AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPsychiatry and PsychologyPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceNamed GroupsHealth Care
Quantitative Trait LociQuantitative Trait, HeritableChromosome MappingCrosses, GeneticGenetic MarkersGenetic LinkageChromosomes, MammalianPhenotypeModels, GeneticEpistasis, GeneticAnimals, CongenicGenotypeInbreedingLod ScoreChromosomes, PlantGenetic VariationMicrosatellite RepeatsBreedingAllelesPolymorphism, Single NucleotideGenomeLinkage DisequilibriumMultifactorial InheritanceGenome-Wide Association StudyMice, CongenicGenes, PlantOryza sativaPhysical Chromosome MappingChromosomesGenetic LociLikelihood FunctionsGenetic Predisposition to DiseaseComputer SimulationZea maysHybridization, GeneticGenome, PlantInheritance PatternsMice, Inbred StrainsBayes TheoremSeedsSelection, GeneticGenetics, PopulationSpecies SpecificityDisease ResistanceAnimals, Outbred StrainsGenetic PleiotropyHaplotypesPedigreeGenetic Association StudiesPlant DiseasesModels, StatisticalMice, Inbred DBAHordeumPolymorphism, GeneticFlowersHybrid VigorFlowering TopsCrops, AgriculturalGenomicsGenome, HumanGene FrequencyMonte Carlo MethodAnimals, Inbred StrainsMice, Inbred C57BLGene Expression ProfilingRecombination, GeneticBrassica napusTriticumArabidopsisMeatEnvironmentMimulusPlant LeavesAlgorithmsBody WeightDNA, PlantGlucosinolatesSus scrofaHeredityBrassica rapaSolanumSequence Analysis, DNANuclear FamilyRats, Inbred BNSyntenyRats, Inbred DahlMolecular Sequence DataHaploidyLycopersicon esculentumHip Dysplasia, CanineCattleData Interpretation, StatisticalRadiation Hybrid MappingMarkov ChainsSorghumEcotypeDatabases, GeneticGenetic TechniquesSwineGene Expression Regulation, Plant
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 DBA
Hordeum
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 C57BL
Gene 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 BN
Synteny
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 C3H
Heterozygote
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 A
Plant 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.

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)

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis | BMC...Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis | BMC...
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
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-244
Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide...Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide...
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 …
https://pubmed.ncbi.nlm.nih.gov/17944808/?dopt=Abstract
Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the...Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the...
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. ...
http://www.diva-portal.org/smash/record.jsf?pid=diva2:910411
Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut...Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut...
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 ...
https://www.cgiar.org/research/publication/genome%E2%80%90wide-expression-quantitative-trait-locus-analysis-in-a-recombinant-inbred-line-population-for-trait-dissection-in-peanut/
Comprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe | Genome Medicine | Full TextComprehensive promoter level expression quantitative trait loci analysis of the human frontal lobe | Genome Medicine | Full Text
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
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0320-1/figures/2
A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare<...
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 ...
https://okayama.pure.elsevier.com/en/publications/a-novel-quantitative-trait-locus-qcl1-involved-in-semi-dwarfism-d
Descripción: Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for...Descripción: Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for...
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 ...
http://repositoriosiidca.csuca.org/Record/RepoKERWA30398
Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studiesIntegrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
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 ...
https://dash.harvard.edu/handle/1/30370942
Frontiers | Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential...Frontiers | Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential...
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
https://www.frontiersin.org/articles/10.3389/fonc.2020.602104/full
Patent WO2009132089A2 - A method to identify asian soybean rust resistance quantitative trait loci ... - Google PatentsPatent WO2009132089A2 - A method to identify asian soybean rust resistance quantitative trait loci ... - Google Patents
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.
http://www.google.com.au/patents/WO2009132089A2?cl=en
High-Resolution Quantitative Trait Locus Mapping Reveals Sign Epistasis Controlling Ovariole Number Between Two Drosophila...High-Resolution Quantitative Trait Locus Mapping Reveals Sign Epistasis Controlling Ovariole Number Between Two Drosophila...
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 ...
https://www.genetics.org/content/173/1/197.abstract
Bayesian hierarchical regression model to detect quantitative trait loci, NC DOCKS (North Carolina Digital Online Collection of...
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 ...
http://libres.uncg.edu/ir/listing.aspx?id=1630
Improving the power of sib pair quantitative trait loci detection by phenotype winsorization.
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
http://www.biomedsearch.com/nih/Improving-power-sib-pair-quantitative/12037405.html
Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping | GeneticsSignificance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping | Genetics
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 ...
http://www.genetics.org/content/177/3/1963
Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local...Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local...
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 ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1300-3
A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis<...A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis<...
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 ...
https://einstein.pure.elsevier.com/en/publications/a-model-selection-approach-for-the-identification-of-quantitative
Identification of quantitative trait locus for abscisic acid responsiveness on chromosome 5A and association with dehydration...
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 ...
https://okayama.pure.elsevier.com/en/publications/identification-of-quantitative-trait-locus-for-abscisic-acid-resp
Quantitative trait locus analysis of unsaturated fatty acids in a rec by Xianzhi Wang, Guo-Liang Jiang et al.Quantitative trait locus analysis of unsaturated fatty acids in a rec by Xianzhi Wang, Guo-Liang Jiang et al.
