Adaptation traits — Adaptation traits contribute to individual fitness and to the evolution of animal genetic resources. By definition, these traits are also important to the ability of the animal genetic resource to be sustained in the production environment.
Additive genetic effects — The effect of an allele on animal performance, independent of the effect of the other allele at a locus. These effects of the two alleles at a locus add up (thus "additive"). Alleles at a locus may have other effects (dominance, epistasis), so that there are not genes that have just "additive" effects and other genes with only "dominance" effects. Additive genetic effects can be inherited; other genetic effects such as dominance and epistasis are the result of allele combinations that are lost between generations. The additive genetic effect that an animal has for a trait is equal to its breeding value.
Allele — One of a pair, or series of alternative forms of a gene that can occur at a given locus on homologous chromosomes.
Amino acids — Any one of a class of organic compounds containing the amino (NH2) group and the carboxyl (COOH) group. Amino acids are combined to form proteins.
Animal model — A system for genetic evaluations that estimates breeding values of individual animals (males, females) at the same time. The system uses production data on all known relatives in calculating a genetic evaluation.
Ancestor — Any individual from which an animal is descended.
Assortative mating — Assigning animals as mates based on phenotypic or genetic likeness. Positive assortative mating is mating animals that are more similar than average. Negative assortative mating is mating animals that are less similar than average.
Autosome — Any chromosome that is not a sex chromosome.
Backcross — The cross produced by mating a first-cross animal back to one of its parent lines or breeds.
Best linear unbiased prediction (BLUP) — A method of genetic prediction (with the properties of smallest variance, linear and unbiasedness) that is particularly appropriate when performance data come from genetically diverse contemporary groups.
Breed — Either a sub-specific group of domestic livestock with definable and identifiable external characteristics that enable it to be separated by visual appraisal from other similarly defined groups within the same species, or a group for which geographical and/or cultural separation from phenotypically similar groups has led to acceptance of its separate identity.
Breeding value — The mean genetic value of an individual as a parent. It can be estimated as the average superiority of an individual's progeny relative to all other progeny under conditions of random mating.
Candidate gene study — A study that evaluates association of specific genetic variants with outcomes or traits of interest, selecting the variants to be tested according to explicit considerations (known or postulated biology or function, previous studies, etc).
Categorical trait — Scores are given usually in a few categories up to several categories (i.e. scores 1-5 for leg movement).
Centromere — Spindle-fiber attachment region of a chromosome.
Chromosome — Microscopically observable linear arrangement of DNA in the nucleus of a cell. Chromosomes carry the genes responsible for the determination and transmission of hereditary characteristics.
Co-dominant alleles — Alleles, each of which produces an independent effect in heterozygotes.
Combining ability — The mean performance of a line when involved in a cross-breeding system. General combining ability is the average performance when a breed or line is crossed with two or more other breeds or lines. Specific combining ability is the degree to which the performance of a specific cross deviates from the average general combining ability of two lines.
Composite (synthetic) breed — A hybrid with at least two and typically more breeds in its background. Composites are expected to be bred to their own kind, retaining a level of hybrid vigor normally associated with traditional cross-breeding systems.
Control line — A line that is randomly selected and randomly mated. Usually used in selection experiments to monitor environment effects in order to estimate genetic change in a selected line.
Correlation coefficient — A measure of the interdependence of two random variables that ranges in value from -1 to +1, indicating perfect negative correlation at -1, absence of correlation at zero, and perfect positive correlation at +1. It determines the degree to which two variables' movements are associated. No cause and effect is implied.
Covariance — The degree to which two measurements vary together. A positive covariance is when two measurements tend to increase together. A negative covariance is when one measurement increases and the other measurement tends to decrease.
Crossbreeding — Matings between animals of different breeds or lines.
Crossover — The process during meiosis when chromosomal segments from different members of a homologous pair of chromosomes break, and part of one will join a part of the other, so that two gametes form possessing new combinations of genes. The frequency of crossover between two loci is proportional to the physical distance between them.
Crossover unit — Each unit is equal to a one percent frequency of crossover gametes.
Cytoplasm — The protoplasm outside a cell nucleus.
Descendant — An individual descended from other individuals.
Diallel cross — When both males and females from each breed (or line) in a set of breeds (or lines) are mated to males and females of each breed (or line) in the set including their own breed (or line).
DNA — Deoxyribonucleic acid, the chemical material which carries information to code for a gene.
Dominant — Applied to one member of an allelic pair of genes, which has the ability to express itself wholly or largely at the exclusion of the expression of the other allele.
