Genetics Glossary - VGL Vocab

A

• Allele: An allele is an alternate version of a gene. This is also known as a variant of a gene. They are caused by differences in the sequence of the DNA at a specific position within a gene.

• Amino acid: Organic molecules that are the building blocks of proteins. There are 20 standard amino acids specified by the information (codon) stored in the DNA.

• Autosomal: Of or relating to the autosomes, which are the non-sex chromosomes. In other words, any other chromosomes besides X and Y (in mammals).

B

• Blood-brain barrier: The blood–brain barrier is a highly selective semipermeable border of endothelial cells (lining the blood vessels in the brain) that protect the brain tissue from any circulating toxins or pathogens.

C

• Carrier: An organism possessing one copy (heterozygous) of a recessive allele. The term “carrier” is often used in the context of disease-associated or otherwise deleterious variants. Because carriers are heterozygous, they do not express the phenotype of the recessive allele. However, carriers can transmit the recessive allele to their offspring and can thus produce affected offspring if their mate also contributes a recessive allele.

• Chimerism: When an organism or tissue contains at least two different complete diploid sets of DNA that originated from more than one zygote. In animals this can happen when two fertilized eggs fuse early during gestation or when twins exchange cells.

• Chromosome: Physical structure that stores the genetic information, composed of long strands of DNA coiled around proteins.

• Co-dominance: Both alleles at a locus are expressed equally in an organism. This can lead to the appearance of a “blended” phenotype, but differs from incomplete dominance.

  • Example: Blood type in humans; a person with blood type AB expresses both A and B proteins on the surface of their red blood cells.

• Codon: A sequence of three consecutive nucleotides in DNA or RNA that specifies the synthesis of a single amino acid (or acts as a start or stop signal) during the translation of mRNA to protein. There are 64 codons, of which 61 specify amino acids and 3 are stop signals.

• Complete penetrance: Traits with complete penetrance will be expressed in all individuals possessing the causal allele.

• Compound Heterozygote: A compound heterozygote has two different mutant alleles at the same genetic locus (one on each chromosome).

  • Example: There are two variants associated with the tiger eye mutation in Puerto Rico Paso Fino horses, TE1 and TE2. The normal wild type variant is N. A horse can be N/N (no tiger eye), N/TE1 or N/TE2 (no tiger eye, heterozygous carriers), TE1/TE1 or TE2/TE2 (tiger eye, homozygous recessive), or TE1/TE2 (tiger eye, compound heterozygote).

D

• De novo: De novo variants are genetic variations that arise in a reproductive cell (i.e., egg or sperm) or the fertilized egg so that they are present in an individual animal but absent from both parents’ DNA.

• Deletion: A type of mutation in which part of the DNA sequence is lost; the loss can be as small as a single base pair or as much as an entire section of a chromosome.

• Dilution (coat color): Dilutions are caused when a variant of a pigmentation gene lightens the coat color of an animal. Dilution mutations can dilute all pigments (both eumelanin and phaeomelanin) or only one pigment type (eumelanin or phaeomelanin). The physical cause of the lightened coat color may vary, from reduction in the amount of pigment produced to inefficient transfer of the pigment from the melanocyte to the hair follicle cells.

  • Examples:

    • In cats, the dilute allele d creates a dilution of all pigments (and thus all coat colors) by causing the clumping and uneven distribution of pigment granules in the hair shaft.

    • In dogs, the Intensity dilution allele In causes an extreme dilution of phaeomelanin (red or yellow pigment), resulting in a cream to white coat in dogs. Eumelanin is not affected.

    • In horses, the dun allele D affects both eumelanin (black) and phaeomelanin (red) pigment, diluting the coat but leaving the head, lower legs, mane and tail undiluted.

• Diploid: Having two complete sets of chromosomes; one set is inherited from the mother, and one set from the father.

• DNA: Deoxyribonucleic Acid, a complex organic molecule that is capable of self-replication and that carries and stores genetic information. DNA is the material of heredity and is found in all known living organisms.

• DNA sequence: The ordered sequence of nucleotides on a strand of DNA. Example: TAAGTCTGACACAAT

• Dominant: A trait is dominant when only one copy of a variant allele is needed for an animal to express the phenotype.