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
https://digitalcommons.unl.edu/agronomyfacpub/813/
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...
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 ...
https://www.gov.uk/dfid-research-outputs/a-germin-like-protein-gene-family-functions-as-a-complex-quantitative-trait-locus-conferring-broad-spectrum-disease-resistance-in-rice
Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae...Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae...
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
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07417-4
Quantitative trait loci analysis of blood pressure in an eight intercr by Marion Elizabeth DeerhakeQuantitative trait loci analysis of blood pressure in an eight intercr by Marion Elizabeth Deerhake
Deerhake, Marion Elizabeth, Quantitative trait loci analysis of blood pressure in an eight intercross mouse study (2008). Summer and Academic Year Student Reports. 2234 ...
https://mouseion.jax.org/strp/2234/
Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene<...
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 ...
https://squ.pure.elsevier.com/en/publications/genome-wide-scans-reveal-a-quantitative-trait-locus-for-withers-h-2
Bone Mineral Density Quantitative Trait Locus 12 disease: Malacards - Research Articles, Drugs, Genes, Clinical TrialsBone Mineral Density Quantitative Trait Locus 12 disease: Malacards - Research Articles, Drugs, Genes, Clinical Trials
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 ...
https://www.malacards.org/card/bone_mineral_density_quantitative_trait_locus_12
Bone Mineral Density Quantitative Trait Locus 11 disease: Malacards - Research Articles, Drugs, Genes, Clinical TrialsBone Mineral Density Quantitative Trait Locus 11 disease: Malacards - Research Articles, Drugs, Genes, Clinical Trials
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 ...
https://www.malacards.org/card/bone_mineral_density_quantitative_trait_locus_11
A combined strategy for quantitative trait loci detection by genome-wide association | BMC Proceedings | Full TextA combined strategy for quantitative trait loci detection by genome-wide association | BMC Proceedings | Full Text
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 ...
https://bmcproc.biomedcentral.com/articles/10.1186/1753-6561-3-S1-S6
Identification of porcine Lhx3 and SF1 as candidate genes for QTL affecting growth and reproduction traits in swine<...
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 ...
https://indiana.pure.elsevier.com/en/publications/identification-of-porcine-lhx3-and-sf1-as-candidate-genes-for-qtl
Detection of Quantitative Trait Loci for Mineral Content of Nelore Lon by Polyana C. Tizioto, Jeremy F. Taylor et al.Detection of Quantitative Trait Loci for Mineral Content of Nelore Lon by Polyana C. Tizioto, Jeremy F. Taylor et al.
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
https://lib.dr.iastate.edu/ans_pubs/166/
Quantitative Trait Loci for salinity tolerance identified under drained and waterlogged conditions and their association with...Quantitative Trait Loci for salinity tolerance identified under drained and waterlogged conditions and their association with...
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.. ...
http://researchrepository.murdoch.edu.au/id/eprint/28274/
Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheatSingle nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat
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 ...
http://krex.k-state.edu/dspace/handle/2097/33970
Genome-Wide Linkage and Association Scans for Quantitative Trait Loci of Serum Lactate Dehydrogenase-The Framingham Heart StudyGenome-Wide Linkage and Association Scans for Quantitative Trait Loci of Serum Lactate Dehydrogenase-The Framingham Heart Study
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 ...
https://open.bu.edu/handle/2144/2809
QTL for Body Composition Traits During Heat Stress Revealed in an Advanced Intercross Line of Chickens | WCGALP Archive
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.. ...
http://wcgalp.org/proceedings/2014/qtl-body-composition-traits-during-heat-stress-revealed-advanced-intercross-line
Quantitative Trait Loci for Root Architecture Traits Correlated with Phosphorus Acquisition in Common Bean - Department of...Quantitative Trait Loci for Root Architecture Traits Correlated with Phosphorus Acquisition in Common Bean - Department of...
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 ...
https://plantscience.psu.edu/research/labs/roots/publications/overviews/quantitative-trait-loci-for-root-architecture-traits-correlated-with-phosphorus-acquisition-in-common-bean
Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs | Genetics...Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs | Genetics...
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).
https://gsejournal.biomedcentral.com/articles/10.1186/s12711-015-0135-3/figures/5
Identification of Quantitative Trait Loci Controlling Floral Morphology of Rice Using a Backcross Population between Common...Identification of Quantitative Trait Loci Controlling Floral Morphology of Rice Using a Backcross Population between Common...
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
http://www.scirp.org/journal/PaperInformation.aspx?paperID=74787&
Quantitative trait loci identification, fine mapping and gene expression profiling for ovicidal response to whitebacked...Quantitative trait loci identification, fine mapping and gene expression profiling for ovicidal response to whitebacked...
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
https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-145
Detecting Major Genes Controlling Robustness of Chicken Body Weight Using Double Generalized Linear ModelsDetecting Major Genes Controlling Robustness of Chicken Body Weight Using Double Generalized Linear Models
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.. ...
http://www.diva-portal.org/smash/record.jsf?pid=diva2:518898
Identification of quantitative trait loci function through analysis of multiple cuticular hydrocarbons differing between...Identification of quantitative trait loci function through analysis of multiple cuticular hydrocarbons differing between...