Dominance genetic effects — The effect that an allele has on animal performance, which depends upon the genotype at the locus. For example, the "a" allele may have a different effect on animal performance in "aa" animals than in "Aa" animals. See additive genetic effects.
Economic trait loci — Loci that have effects on traits of economic importance.
Economic value — A measure of the contribution an individual trait makes to the overall economic value of an animal.
Environment — The aggregate of all the external conditions and influences affecting the life and development of the organism.
Environmental correlation — When two traits tend to change in association with each other as a result of environmental effects.
Environmental variance — Variation in phenotype which results from variation in environmental effects.
Estimated breeding value — A prediction of a breeding value. See breeding value.
Epistasis — When the gene at one locus affect the expression of the gene at another locus.
Exon — A sequence of DNA that is expressed (transcribed) into RNA , then translated into protein. Adjacent exons may be separated by an intron, which is later removed from the RNA transcript via a splicing mechanism.
F1 — Animals resulting from crossing parents from different lines or breeds.
F2 — Animals resulting from matings among F1 parents.
F3 — Animals resulting from matings among F2 parents.
Family size — The mean number of offspring per parent that successfully reproduce.
Full sibs — Individuals having the same male and female parents.
Gamete — A sperm or egg cell containing the haploid (1n) number of chromosomes .
Gene — A functional hereditary unit that occupies a fixed location on a chromosome, has a specific influence on phenotype, and is capable of mutation to various allelic forms.
Gene ontology (GO) — A bioinformatics initiative to unify the representation of gene and gene product attributes across all species. The project aims to maintain and develop controlled vocabulary of gene and gene product attributes; annotate genes and gene products, and assimilate and disseminate annotation data; and provide tools for easy access to all aspects of the data provided by the project.
Generation interval — The average age of the parents when the progeny that will replace them are born.
Genetic correlation — When two traits tend to change in the same or opposite directions as a result of genetic effects.
Genetic distances — A measure of gene differences between populations (hence genetic relationships among them) described by some numerical quantity; usually refer to the gene differences as measured by a function of gene frequencies.
Genetic drift — Changes in gene frequency in small breeding populations due to chance fluctuations.
Genetic gain — The amount of increase in performance that is achieved through genetic selection after one generation of selection.
Genetic maps — See linkage map.
Genetic marker — A gene or DNA sequence having a known location on a chromosome and associated with a particular gene or trait; a gene phenotypically associated with a particular, easily identified trait and used to identify an individual or cell carrying that gene.
Genetic variance — Variation in phenotype which results from variations in genetic composition among individuals.
Genome — The complete set of genes and non-coding sequences present in each cell of an organism, or the genes in a complete haploid set of chromosomes of a particular organism.
Genomics — A discipline in genetics concerned with the study of the genome of an organism. The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. It also studies intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome.
Genotype — The genetic constitution of one or a few gene(s) or locus (loci), or total genetic make-up (genes) of an individual organism.
Genotype-environment interaction — When the difference in performance between two genotypes differs, depending upon the environment in which performance is measured. This may be a change in the magnitude of the difference or a change in rank of the genotypes.
Genotype-phenotype correlation — The association between the presence of a certain mutation or mutations (genotype) and the resulting physical trait, abnormality, or pattern of abnormalities (phenotype).
Genome-wide association study (GWAS) — A study that evaluates association of genetic variation with outcomes or traits of interest by using very large number of markers across the genome.
Germplasm — The germinal material or physical basis of heredity; the sum total of the genes.
GO — (see Gene Ontology)
GO Term — A GO Term is a unique identifier for a gene annotation, represented in the form of a alphanumeric code, e.g. GO:0000016. The definition usually includes a term name, a definition with cited sources, and a namespace indicating the domain to which it belongs.
Grade-up — The process of repeated backcrossing to one parental line to produce a population that is nearly purebred.
Half sibs — Individuals that share only one common parent.
Haplotype — A set of alleles at a closely linked group of loci, so closely linked that the allelic set behaves almost as one allele in terms of inheritance.
Hardy-Weinberg law — A population is in genotypic equilibrium if p and q are the frequencies of alleles A and a, respectively, and p2, 2pq and q2 are the genotypic frequencies of AA, Aa, and aa under the condition of random mating.
Heritability — Degree to which a given trait is controlled by inheritance; proportion of total phenotypic variation that is attributable to genetic variation (in contrast to environment-caused variation).
Heterosis — The degree to which the performance of a crossbred animal is better or worse than the average performance of the parents.
