Glossary of Genetic Terms

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Allele
An alternate form of a gene or locus. A locus can have many different alleles which may differ from each other by as little as a single base or by the complete absence of a sequence.
Anchor locus
A well-mapped locus that is chosen as a marker to "anchor" a particular genomic region to a framework map that is being constructed in a linkage study with a new cross.
Anonymous locus
An isolated DNA region with no known function but with at least two allelic states that can be followed through some form of DNA analysis in mapping studies.

Backcross
A cross between one animal type that is heterozygous for alleles obtained from two parental strains and a second animal type from one of those parental strains. The term is often used by itself to describe the two generation breeding protocol of an outcross followed by a backcross used frequently in linkage analysis.

Chi-squared
A statistical test used most often by geneticists to ascertain whether experimental data provide significant evidence for linkage between two loci.
Chimera
An individual mouse, or other mammal, that is derived from the fusion of two or more preimplantation embryos or an embryo and ES cells.
Codominance
Defined for pairs of alleles. The situation in which an animal heterozygous for two alleles (A1 and A2 at the A locus) expresses both of the phenotypes observed in the two corresponding homozygotes. Thus, the heterozygote (A1/A2) and both homozygotes (A1/A1 and A2/A2) are all distinguishable from each other and A1 and A2 would be considered to be "codominant". This term has also been co-opted to describe DNA markers defined by alternative visible allelic forms such as different sized restriction fragments or PCR products.
Commensal
Pertaining to populations of house mice that depend on human-built habitats and/or food production for survival.
Concordance
For two or more loci or traits typed in offspring from a backcross or RI strain, the presence of alleles (or expression of a trait) derived from the same parental chromosome.
Cross
Refers to one or more mating units set up with males and females that each have a designated genotype chosen to carry out a particular genetic analysis.
Crossover product
A chromosome homolog that was formed through the recombination of alleles at different loci present on opposite homologs in one of the parents of the animal in which it is observed.

Deme
A breeding group unit. In natural populations of mice, a deme usually consists of one breeding male with a harem of up to 8 females.
Discordance
The opposite of concordance. Inheritance of only one of two alleles or traits associated with a particular parental chromosome.
domesticus
Short form of M. m. domesticus, a subspecies within the M. musculus group that resides in Western Europe, Africa, and throughout the New World. It is the primary component of the traditional inbred strains.
Dominant
A relative term describing the relationship of one allele to a second at the same locus when an animal heterozygous for these alleles expresses the same phenotype as an animal homozygous for the first allele. The second allele of the pair is considered recessive.

Expressivity
Pertaining to observed quantitative differences in the expression of a phenotype among individuals that have the same mutant genotype. When quantitative differences are observed, a phenotype is said to show "variable expressivity" which can be caused by environmental factors, modifier genes or chance.

F1
The first filial generation; the offspring of an outcross between two inbred strains.
Feral
Pertaining to wild populations of animals derived from commensal ancestors; house mice that live apart from, and independent of, humans.
Filial generation
Pertaining to a particular generation in a sequence of brother-sister matings that can be carried out to form an inbred strain. The first filial generation, symbolized as F1, refers to the offspring of a cross between mice having non-identical genomes. When F1 siblings are crossed to each other, their offspring are considered to be members of the second filial generation or F2, with subsequent generations of brother-sister matings numbered with integer increments.

Genetic drift
Refers to the constant tendency of genes to evolve even in the absence of selective forces. Genetic drift is fuelled by spontaneous neutral mutations that disappear or become fixed in a population at random. Inbred lines separated from a common ancestral pair can drift rapidly apart from each other.
Genome
The total genetic information present within a single cell nucleus of an animal. The haploid genome content of the mouse is 3 x109 bp.
Genotype
For any one animal, the set of alleles present at one or more loci under investigation. At any one autosomal locus, a genotype will be either homozygous (with two identical alleles) or heterozygous (with two different alleles).

Heterozygote
An animal with two distinguishable alleles at a particular locus under analysis. In this case, the locus is considered to be heterozygous.
Histocompatible
Pertaining to a genetic state in which cells from two animals can be cross-transplanted without immunological rejection. The opposite of histoincompatible. Histocompatibility is controlled predominantly by genes in the Major Histocompatiblity Complex or MHC.
Homolog
This term is used by geneticists in two different senses: (1) One member of a chromosome pair in diploid organisms, and (2) A gene from one species, for example the mouse, that has a common origin and functions the same as a gene from another species, for example humans, Drosophila, or yeast.
Homozygote
An animal with two identical alleles at a particular locus under analysis. In this case, the locus is considered to be homozygous.
House mouse
An animal that is a member of the species M. musculus.
Hybrid sterility
Pertaining to the sterility of animals produced from matings between members of two different species, such as M. musculus and M. spretus. In this case, and in general, only the male hybrids are sterile while the females are fertile.
Hybrid zone
A narrow geographical line that separates the natural ranges of two distinct animal populations. The best-characterized house mouse hybrid zone occurs in Central Europe and separates M. m. domesticus to the west and M. m. musculus to the east.

Imprinting, Genomic
The situation in which the expression of a gene varies depending on its parental origin. Only a small subset of genes in the mammalian genome are imprinted.
Inbred
Animals that result from the process of at least twenty sequential generations of brother-sister matings. This process is called inbreeding.
Incross
A cross between two animals that have the same homozygous genotype at designated loci; for example, between members of the same inbred strain.
Intercross
A cross between two animals that have the same heterozygous genotype at designated loci; for example, between sibling F1 hybrids that were derived from an outcross between two inbred strains. .
Interspecific cross
A cross between mice from two different species, most often M. musculus (represented by a traditional laboratory strain) and M. spretus for the purpose of linkage analysis. The interspecific cross is carried out to take advantage of the high level of polymorphism between the two parents.
Intersubspecific cross
A cross between two subspecies. In the case of mouse genetics, this refers most often to a cross between a traditional inbred strain that is predominantly M. m. domesticus and one of the other subspecies in the M. musculus complex, usually M. m. musculus or M. m. castaneus or a combination of both (within the faux species M. m. molossinus).