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
https://www.semanticscholar.org/paper/Identification-of-quantitative-trait-loci-function-Gleason-James/28f298cca82029eb826b18eb2b24f74596235582
QTL mapping and gene markers for resistance to infectious diseases in sheep and cattle. | WCGALP Archive
Infectious disease has a significant economic impact in livestock production systems worldwide. Selection using DNA markers closely linked to, or within genes controlling resistance traits is increasingly prevalent. We review the state of quantitative trait loci (QTL) studies based on genome wide screens or targeted candidate gene studies for sheep and cattle. Infectious diseases considered include gastrointestinal nematodes, mastitis, trypanosomiasis, dermatophilosis, footrot, fasciolosis, tick and tickborne diseases. We discuss the problems and methods of moving from QTL results to quantitative trait nucleotides (QTN) by fine mapping, and comparative mapping. We highlight the utility of integrating QTL studies with large scale transcriptome studies to obtain positional-functional candidate genes, followed by gain/loss of function studies. We close with markers shown to have utility in industry applications.. ...
http://wcgalp.org/proceedings/2006/qtl-mapping-and-gene-markers-resistance-infectious-diseases-sheep-and-cattle
Fine mapping of Lvm1: a quantitative trait locus controlling heart size independently of blood pressure - DROFine mapping of Lvm1: a quantitative trait locus controlling heart size independently of blood pressure - DRO
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. ...
http://dro.deakin.edu.au/view/DU:30075169
African Journal of Agricultural Research - quantitative trait loci (qtl) mapping of resistance to coffee berry disease ...African Journal of Agricultural Research - quantitative trait loci (qtl) mapping of resistance to coffee berry disease ...
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
https://academicjournals.org/journal/AJAR/article-abstract/5CDC01C64605
Resistance to Melampsora larici-epitea leaf rust in Salix : analyses of quantitative trait lociResistance to Melampsora larici-epitea leaf rust in Salix : analyses of quantitative trait loci
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 ...
http://su.diva-portal.org/smash/record.jsf?pid=diva2:417653
A polymerase chain reaction-based linkage map of broccoli and identification of quantitative trait loci associated with harvest...A polymerase chain reaction-based linkage map of broccoli and identification of quantitative trait loci associated with harvest...
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 ...
https://experts.illinois.edu/en/publications/a-polymerase-chain-reaction-based-linkage-map-of-broccoli-and-ide
A genome-wide scan for quantitative trait loci affecting limb bone lengths and areal bone mineral density of the distal femur...A genome-wide scan for quantitative trait loci affecting limb bone lengths and areal bone mineral density of the distal femur...
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
https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-9-63
Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA<...
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) ...
https://research.wur.nl/en/publications/regulatory-network-identification-by-genetical-genomics-signaling
Quantitative trait loci affecting initial sensitivity and acute functional tolerance to ethanol-induced ataxia and brain cAMP...Quantitative trait loci affecting initial sensitivity and acute functional tolerance to ethanol-induced ataxia and brain cAMP...
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 ...
https://experts.colorado.edu/display/pubid_34602
Quantitative trait loci and molecular markers associated with wheat allelopathy<...Quantitative trait loci and molecular markers associated with wheat allelopathy<...
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 ...
https://researchoutput.csu.edu.au/en/publications/quantitative-trait-loci-and-molecular-markers-associated-with-whe
The role of bovine causal genes underlying dairy traits in Spanish Churra sheepThe role of bovine causal genes underlying dairy traits in Spanish Churra sheep
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 …
https://pubmed.ncbi.nlm.nih.gov/21749424/
The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction...The prostate cancer risk variant rs55958994 regulates multiple gene expression through extreme long-range chromatin interaction...
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 ...
https://advances.sciencemag.org/content/5/7/eaaw6710
A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic...A Comparison of the Sensitivity of the BayesC and Genomic Best Linear Unbiased Prediction (GBLUP) Methods of Estimating Genomic...
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
http://pakdel.iut.ac.ir/comparison-sensitivity-bayesc-and-genomic-best-linear-unbiased-prediction-gblup-methods-estimating
HKU Scholars Hub: Expression QTL analysis of a gene expression signature which predicts advanced non-alcoholic fatty liver...HKU Scholars Hub: Expression QTL analysis of a gene expression signature which predicts advanced non-alcoholic fatty liver...
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, ...
http://hub.hku.hk/handle/10722/195788
High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions...High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions...
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 ...
http://www.plantphysiol.org/content/159/4/1644.full
Examining the candidacy of ghrelin as a gene responsible for variation in adult stature in a United Kingdom population with...Examining the candidacy of ghrelin as a gene responsible for variation in adult stature in a United Kingdom population with...
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
https://www.rdm.ox.ac.uk/publications/25167
Kidney Specificity of Rat Chromosome 1 Blood Pressure Quantitative Trait Locus Region | HypertensionKidney Specificity of Rat Chromosome 1 Blood Pressure Quantitative Trait Locus Region | Hypertension
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http://hyper.ahajournals.org/content/early/2002/08/12/01.HYP.0000029106.10586.4C
中国农业科学院作物科学研究所中国农业科学院作物科学研究所
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 ...
http://icscaas.com.cn/xwdt/zxlw/120601.htm
Abundant contribution of short tandem repeats to gene expression variation in humans | Haldanes SieveAbundant contribution of short tandem repeats to gene expression variation in humans | Haldanes Sieve
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: http://dx.doi.org/10.1101/017459 Expression quantitative trait loci (eQTLs) are a key tool to dissect cellular processes mediating complex diseases.…
https://haldanessieve.org/2015/04/03/abundant-contribution-of-short-tandem-repeats-to-gene-expression-variation-in-humans/
Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP...Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP...