Heterozygote, adj. heterozygous — An organism with unlike members of any given pair or series of alleles, which consequently produces unlike gametes.
Homologous chromosomes — Chromosomes which occur in pairs and are similar in size and shape, one having come from the male and one from the female parent.
Homozygote, adj. homozygous — An organism whose chromosomes carry identical members of a given pair of genes. The gametes are therefore all alike with respect to this locus.
Inbreeding — Matings among related individuals, which results in progeny that have less heterozygosity and hence more homozygous gene pairs than the average of the population.
Inbreeding coefficient — A measurement of the increase in homozygosity; each unit is equal to a 1% increase in homozygosity relative to the average homozygosity in the base population.
Inbreeding depression — The decreased performance normally associated with accumulation of inbreeding. Many recessive genes result in undesired traits or decreased performance when they are expressed. Inbred animals have more recessive genes in the homozygous condition that are expressed and result in reduced performance or undesired traits.
Independent culling — When animals are culled if they do not meet all of the minimum levels of performance for a set of traits.
Introgression — A breeding strategy for transferring specific favorable alleles from a donor population to a recipient population. This would, for example, be of great interest for genes responsible for disease resistance, which could be introgressed into a susceptible but otherwise economically superior breed.
Intron — A piece of nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated.
Karyotype — The appearance of the metaphase chromosomes of an individual or species, which shows the comparative size, shape, and morphology of the different chromosomes.
Lethal gene — A gene that results in the death of the animal.
Liability — Both internal (e.g., genetic merit) and external (e.g., nutrition, disease, exposure) forces that influence the expression of a threshold character (e.g., disease, conception, abnormalities, etc.).
Line-breeding — Mating of selected individuals from successive generations to produce animals with a high relationship to one or more selected ancestors. It is a mild form of inbreeding.
Linkage — Association of genes physically located on the same chromosome. A group of linked genes is called a linkage group.
Linkage map — A linear map of an experimental population that shows the position of its known genes and/or genetic markers relative to each other in terms of recombination frequency.
Linkage disequilibrium — In population genetics, refers to the non-random association between alleles at two or more loci, that may or may not be on the same chromosome. It is also referred to as gametic (phase) disequilibrium.
Locus, pl. loci — A fixed position on a chromosome occupied by a given gene or one of its alleles.
MAF — (see Minor Allele Frequency).
Major gene — A gene that has an easily recognizable and measurable effect on a characteristic.
Marker — Specific and identifiable sequences of the DNA molecule. These markers may or may not be functional genes.
Marker-assisted selection (MAS) — Selection for specific alleles using genetic markers.
Maternal heterosis — The advantage of the crossbred mother over the average of purebred mothers.
Mating systems — The rules which describe how selected breeds and/or individuals will be paired at mating.
Meiosis — The process by which the chromosome number of a reproductive cell becomes reduced to half the diploid (2n) or somatic number and results in the formation of eggs or sperm.
Migration — Movement of animals, and consequently genes, from one population to another.
Minor allele frequency (MAF) — Refers to the frequency at which the less common allele occurs in a given population.
Mitochondria — Small bodies in the cytoplasm of most plant and animal cells responsible for energy production.
Mitosis — Cell division process in which there is first a duplication of chromosomes, followed by migration of chromosomes to the ends of the spindle and a dividing of the cytoplasm, resulting in the formation of two cells with diploid (2n) number of chromosomes.
Molecular genetics — The branch of genetic studies that deals with hereditary transmission and variation on the molecular level. It deals with the expression of genes by studying the DNA sequences of chromosomes.
Multiple alleles — Three or more alternative forms of a gene representing the same locus in a given pair of chromosomes.
Mutation — A sudden change in the genotype of an organism. The term is most often used in reference to point mutations (changes in base sequence within a gene), but can refer to chromosomal changes.
Natural selection — Natural processes favoring reproduction by individuals that are better adapted, and tending to eliminate those less adapted to their environment.
Nucleus — Part of a cell containing chromosomes and surrounded by cytoplasm.
Outcrossing — Mating of individuals that are less closely related than the average of the population.
Overdominance — A form of dominance where the performance of the heterozygote exceeds that of the best homozygote.
Partial dominance — A form of dominance where the performance of the heterozygote is intermediate between the two homozygotes, but more closely resembles the performance of the homozygous dominant type.
Pedigree — Usually refers to pedigree chart or what a pedigree chart represents in genetics. It is a document to record the ancestry of an individual. A pedigree can also be used to illustrate the family structure or breeding scheme.