• Duplication: A type of mutation in which a gene or part of the sequence of a gene is duplicated.

E

• Epistasis: A type of interaction between genes in which the genotype at one locus masks the phenotype or expression of an allele of another gene/locus.

  • Example: A dominant allele for orange coat color (denoted O) can exist on the X chromosome of cats. This dominant orange is separate from the autosomal gene controlling agouti/black coat color (Agouti) and has an epistatic effect on the agouti gene. A male cat (X/Y) with the dominant orange allele (O) will be orange regardless of its genotype at the agouti locus.

• Exon: A section of DNA in a gene that codes for the amino acids of a protein product. After intervening intron sequences have been removed, exons are spliced together to form mature messenger RNA. This messenger RNA (or mRNA) is then translated into a protein.

• Expression (of a gene): The phenotypic outcome produced by transcription and translation of a gene; the way in which a gene manifests as a phenotype.

F

• Fixed: An allele is described as being fixed in a population when it is the only allele for a given gene present in the population. In other words, all individuals in the population will be homozygous for that variant.

  • Example: One of the defining traits of the Russian Blue cat breed is its dilute gray (“blue”) coat, which is a recessive trait. All Russian Blue cats genotype as d/d, and the dominant D allele is absent from the population. Therefore this breed is fixed for dilute.

• Frameshift mutation: The insertion or deletion of base pairs in a DNA sequence, in which the number of added or deleted base pairs is not a multiple of three, thus shifting the triplet reading frame of the gene product (protein). This results in the synthesis of a protein with amino acids different from those normally specified by the gene.

G

• Gene: A sequence of DNA occupying a particular fixed location (locus) on a chromosome. For those genes that code for proteins, the sequence of DNA comprising a gene directs the synthesis of the protein product. Genes are the basic unit of heredity.

• Genome: An organism's complete DNA sequence found in one set of its chromosomes. This includes the DNA that makes up the 20,000+ genes of mammals as well as all non-coding regions of DNA.

• Genotype: An organism’s set of genes; the genetic makeup of that organism. In practice and in the context of genetic testing, the term “genotype” is used to reference a particular gene of interest and to specify for the individual being tested what alleles are present at that locus.

• Germ line: Cells that pass on genetic information from one generation to the next. Specifically, egg and sperm cells are called germ cells while all other cells of the body are called somatic cells.

H

• Haplotype: A haplotype is defined as a combination of alleles being inherited together; a set of DNA polymorphisms found on the same chromosome.

• Heteroplasmy: Heteroplasmy occurs when there is more than one type of mitochondrial DNA (mtDNA) in an individual.

• Heterozygous: Possessing two different alleles at a particular locus.

• Homozygous: Possessing identical alleles at a particular locus. In diploid organisms, which have two copies of each autosomal gene, this means possessing two copies of the same variant.

I

• Incomplete Dominance: A trait is incompletely dominant when the phenotype is dependent on how many copies of the variant allele is present. In other words the phenotype is different if there are zero, one, or two copies of the allele. Typically the heterozygotes have an intermediate phenotype between the two homozygous conditions.

  • Example: A horse with a red base color and one copy of the cream allele has an intermediate phenotype of Palomino, while two copies of the cream allele creates a paler Cremello color.

• Incomplete penetrance: Conditions or traits with incomplete penetrance will be expressed in only some of the individuals who possess the trait-associated allele; some individuals with the allele may never express the trait.

• Insertion: The addition of DNA base pairs to an existing DNA sequence. Insertions may be as small as a single base pair or as large as an entire section of chromosome that encompasses multiple genes.

• Intron: A section of DNA in a gene that does not code for protein. Introns are intervening sequences between the coding regions of genes, which are called exons. The non-coding introns are spliced out of pre-messenger RNA, leaving only coding exons in the resulting messenger RNA. Each gene may contain multiple introns.

• Intronic mutation: A mutation that occurs in the intron, or portion of a gene that does not code for a protein.

J

K

L

• Lethal mutation (lethal allele): A lethal mutation causes premature death of an organism. Lethal mutations may lead to mortality at any stage of an organism's development, including after birth, but often act in the early stages of embryonic or fetal development.

  • Embryonic lethal: A genotype is considered embryonic lethal if it causes termination of embryonic development. Some individuals with embryonic lethal mutations can survive to term but are nonviable.