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
https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0360-x/figures/1
An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important...
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 ...
http://connection.ebscohost.com/c/articles/94445140/integrated-genetic-map-based-four-mapping-populations-quantitative-trait-loci-associated-economically-important-traits-watermelon-citrullus-lanatus
Integrative Analysis Identifies <i>BTN3A2</i> as a Novel Schizophrenia Risk Gene----Chinese...Integrative Analysis Identifies <i>BTN3A2</i> as a Novel Schizophrenia Risk Gene----Chinese...
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 ...
http://english.cas.cn/newsroom/research_news/201906/t20190627_212205.shtml
Pesquisa | Portal Regional da BVSPesquisa | Portal Regional da BVS
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 ...
https://pesquisa.bvsalud.org/portal/?lang=pt&q=au:%22Jia,%20Ledong%22
Chromosome substitution strains: gene discovery, functional analysis, and systems studies, Mammalian Genome | 10.1007/s00335...Chromosome substitution strains: gene discovery, functional analysis, and systems studies, Mammalian Genome | 10.1007/s00335...
Read Chromosome substitution strains: gene discovery, functional analysis, and systems studies, Mammalian Genome on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
https://www.deepdyve.com/lp/springer_journal/chromosome-substitution-strains-gene-discovery-functional-analysis-and-VUdOVpJw0u
USE OF TRANSPOSABLE ELEMENTS AND RFLP MAPPING TO CLONE QUANTITATIVE TRAIT LOCI | SBIR.govUSE OF TRANSPOSABLE ELEMENTS AND RFLP MAPPING TO CLONE QUANTITATIVE TRAIT LOCI | SBIR.gov
THIS PROPOSED RESEARCH REPRESENTS A UNIQUE COMBINATION OF TECHNOLOGIES AND SUBSEQUENT OPPORTUNITY TO EXAMINE THE MOLECULAR BASIS OF TRAITS EXHIBITING QUANTITATIVE EXPRESSIONAND INHERITANCE. IT HAS BEEN OBSERVED THAT THERE ARE OFTEN STRONG ASSOCIATIONS BETWEEN PATTERNS OF VARIATION OF ISOZYME MARKERS AND PLANT MORPHOLOGICAL CHARACTERS WHICH SHOW QUANTITATIVE INHERITANCE. RECENTLY, HELENTJARIS, EDWARDS, AND STUBER (UNPUBLISHED DATA) HAVE EXTENDED THIS TYPE OF ANALYSIS USING RESTRICTION FRAGMENT LENGTH POLYMORPHISMS (RFLP). SEVERAL RFLP LOCI WERE IDENTIFIED WHICH WERE PREDICTIVE FOR PLANT HEIGHT. ROBERTSON HAS SUGGESTED THAT GENETIC LOCI RESULTING IN DWARF PLANTS ARE GOOD CANDIDATES FOR LOCI INVOLVED IN THE QUANTITATIVE INHERITANCE OF PLANT HEIGHT. THE DWARF LOCUS, D3, MAPS IN ONE OF THE AREAS OF THE GENOME IDENTIFIED AS SIGNIFICANTLY CONTRIBUTING TO PLANT HEIGHT. WE PROPOSE TO TAKE ADVANTAGE OF THIS EASILY RECOGNIZABLE PHENOTYPE TO CLONE A DWARF ALLELE USING THE STRATEGY OF INSERTION MUTAGENESIS ...
https://www.sbir.gov/sbirsearch/detail/245524
COL4A2 | Cancer Genetics Web
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 ...
http://www.cancerindex.org/geneweb/COL4A2.htm
The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived...
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. ...
http://www.ikmb.uni-kiel.de/publications/age-related-markers-lipofuscin-and-apoptosis-show-different-genetic-architecture-qtl
The Genetic Architecture of Maize (Zea mays L.) Kernel Weight Determination | Vien Khoa Hoc Ky Thuat Nong Nghiep Mien NamThe Genetic Architecture of Maize (Zea mays L.) Kernel Weight Determination | Vien Khoa Hoc Ky Thuat Nong Nghiep Mien Nam
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 ...
https://iasvn.org/en/tin-tuc/The-Genetic-Architecture-of-Maize-
Exploring hepsin functional genetic variation association with disease specific protein expression in bipolar disorder:...
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 ...
https://mayoclinic.pure.elsevier.com/en/publications/exploring-hepsin-functional-genetic-variation-association-with-di
Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana |...Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana |...
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 ...
https://www.pnas.org/content/116/36/17890.abstract
Lack of Association between SLC30A8 Variants and Type 2 Diabetes in Mexican American FamiliesLack of Association between SLC30A8 Variants and Type 2 Diabetes in Mexican American Families
|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
https://www.hindawi.com/journals/jdr/2016/6463214/
MPD: Data set: Beamer1MPD: Data set: Beamer1
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 ...
https://phenome.jax.org/projects/Beamer1
Trypanosoma cruzi Infection in Genetically Selected Mouse Lines: Genetic Linkage with Quantitative Trait Locus Controlling...Trypanosoma cruzi Infection in Genetically Selected Mouse Lines: Genetic Linkage with Quantitative Trait Locus Controlling...