Penetrance — The proportion of the individuals with a particular gene combination that express the corresponding trait.
Permanent environmental effects — Environmental effects that result in permanent effects on the phenotypic expression of a trait. For example, severe mastitis during lactation may have a permanent effect on milk production and litter weaning weight for an animal in subsequent litters.
Phene — Genetically determined characteristic which can be possessed by an organism. A synonym of trait.
Phenome — The set of all phenotypes expressed by a cell, tissue, organ, organism, or species.
Phenotype — Actual exhibit of observable traits. Normally, it refers to physical characteristic of an individual such as size, shape, color, or performance.
Phenotypic correlation — When two traits tend to change in the same or different direction as a net result of genetic and environmental effects.
Phenotypic value — A performance record; a measure of an animal's performance for a trait.
Phenotypic variation — Variation in phenotype which results from variation in genetic and environmental effects on the individuals.
Pleiotropy — The property of a gene whereby it affects two or more characters, so that if the gene is segregating, it causes simultaneous variation in the characters it affects.
Polymorphism — Where DNA or genes have more than two forms or alleles in the population.
Population — Entire group of organisms of a kind that interbreed.
Population genetics — The branch of genetics which deals with frequencies of alleles in groups of individuals.
Progeny — Offspring or individuals resulting from specific matings.
Progeny test — A test used to help predict an individual's breeding values, involving multiple matings of that individual and evaluation of its offspring.
Protein — Any of a group of complex nitrogenous organic compounds that contain amino acids as their basic structural units, occur in all living matter, and are essential for the growth and repair of animal tissue.
Qualitative trait — A trait that can generally be classified into a limited number of categories, and the animal can be said to "possess" the quality or not. Examples include hair color, skin color, and ear stature.
Quantitative trait — A trait that is represented by an almost continuous distribution of measurements. Examples include average daily gain, backfat thickness, and height.
Quantitative trait locus (QTL) — A locus that affects a quantitative trait.
Random mating — A mating system in which animals are assigned as breeding pairs at random, without regard to genetic relationship or performance.
Recessive — Applies to one member of an allelic pair which lacks the ability to manifest itself when the other, dominant, member is present.
Reciprocal cross — A breeding scheme where males of breed A are mated to females of breed B and males of breed B are mated females of breed A.
Reciprocal recurrent selection — A method of selection for combining ability or heterosis. Selection within two lines is based on the performance of crossbred progeny produced by crossing the two lines.
Recombination — The observed new combinations of DNA segments, or loci, or traits, which are different from those combinations exhibited by the parents.
Recurrent selection — A method of selection for combining ability or heterosis. Selection within one line is based on performance of crossbred progeny from matings with a "tester" line.
Repeatability — The proportion of total phenotypic variation that is attributable to variations caused by genetic and permanent environmental effects. It is a measure of the degree to which early measures of a trait can predict later records of the same trait.
RNA — Ribonucleic acid, involved in the transcription of genetic information from DNA.
Segregation — The separation of paired alleles at loci during germ cell formation.
Selection — Any natural or artificial process favoring the survival and propagation of certain individuals in a population.
Selection criteria — The character(s) upon which selection decisions are based, with the intent of changing the character(s) in the selection objective.
Selection differential — The difference in mean performance of the selected group of animals relative to the mean performance of all animals available for selection.
Selection index — The combining of measurements from several sources into an estimate of genetic value; when more than one measurement on a trait, and/or measurements of the trait on relatives, and/or measurements of more than one trait are combined into a single estimate of overall genetic value.
Selection intensity — The proportion of animals selected to be parents relative to the total number available for selection. The smaller the proportion selected, the higher the selection intensity.
Selection objective — The character(s) which are intended to be modified by selection.
Sequence — The linear arrangement of nucleotides that make up unbranched polymer chains of DNA or RNA.
Sex chromosomes — The X or Y chromosomes.
Sex-influenced — Traits for which the expression depends on the sex of the individual.
Sex-limited — A trait that can be expressed only in one sex, such as milk production.
Sex linked — Genes that are located on the sex (X or Y) chromosomes.
Single-nucleotide polymorphism (SNP) — A single base pair change in the DNA sequence at a particular point compared with the "common" or "wild-type" sequence.
SNP — Abbreviation for Single-Nucleotide Polymorphism.
Synthetic breed — See composite breed.
Trait — A distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or a combination of the two.
Variant allele — The allele at a particular SNP that is the least frequent in a population.
Zygote — The cell produced by the union of mature gametes (egg and sperm) in reproduction.
Standardized Genetics Nomenclature