Linkage
Pertaining to the situation where two loci are close enough to each on the same chromosome such that recombination between them is reduced to a level significantly less than 50%.
Linkage group
A set of loci in which all members are linked either directly or indirectly to all other member of the set. Essentially equivalent to the genetic information associated with any single chromosome.
Locus
Any genomic site, whether functional or not, that can be mapped through formal genetic analysis.

Multifactorial
A trait controlled by at least two factors, which may be genetic or environmental; polygenic traits represent a subset of multifactorial traits.
Mus
The name of the genus that contains all house mice (M. musculus) and other closely related species.
musculus
Abbreviated form of M. musculus, the species that is synonymous with the house mouse.
Mutant allele
This term is defined differently by formal geneticists and population biologists. The formal genetic definition is an allele that exerts a deleterious effect on phenotype. The population definition is an allele that is present at a frequency of less than 1% in a natural population; according to this definition, a mutant allele in one population may be considered non-mutant (wild-type) in another population.
Mutation
An allele present in a progeny that is not present in the genome of either its parents.

N2, N3, N4 etc.
Used to describe the generation of backcrossing and the offspring that derive from it. The N2 generation describes offspring from the initial cross between an F1 hybrid and one of the parental strains. Each following backcross generation is numbered in sequence.

Outcross
A cross between genetically unrelated animals.

Parental
An inbred strain of animals that is used in the initial cross of a multi-generational breeding protocol; the meiotic products and offspring that retain the same set of designated alleles as one of the parental strains.
Penetrance
Pertaining to the failure of some animals with a mutant genotype to express the associated mutant phenotype. In any case where less than 100% of genotypically mutant animals are phenotypically mutant, the phenotype is said to be "incompletely penetrant". Incomplete penetrance is usually a matter of chance or modifiers in the genetic background.
Phenotype
The physical manifestation of a genotype within an animal. A mutant phenotype is caused by a mutant genotype and is manifested as an alteration within an animal that distinguishes it from the wild-type.
Polygenic
Pertaining to a phenotype that results from interactions among the products of two or more genes with alternative alleles.
Polymorphic
A term formulated by population geneticists to describe loci at which there are two or more alleles that are each present at a frequency of at least one percent in a population of animals. The term has been co-opted for use in transmission genetics to describe any locus at which at least two alleles are available for use in breeding studies, irrespective of their actual frequencies in natural populations.

Quantitative trait
A phenotype that can vary in a quantitative manner when measured among different individuals. The variation in expression can be due to combinations of genetic and environmental factors, as well as chance. Quantitative traits are often controlled by the cumulative action of alleles at multiple loci.

Recessive
A relative term describing the relationship of one allele to a second at the same locus when an animal heterozygous for these alleles expresses the same phenotype as an animal homozygous for the second allele. The second allele of the pair is considered dominant.
Recombinant
The result of a crossover in a doubly heterozygous parent such that alleles at two loci that were present on opposite homologs are brought together on the same homolog. The term is used to describe the chromosome as well as the animal in which it is present.
Recombinant congenic strain
A variation on recombinant inbred strains in which the initial outcross is followed by several generations of backcrossing prior to inbreeding.
Recombinant inbred (RI) strain
A special type of inbred strain formed from an initial outcross between two well-characterized inbred strains followed by at least twenty generations of inbreeding.
RI strain
See Recombinant inbred strain.

spretus
Abbreviated form of M. spretus, a species commonly used in interspecific matings for the generation of linkage maps.
Strain
Refers to a group of mice that are bred within a closed colony in order to maintain certain defining characteristics. Strains can be inbred or non-inbred.
Strain Distribution Pattern (SDP)
The distribution of two segregating alleles at a single locus across a group of animal samples used for analysis in a linkage study. Used in the context of backcross data and data obtained from RI strains.
Sympatric
Closely related species that have overlapping ranges in nature but do not interbreed. In different parts of its range, M. musculus is sympatric with M. macedonicus, M. spicilegus, and M. spretus.
Syngenic
Literally "of the same genotype". Used most frequently by immunologists to describe interactions between cells from the same inbred strain.
Syntenic
Two loci known to be in the same linkage group. Conserved synteny refers to the situation where two linked loci in one species (such as the mouse) have homologs that are also linked in another species (such as humans).

Targeting, Gene
A technology that allows an investigator to direct mutations to a specific locus in the mouse genome. Also called targeted mutagenesis.
Transgene
A fragment of foreign DNA that has been incorporated into the genome through the manipulation of preimplantation embryos.
Transgenic
Pertaining to an animal or locus that contains a transgene.
Translocation
Pertaining to a novel chromosome formed by breakage and reunion of DNA molecules into a non-wild-type configuration.

Unequal crossover
A crossover event that occurs between non-allelic sites. Can lead to the duplication of sequences on one homolog and the deletion of sequences on the other.

Variant
Literally, an alternative form. Used in conjunction with locus, phenotype or mouse strain. A "DNA variant" is equivalent to an alternative DNA allele. A variant mouse usually refers to one that carries a mutant allele or expresses a mutant phenotype.

Wild-type
Animal or allele that functions normally and represents a common type found in natural populations at a frequency of at least one percent.

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