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.
https://www.hindawi.com/journals/mi/2014/952857/
Quantitative trait loci for peripheral blood cell counts: a study in baboons | SpringerLinkQuantitative trait loci for peripheral blood cell counts: a study in baboons | SpringerLink
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
https://link.springer.com/article/10.1007%2Fs00335-007-9022-8
Identification of quantitative trait loci for non-insulin-dependent diabetes mellitus that interact with body weight in the...
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
http://www.biomedsearch.com/nih/Identification-quantitative-trait-loci-non/9824537.html
Influence of dent corn genetic backgrounds on QTL detection for plant-height traits and their relationships in high-oil maize -...
QTL mapping for plant-height traits has not been hitherto reported in high-oil maize. A high-oil maize inbred 'GY220' was crossed with two dent maize inbreds ('8984' and '8622') to generate two connected F2:3 populations. Four plant-height traits were evaluated in 284 and 265 F2:3 families. Single-trait QTL mapping and multiple-trait joint QTL mapping was used to detect QTLs for the traits and the genetic relationship between plant height (PH) and two other plant-height traits. A total of 28 QTLs and 12 pairs of digenic interactions among detected QTLs for four traits were detected in the two F2:3 families. Only one marker was shared between the two populations. Joint analysis of PH with ear height (EH) and PH with top height (TH) detected 32 additional QTLs. Our results showed that QTL detection for PH was dependent on the genetic background of dent corn inbreds. Multiple-trait joint QTL analysis could increase the number of detected QTLs ...
http://psjd.icm.edu.pl/psjd/element/bwmeta1.element.element-from-psjc-f171616c-6cc6-3266-93ec-31cbe0ff9686
DSpace at EWHA: An integrated map of structural variation in 2,504 human genomesDSpace at EWHA: An integrated map of structural variation in 2,504 human genomes
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 ...
http://dspace.ewha.ac.kr/handle/2015.oak/217677
Variability assessment of aromatic and fine rice germplasm in Bangladesh based on quantitative traitsVariability assessment of aromatic and fine rice germplasm in Bangladesh based on quantitative traits
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 ...
https://cgspace.cgiar.org/handle/10568/76729
iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental...iMEGES: integrated mental-disorder GEnome score by deep neural network for prioritizing the susceptibility genes for mental...
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),
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2469-7/figures/3
Study Examines Cross-Species Interactions | Chancellors Faculty Excellence Program | NC State UniversityStudy Examines Cross-Species Interactions | Chancellors Faculty Excellence Program | NC State University
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 ...
https://facultyclusters.ncsu.edu/study-examines-cross-species-interactions/
Frontiers | Genetic and Expression Analysis of COPI Genes and Alzheimers Disease Susceptibility | GeneticsFrontiers | Genetic and Expression Analysis of COPI Genes and Alzheimers Disease Susceptibility | Genetics
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,
https://www.frontiersin.org/articles/10.3389/fgene.2019.00866/full
KRISP Paper - HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter RegionKRISP Paper - HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region
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 ...
http://www.krisp.org.za/publications.php?pubid=155
Pathophysiological, genetic and gene expression features of a novel rodent model of the cardio-metabolic syndrome. - Radcliffe...Pathophysiological, genetic and gene expression features of a novel rodent model of the cardio-metabolic syndrome. - Radcliffe...
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
https://www.rdm.ox.ac.uk/publications/17408
Associating disease-related genetic variants in intergenic regions to the genes they impact [PeerJ Preprints]Associating disease-related genetic variants in intergenic regions to the genes they impact [PeerJ Preprints]
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,
https://peerj.com/preprints/507/
QTL Cloning at North Carolina State University and USDA-ARS, Raleigh, NC - TCAPQTL Cloning at North Carolina State University and USDA-ARS, Raleigh, NC - TCAP
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.. ...
https://www.triticeaecap.org/qtl-cloning-at-north-carolina-state-university-and-usda-ars-raleigh-nc/
NASC Collection InfoNASC Collection Info
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 ...
http://arabidopsis.info/CollectionInfo?id=140

No data available that match "quantitative trait loci"


Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk: Cell ReportsLinkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk: Cell Reports
Methylation Quantitative Trait Loci Identification. Methylation quantitative trait loci associated with the entire set of GWAS- ... Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.. PLoS Genet. 2010; 6: e1000952 ... Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.. PLoS Genet. 2010; 6: e1000952 ... Detection and interpretation of expression quantitative trait loci (eQTL).. Methods. 2009; 48: 265-276. View in Article *Scopus ...
https://www.cell.com/cell-reports/references/S2211-1247
Mapping Quantitative Trait Loci for Resistance to Rice BlastMapping Quantitative Trait Loci for Resistance to Rice Blast
... Y. Jia and G. Liu...This article is in the public domain and not ... Quantitative trait loci (QTLs) conferring resistance to rice blast, caused by Magnaporthe oryzae, have been under-explored. In ...