• Locus: The location of a particular gene on a chromosome. Plural is loci.

M

• Mendelian (Mendelian inheritance): Pattern of inheritance that follows the principles proposed by botanist Gregor Mendel. Mechanistically, Mendelian inheritance follows the law of segregation and the law of independent assortment.

  • Law of segregation: Alleles segregate when gametes (sperm and egg) are formed during meiosis (division of cells to form specialized reproductive cells). Each gamete thus carries only one version of the gene (one allele).

  • Law of independent assortment: The alleles of any one gene will segregate independently from the alleles of other genes (with the exception of genes located close together on a chromosome).

Single locus autosomal dominant, autosomal recessive, and X-linked inheritance patterns follow Mendel’s laws and are said to be Mendelian. Non-Mendelian inheritance patterns can be caused by epistasis and other complex genetic phenomena including multiple genes and environmental components.

• Melanocyte: A specialized cell that produces melanin. Found in the skin, some structures of the eye, the inner ear, and several other tissues.

• Melanoma: A type of cancer, typically in the skin, that arises from changes in an individual’s melanocytes.

• Microsatellite: Regions of repeated DNA found abundantly throughout the genome, often in non-coding areas, and which are highly variable and prone to mutation (see short tandem repeats). The various forms of a given microsatellite (identified by differences in the number of repeats) are referred to as alleles, and these are inherited in a Mendelian fashion. Genetic variation at the microsatellite level can be used to identify individuals (see microsatellite marker).

• Microsatellite marker: Specific microsatellite sequences (short tandem repeats) found at a particular location on a chromosome that are often used in various kinds of genetic analyses. Microsatellite markers can be used to identify individuals and have applications in forensics, parentage analysis, and studies of populations.

• Missense mutation: A specific type of change in the nucleotide sequence of an organism’s DNA in which a single change in the DNA causes a change in the building block (amino acid) of the gene product (protein).

• Mitochondria: Mitochondria (singular: mitochondrion) are membrane bound organelles, or specialized parts of cells. They play a key role in generating cellular energy known as adenosine triphosphate (ATP). Mitochondria possess their own independent genome separate from the DNA found in the nucleus (see: mitochondrial DNA).

• Mitochondrial DNA: DNA found specifically in the mitochondria. Mitochondrial DNA is a single, circular chromosome. In mammals, this DNA is transmitted primarily from mother to offspring via maternal egg cells.

• Mitotype: Mitochondrial haplotype; a set of variants (alleles) that are inherited together on the mitochondrial DNA.

• Mode of inheritance: The manner in which a trait is inherited across generations; the pattern of transmission of a genetic trait.

  • Examples: autosomal recessive inheritance, autosomal dominant, X-linked inheritance.

• Modifier: A gene that affects (or modifies) the phenotypic outcome, actions, or product of another gene.

• Mutation: A change in the nucleotide sequence of DNA. A mutation can be small (e.g. single base pair) or large (e.g. segment of a chromosome encompassing multiple genes). Mutations create alleles, which are alternate versions of a gene.

N

• Nonsense mutation: A specific type of change in the nucleotide sequence of an organism’s DNA in which a single change in the DNA causes a premature stop or truncation of the gene product (protein).

• Nucleotide: An organic molecule that is the basic structural unit of DNA (and RNA). Nucleotides consist of a nitrogenous base, a five-carbon sugar molecule, and a phosphate group. In DNA, the nitrogenous bases are Adenine (A), Guanine (G), Thymine (T), and Cytosine (C). In RNA, Uracil (U) replaces Thymine (T).

O

P

• Penetrance: The proportion of individuals in a population that have a particular variant and express the trait caused by that variant. In other words, when a variant causes a trait but not everyone with the variant has the phenotype, the allele is said to be incompletely penetrant.

• Phenotype: The expressed characteristic or trait of an organism; this can include an organism’s appearance, physical features, biochemistry, physiology, and behaviors. An organism’s phenotype can result from the genetic makeup (genotype) or can result from the interaction of genes and the environment.

  • Examples of phenotypes: coat color, blood type, disease status, etc.

