet sorghumExtracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Subtherapeutic antibiotic use in swine: Antibiotics are commonly used in commercial swine production in the United States and around the world. They are used for disease treatment, disease prevention and control, and growth promotion.Squamosa promoter binding protein: The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.

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

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)

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

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)

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

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)

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

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)

(5/4986) 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.

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)

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

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)

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

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)

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

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)

expression quantitative

  • Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests. (howard.edu)
  • Genetic association of a MAPK8 expression quantitative trait locus with pre-capillary pulmonary hypertension in sickle cell disease. (howard.edu)


  • Fourteen SNPs were found significantly associated with reproductive traits. (bl.uk)
  • Simultaneous analysis of common and rare variants in complex traits: Application to SNPs (SCARVAsnp). (howard.edu)
  • When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). (pubmedcentralcanada.ca)


  • Traits such as size, obesity or longevity vary greatly among individuals, and have continuously distributed phenotypes that do not show simple Mendelian inheritance. (royalsocietypublishing.org)
  • However one of their most important applications is in the search for Mendelian and Quantitative Trait Loci (QTL) [ 5 , 6 ]. (pubmedcentralcanada.ca)


  • 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). (ahajournals.org)
  • 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. (ahajournals.org)
  • This analysis revealed 13 putative QTLs on seven different chromosomes with effects on five different traits: ovulation rate (OR), teat number (TN), prenatal survival (PS), total born alive (TBA) and litter size (LS). (bl.uk)


  • Use of these QTL to improve crop species, however, is hindered because the genes contributing to the trait are not known. (www.gov.uk)
  • Quantitative genetics, or the genetics of complex traits, is the study of those characters which are not affected by the action of just a few major genes. (royalsocietypublishing.org)
  • Analyses using dense molecular markers are greatly increasing information about the architecture of these traits, but while some genes of large effect are found, even many dozens of genes do not explain all the variation. (royalsocietypublishing.org)
  • Quantitative genetics , also referred to as the genetics of complex traits , is the study of such characters and is based on a model in which many genes influence the trait and in which non-genetic factors may also be important. (royalsocietypublishing.org)
  • On the premise that many genes and the environment act and interact to determine the trait, founders recognized that it would be difficult if not impossible to determine the action of individual trait genes. (royalsocietypublishing.org)
  • Ultimately, we want to know at the molecular level not just which genes are involved, whether structural or regulatory, but what specific nucleotide change in each gene or alternatively copy number variant is responsible for the quantitative trait effect, and how the genes are controlled. (royalsocietypublishing.org)


  • To test for possible epistatic interactions between variants, transmission disequilibrium test analyses were further stratified by genotype at other loci, and novel log linear analyses were performed using the haplotype relative risk model. (bmj.com)
  • Genetic variants from three distinct loci have recently been shown to be associated with CD. (bmj.com)
  • A novel approach for the simultaneous analysis of common and rare variants in complex traits. (howard.edu)

genetic variation

  • There is extensive genetic variation in natural populations, but better estimates of covariances among multiple traits and their relation to fitness are needed. (royalsocietypublishing.org)
  • We are indeed becoming increasingly able to peer inside the box and can ask whether our statistical models of genetic variation in traits are so unrealistic that the edifice may topple. (royalsocietypublishing.org)
  • There is abundant evidence of genetic variation in these traits among pig breeds. (bl.uk)
  • Finally, genetic variation in a 250 kb cytokine gene cluster on chromosome 5q31 ( IBD5 locus and risk haplotype) has been strongly associated with CD in a Canadian Caucasian population. (bmj.com)


  • Genome‐wide association studies have successfully identified many novel genetic loci for various human complex diseases and quantitative traits. (els.net)
  • Over the past three years, GWAS have been playing an important role in identifying novel genetic loci for various human complex diseases and quantitative traits. (els.net)


  • The quantitative genetics approach has diverse applications: it is fundamental to an understanding of variation and covariation among relatives in natural and managed populations, of the dynamics of evolutionary change, and of methods for animal and plant improvement and alleviation of complex disease. (royalsocietypublishing.org)
  • Complex interactions between susceptibility loci have been shown in animal models, and we tested for potential gene-gene interactions between the three CD associated loci. (bmj.com)


  • 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. (ahajournals.org)
  • LDL size phenotype is heritable 8 and most segregation analyses suggest the existence of a major locus for the trait. (ahajournals.org)


  • Statistical methods were invented by Fisher (1918) and Wright (1921) , the analysis of variance and path coefficients, respectively, to partition the variation and describe the resemblance between relatives, and such tools and methods developed in quantitative genetics have had widespread application in disciplines way outwith their original targets. (royalsocietypublishing.org)


  • 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. (ahajournals.org)
  • Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). (pubmedcentralcanada.ca)


  • The framework can also be used for the analysis of traits such as litter size that take a few discrete values, and of binary characters such as survival to adulthood that have a polygenic basis. (royalsocietypublishing.org)
  • SILAC-based quantitative proteomic analysis of gastric cancer secretome. (howard.edu)


  • Thus, we have localized 2 major quantitative trait loci that influence variation in cholesterol concentrations of small LDL particles. (ahajournals.org)


  • A Large White - Meishan F2 population was scanned for QTL with effects on reproductive traits. (bl.uk)


  • 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. (ahajournals.org)


  • The aims of this study were to identify quantitative trait loci (QTL) affecting reproductive traits and to identify and characterise positional candidate gene(s) underlying the QTL. (bl.uk)
  • A genome-wide association study was performed on a diverse population of different breeds and crosses lines, for reproductive traits including LS, TBA, number of stillborn piglets, and number of mummified piglets. (bl.uk)


  • Both the dichotomous and continuous traits studied above are based on LDL particle size distributions rather than concentrations. (ahajournals.org)


  • 8 Secondly, we have described an association between IBD and the TNF −857C/T promoter polymorphism (located within the chromosome 6, IBD3 locus) in a British Caucasian population. (bmj.com)


  • Plant disease resistance governed by quantitative trait loci (QTL) is predicted to be effective against a broad spectrum of pathogens and long lasting. (www.gov.uk)