https://www.apsnet.org/publications/phytopathology/2011/February/Pages/101_2_176.aspx
Honesty, power and bootstrapping in composite interval quantitative trait locus mappingHonesty, power and bootstrapping in composite interval quantitative trait locus mapping
Quantitative bootstrap support-the proportion of bootstrap replicates in which a significant likelihood maximum occurred in a ... "Honesty, power and bootstrapping in composite interval quantitative trait locus mapping" written by Philip M. Service, ... Inheritance and Identification of a Major Quantitative Trait Locus (QTL) that Confers Resistance to Meloidogyne incognita and a ... Inheritance and Identification of a Major Quantitative Trait Locus (QTL) that Confers Resistance to Meloidogyne incognita and a ...
https://scirp.org/journal/papercitationdetails.aspx?paperid=33620&JournalID=613
RFA-RM-09-006: Novel statistical methods for human gene expression quantitative trait loci (eQTL) analysis (R01)RFA-RM-09-006: Novel statistical methods for human gene expression quantitative trait loci (eQTL) analysis (R01)
Novel statistical methods for human gene expression quantitative trait loci (eQTL) analysis (R01) RFA-RM-09-006. Roadmap ... Title: Novel statistical methods for human gene expression quantitative trait loci (eQTL) analysis (R01) ... known as expression quantitative trait loci, or eQTLs) can serve as a tool to functionally characterize a disease-associated ... It has been shown that levels of gene expression, when treated as a quantitative trait, are heritable in a variety of organisms ...
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-09-006.html
Detection and Localization of Quantitative Trait Loci Affecting Fatness in Broilers | The Poultry Site Detection and Localization of Quantitative Trait Loci Affecting Fatness in Broilers | The Poultry Site
Mapping of quantitative trait loci affecting quality and production traits in egg layers. Poult. Sci. 81:919-927. Van Kaam, J. ... Whole genome scan in chickens for quantitative trait loci affecting carcass traits. Poult. Sci. 78:1091-1099. Van Kaam, J. B. C ... Mapping of quantitative trait loci for body weight at three, six, and nine weeks of age in broiler layer cross. Poult. Sci. 81: ... Quantitative trait loci affecting fatness in the chicken. Anim. Genet. 33:428-435. Jennen, D. G. J., R. P. M. A. Crooijmans, B ...
https://www.thepoultrysite.com/articles/detection-and-localization-of-quantitative-trait-loci-affecting-fatness-in-broilers
Quantitative trait loci affecting starvation resistance in Drosophila melanogaster - PubMedQuantitative trait loci affecting starvation resistance in Drosophila melanogaster - PubMed
Starvation resistance is a quantitative trait controlled by multiple interacting genes and exhibits considerable genetic ... The ability to withstand periods of scarce food resources is an important fitness trait. ... Quantitative trait loci affecting starvation resistance in Drosophila melanogaster Susan T Harbison et al. Genetics. 2004 Apr. ... Quantitative trait loci affecting starvation resistance in Drosophila melanogaster Susan T Harbison 1 , Akihiko H Yamamoto, ...
https://pubmed.ncbi.nlm.nih.gov/15126400/
Block network mapping approach to quantitative trait locus analysis - PubMedBlock network mapping approach to quantitative trait locus analysis - PubMed
Block Network Mapping provides an alternative data-driven approach to mapping quantitative trait loci that leverages ... Bayesian multiple quantitative trait loci mapping for complex traits using markers of the entire genome. Huang H, Eversley CD, ... Block network mapping approach to quantitative trait locus analysis Zeina Z Shreif 1 , Daniel M Gatti 2 , Vipul Periwal 3 ... Block network mapping approach to quantitative trait locus analysis Zeina Z Shreif et al. BMC Bioinformatics. 2016. . ...
https://www.ncbi.nlm.nih.gov/pubmed/?term=28007037
RGD Reference Report - Genome-wide scan for quantitative trait loci influencing spatial navigation and social recognition...RGD Reference Report - Genome-wide scan for quantitative trait loci influencing spatial navigation and social recognition...
Here we report a genome-wide scan for quantitative trait loci (QTLs) affecting spatial learning and memory and social ... Genome-wide scan for quantitative trait loci influencing spatial navigation and social recognition memory in Dahl rats.. ... Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) ...
https://rgd.mcw.edu/rgdweb/report/reference/main.html?id=1581615
RGD Reference Report - Identification of quantitative trait loci influencing alcohol consumption in the high alcohol drinking...RGD Reference Report - Identification of quantitative trait loci influencing alcohol consumption in the high alcohol drinking...
Identification of quantitative trait loci influencing alcohol consumption in the high alcohol drinking and low alcohol drinking ... To identify quantitative trait loci (QTLs) contributing to alcohol consumption, reciprocal HAD and LAD matings in conjunction ... Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) ...
https://rgd.mcw.edu/rgdweb/report/reference/main.html?id=631230
A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population | BMC...A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population | BMC...
That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated ... Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained ... Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait. ... From: A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-266/figures/2
Analysis of a hierarchial Bayesian method for quantitative trait loci , NC DOCKS (North Carolina Digital Online Collection of...