• Pigment: A compound that selectively absorbs certain wavelengths of light while reflecting others, which creates the appearance of a particular color. In mammals, the pigment eumelanin is responsible for shades of black and brown coloration, and the pigment phaeomelanin is responsible for shades of yellow and red.

• Pleiotropy: Occurs when a single gene affects multiple phenotypic characteristics.

  • Example: The mutation responsible for leopard complex spotting in horses affects coat pigmentation as well as vision in low light conditions.

• Polymorphism: The occurrence of two or more different sequence variants at a particular locus.

Q

R

• Recessive: A trait is recessive when two copies of a variant allele are needed to produce (express) the phenotype.

• RNA: Ribonucleic Acid, a single-stranded organic molecule composed of nucleotides. Like DNA, RNA is a nucleic acid made up of a chain of nucleotides; unlike DNA, it is single-stranded instead of double helix, has a ribose sugar backbone instead of a deoxyribose sugar backbone, and contains the nitrogenous base uracil (U) in place of thymine (T). One of the main roles of RNA in the cell is to be the messenger or intermediate of genetic information. DNA is used as the template to make RNA in a process known as transcription, and then RNA is used as a template to make protein products by the process of translation.

S

• Self-color (coat coloration): Term used in cat and dog breeding. The individual hairs of an animal described as “self-colored” are unbanded along the hair shaft, resulting in the appearance of a solid, uniform color from the tip of the hair to the base of the hair. (In contrast, mammals with agouti banded hair have alternating areas of black and red pigments along individual hair shafts, creating a banding pattern.)

• Sex-linked: A gene that is sex-linked resides on one of the sex-determining chromosomes. In mammals, these are the X or Y chromosomes. Sex-linked traits follow a different inheritance pattern than non-sex-linked traits (autosomal traits) because of the way sex chromsomes are inhertied. In other words males have one X and one Y and females have two X chromosomes. Many sex-linked traits in mammals are X-linked recessive, meaning the causal variant is located on the X chromosome and females need two copies to have the trait where males will only need one.

• Short tandem repeats (STR): A repetitive pattern found in DNA in which a short sequence of nucleotide base pairs, usually 1-6 base pairs, is tandemly repeated as a unit (i.e. one repeat right after the next). STRs occur most frequently in noncoding regions of the genome.

• Single nucleotide polymorphism (SNP): A type of genetic variation in which a single base is substituted at a specific location. For example in the stretch of sequence TAAGTCTGACACAAT if the first G was substituted for a T then the sequence would become TAATTCTGACACAAT. That SNP would be denoted as a G>T variant.

• Splice site: Places in the DNA that have specific information on how a gene is put together. During the process of transcription, DNA is copied into RNA. There are regions of the DNA that code for proteins (exons) and non-coding regions that are intervening (introns). At the junction of intron-exon boundaries, there is specific sequence information that tells the cellular machinery to remove (splice) the introns out of the RNA and bring the exons together. Splice sites, then, are where splicing occurs at these intron-exon boundaries. During splicing, the non-coding introns are removed from precursor messenger RNA (pre-mRNA), which then produces mature messenger RNA (mature mRNA) that contains only coding exons. Changes in the genetic sequence of a splice site can affect splicing and subsequently produce an altered gene product.

• Splice variant: A mutation that disrupts the normal splicing, or removal of an intron, that occurs when a gene is transcribed.

T

• Transcription: The molecular process by which a DNA sequence is transcribed into RNA (usually messenger RNA, mRNA).

• Translation: The molecular process by which transcribed RNA directs the synthesis of a protein product by encoding a sequence of amino acids.

U

V

• Variant: An alternate form or version of a gene, also known as an allele. A variant is defined as a change in the DNA sequence when comparing individuals in a population.

W

• Wild type: The wild type version of a gene (the wild-type allele) is the allele that existed before a mutation occurred in the population.

X

• X-linked: A gene that is X-linked resides on the X chromosome.

  • Because males (X/Y genotype) have only one X chromosome, they will express an X-linked trait if they inherit one copy of the trait-associated allele, regardless of whether the mode of inheritance is dominant or recessive.

  • In contrast, females (X/X genotype) will only express a X-linked recessive trait if they inherit two copies of the trait-associated allele.

Y

Z

• Zygote: The single cell formed by the union of gametes (sperm and egg); a fertilized egg.