Analysis of a hierarchial Bayesian method for quantitative trait loci UNCW Author/Contributor (non-UNCW co-authors, if there ... Analysis of a hierarchial Bayesian method for quantitative trait loci PDF (Portable Document Format). 198 KB. Created on 1/1/ ... Abstract: Simulations were performed to compare two methods that detect quantitative trait loci on plant data. Karl Bromans ... that the hierarchical Bayesian model and Bromans interval mapping algorithm are able to detect quantitative trait loci (QTL) ...
http://libres.uncg.edu/ir/listing.aspx?id=1721
Identification and mapping of late blight resistance quantitative trait loci in tomato accession PI 163245<...
Ohlson, EW, Ashrafi, H & Foolad, MR 2018, Identification and mapping of late blight resistance quantitative trait loci in ... Identification and mapping of late blight resistance quantitative trait loci in tomato accession PI 163245. Plant Genome. 2018; ... The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this ... The purpose of this study was to identify and map quantitative trait loci (QTLs) associated with LB resistance in this ...
https://pennstate.pure.elsevier.com/en/publications/identification-and-mapping-of-late-blight-resistance-quantitative
A genome-wide search for quantitative trait loci underlying asthma.<...
A genome-wide search for quantitative trait loci underlying asthma.. S.E. Daniels, S. Bhattacharrya, A. James, N.I. Leaves, A. ... A genome-wide search for quantitative trait loci underlying asthma. / Daniels, S.E.; Bhattacharrya, S.; James, A.; Leaves, N.I ... Dive into the research topics of A genome-wide search for quantitative trait loci underlying asthma.. Together they form a ... title = "A genome-wide search for quantitative trait loci underlying asthma.",. abstract = "ASTHMA now affects one child in ...
https://research-repository.uwa.edu.au/en/publications/a-genome-wide-search-for-quantitative-trait-loci-underlying-asthm
Mapping quantitative trait Loci associated with graft (In)compatibility in apricot (Prunus armeniaca L.) - Universidad de...Mapping quantitative trait Loci associated with graft (In)compatibility in apricot (Prunus armeniaca L.) - Universidad de...
... segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single- ... information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, ... Mapping quantitative trait Loci associated with graft (In)compatibility in apricot (Prunus armeniaca L.) - Pina, A. et al - ART ... Home , Articles , Mapping quantitative trait Loci associated with graft (In)compatibility in apricot (Prunus armeniaca L.) , ...
https://zaguan.unizar.es/record/102119/files/?ln=en
Genome-wide identification of splicing quantitative trait loci (sQTL) in diverse ecotypes of Arabidopsis thaliana - Fingerprint...
Dive into the research topics of Genome-wide identification of splicing quantitative trait loci (sQTL) in diverse ecotypes of ... Genome-wide identification of splicing quantitative trait loci (sQTL) in diverse ecotypes of Arabidopsis thaliana. Waqas ...
https://www.research.ed.ac.uk/en/publications/genome-wide-identification-of-splicing-quantitative-trait-loci-sq/fingerprints/
The nature and identification of quantitative trait loci: a communitys view. | BiologyThe nature and identification of quantitative trait loci: a community's view. | Biology
The nature and identification of quantitative trait loci: a communitys view. Share this page: ...
https://bio.as.uky.edu/nature-and-identification-quantitative-trait-loci-communitys-view
Missing heritability in Parkinsons disease: the emerging role of non-coding genetic variation | SpringerLinkMissing heritability in Parkinson's disease: the emerging role of non-coding genetic variation | SpringerLink
Quantitative trait loci. One approach to select variants from the overwhelming number of trait-/disease-associated variants is ... Hannon E, Gorrie-Stone TJ, Smart MC et al (2018a) Leveraging DNA-methylation quantitative-trait loci to characterize the ... to prioritize them based on information on quantitative trait loci (QTL). QTLs are genomic loci that correlate with a ... In mice, an IGF2 locus enhancer element interacting with the TH locus was shown through deletion to be required for TH ...
https://link.springer.com/article/10.1007/s00702-020-02184-0
A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and...A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and...
... were assessed by using the maximum-likelihood binomial method extended to quantitative trait linkage and the quantitative trait ... A new genome-wide significant malaria locus on chromosome 17p12 and a new suggestive locus on chromosome 19p13.12 are reported ... The objective of the present study was to identify malaria resistance loci in individuals living in Burkina Faso. A genome scan ... Moreover, there was evidence that confirmed the influence of chromosomes 5q31 and 6p21.3 as loci controlling mild malaria or ...
https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-13-198
Berry and phenology-related traits in grapevine (Vitis viniferaL.): From Quantitative Trait Loci to underlying genes | BMC...Berry and phenology-related traits in grapevine (Vitis viniferaL.): From Quantitative Trait Loci to underlying genes | BMC...
QTL (Quantitative Trait Loci) analysis was carried out based on single marker and interval mapping methods. QTLs were ... and an average map distance between loci of 4.2 cM. Segregating traits were evaluated in three growing seasons by recording ... These traits result from complex developmental processes modified by genetic, physiological and environmental factors. In order ... Clusters of QTLs for different characters were detected, suggesting linkage or pleiotropic effects of loci, as well as regions ...
https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-38
Quantitative Trait Loci for Interhemispheric Commissure Development and Social Behaviors in the BTBR T|sup|+|/sup| tf/J Mouse...
Quantitative Trait Loci for Interhemispheric Commissure Development and Social Behaviors in the BTBR T+ tf/J Mouse Model of ... Dive into the research topics of Quantitative Trait Loci for Interhemispheric Commissure Development and Social Behaviors in ...
https://ucdavis.pure.elsevier.com/en/publications/quantitative-trait-loci-for-interhemispheric-commissure-developme/fingerprints/
A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss)<...
Baerwald, M. R., Petersen, J. L., Hedrick, R., Schisler, G. J., & May, B. (2011). A major effect quantitative trait locus for ... Baerwald, M. R. ; Petersen, J. L. ; Hedrick, Ronald ; Schisler, G. J. ; May, B. / A major effect quantitative trait locus for ... A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss). / ... Baerwald MR, Petersen JL, Hedrick R, Schisler GJ, May B. A major effect quantitative trait locus for whirling disease ...
https://ucdavis.pure.elsevier.com/en/publications/a-major-effect-quantitative-trait-locus-for-whirling-disease-resi
Quantitative trait locus - PDFSEARCH.IO - Document Search EngineQuantitative trait locus - PDFSEARCH.IO - Document Search Engine
... www.nature.com/naturegenetics ARTICLES Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates ...
https://www.pdfsearch.io/document/Quantitative+trait+locus
Linkage analysis of extremely discordant and concordant sibling pairs identifies quantitative-trait loci that influence...
We performed a genomewide scan for quantitative-trait loci (QTLs) that influence variation in the personality trait of ... One locus, on chromosome 1, is syntenic with that reported from QTL mapping of rodent emotionality, an animal model of ... These five loci met or exceeded the 5% genomewide significance threshold of 3.8 (negative logarithm of the P value). QTLs on ... be used to ascertain phenotypically extreme individuals and thereby increase power to detect genetic linkage in complex traits ...
https://www.neuroscience.ox.ac.uk/publications/32324
Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilersGenetic parameters and mapping quantitative trait loci associated with tibia traits in broilers
... Author. * Ragognetti, B. N. N. ... Quantitative trait loci (QTL) were identified for tibia traits to expand our knowledge of the genetic architecture of the ... Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers. Genetics And Molecular ... Body weight at 42 days of age was included in the model as a covariate for selection effect of bone traits. Two QTL were found ...
https://repositorio.unesp.br/handle/11449/161274
Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic...
title = "Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic ... Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic ... Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic ... Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children : a genetic ...
https://arizona.pure.elsevier.com/en/publications/expression-quantitative-trait-locus-fine-mapping-of-the-17q1221-a
Multiple genetic loci for bone mineral density and fracturesMultiple genetic loci for bone mineral density and fractures
Methods: We performed a quantitative trait analysis of data from 5861 Icelandic subjects (the discovery set), testing for an ... as were loci at 18q21, close to the receptor activator of the nuclear factor-kappaB gene (RANK), and loci at 2p16 and 11p11. ... Multiple genetic loci for bone mineral density and fractures N Engl J Med. 2008 May 29;358(22):2355-65. doi: 10.1056/ ... We then tested for an association between 74 SNPs (most of which were implicated in the discovery set) at 32 loci in ...
https://pubmed.ncbi.nlm.nih.gov/18445777/?dopt=Abstract
Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa (Woods 2021) - genetic map | ICGRCQuantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa (Woods 2021) - genetic map | ICGRC
Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa (Woods 2021) - genetic map. Contact ... Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa (Woods 2021) - genetic map ... Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa (Woods 2021) - genetic map ...
https://icgrc.info/GeneticMap/1611264
Items where Subject is Quantitative genetics (esp. Quantitative Trait Loci (QTL) articles) - DAF eResearch Archive (eRABBB)Items where Subject is "Quantitative genetics (esp. Quantitative Trait Loci (QTL) articles)" - DAF eResearch Archive (eRABBB)
Items where Subject is "Quantitative genetics (esp. Quantitative Trait Loci (QTL) articles)". Up a level. ... Schmidt, A. L., McIntyre, C. L., Thompson, J., Seymour, N. P. and Liu, C. J. (2005) Quantitative trait loci for root lesion ... Zwart, R.S., Thompson, J.P., Sheedy, J.G. and Nelson, J.C. (2006) Mapping quantitative trait loci for resistance to ... Christeller, J. T., McGhie, T. K., Johnston, J. W., Carr, B. and Chagné, D. (2019) Quantitative trait loci influencing ...
https://era.daf.qld.gov.au/view/subjects/QH452=2E7.html
Genome-wide Two-marker linkage disequilibrium mapping of quantitative trait loci | BMC Genomic Data | Full TextGenome-wide Two-marker linkage disequilibrium mapping of quantitative trait loci | BMC Genomic Data | Full Text
We extend the single-marker LD mapping to include two linked loci and explicitly incorporate their LD information into genetic ... overlooking the rich information contained within adjacent linked loci. ... the alleles of multiple tightly linked loci on the same chromosome co-segregate and are passed non-randomly from generation to ... Yang, J., Zhu, W., Chen, J. et al. Genome-wide Two-marker linkage disequilibrium mapping of quantitative trait loci. BMC Genet ...
https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-15-20

No FAQ available that match "quantitative trait loci"