dog foot print and dna diagram

Essays on Dog Genetic Diversity

Inspired by conversations hosted by Jemima Harrison

The purpose of this website is to host essays and information about maintaining viable populations of healthy pure bred dogs

Chapter08[Previous Section]|| Chapter10[Next Section]


copyright © 2009 by Dr Susan Thorpe-Vargus

Appendix: GLOSSARY

Expanded from a glossary originally assembled by Dr Susan - Thorpe Vargas that accompanies her article "Essays For The Dog Breeder


A chromosome with the centromere located close to one end.


Alternative forms of a genetic locus; a single allele for each locus is inherited separately from each parent, each locus may have multiple alleles possible however only two are available at a time, one from each parent.


Natural process of cell death.

Assortative Mating

The mating of individuals that are phenotypically similar. Assortative mating means mating like with like.


A chromosome not involved in sex determination.

Autosomal chromosomes

see Autosomes


The progeny resulting from the mating of a two-breed cross animal to one of the parental breeds. For example, using two breeds designated as P1, and P2, backcross progeny would be produced by mating the two-breed cross animal (Pl x P2) with either of the P1 or P2 parental breeds.

Base pair (bp)

Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs.

Candidate gene

a gene which researchers feel is likely to be one which performs a particular function because it performs a similar function in another species. Further research will be required to determine if it is or is not the gene being sought.


A structure that appears in pairs within the cell during the interphase portion of cell division. During prophase the two asters migrate to opposite poles of the cell and begin organizing spindle fibers which will guide the duplicated chromosomes toward the asters prior to completion of cell division.


A structure which joins two paired chromosomes together.


The tangled fibrous complex of DNA and protein within a eukaryotic nucleus. See: chromosome.


The self-replicating genetic structures of cells containing the cellular DNA that bears in its nucleotide sequence the linear array of genes.


Alleles of a gene which will both express in a heterozygous individual. ExHumanB blood type.


The basic unit of the genetic code, comprising three-nucleotide sequences of messenger ribonucleic acid (mRNA), each of which is translated into one amino acid in protein synthesis.

Coefficient of Relationship (CR)

The probability that any two individuals share a given gene because they descend from a common ancestor. Numerically it is twice the COI (Coefficient of Inbreeding).

Complete (simple) dominant

An allele which will be expressed in the phenotype even if in a heterozygous pairing with another allele.

Constitutive heterochromatin

Condensed segments of the chromosome which are transcriptionally inactive in all cells.

Contig map

A chromosome map that is formed by rendering chromosomes into small pieces, cloning them then forming a "library" of overlapping cloned segments.

Cross Breeding

The mating of two recognized breeds to establish a new variety or to improve an existing one.


The progeny resulting from the mating of animals belonging to different breeds.

Crossing over

See [[#recombination_homologous|recombination]].


A scientist who studies cellular genetics.


The protoplasm of a cell exclusive of that of the nucleus, it consists of a continuous aqueous solution (cytosol) and the organelles and inclusions suspended in it and is the site of most of the chemical activities of the cell.

DNA (deoxyribonucleic acid)

The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner.


Term used to note that more than one codon can represent an amino acid.


Process of cellular development into different types of tissue.


A full set of genetic material, consisting of paired chromsomes one chromosome from each parental set. Most animal cells except the gametes have a diploid set of chromosomes. See haploid

Disassortative Mating

The opposite of assortative mating, i.e., the mating of dissimilar phenotypes.


A gene is said to be dominant if it expresses its phenotype even in thepresence of a recessive gene.


A process by which the expression of one gene will prevent the expression or influence the expression of another.


The protein-coding DNA sequences of a gene. See [[#intron|entron]].


Portion of the chromosome that is transcriptionally active.


The process by which a gene's coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into a protein like mRNA.

Facultive heterochromatin

Bunched segments of the chromosome that are transcriptinally inactive and which vary by cell type.

Founder effect

Changes in allele frequencies that occur when a sub-population if formed from a larger one. Founders of the sub-population may have among them greater or lesser percentages of particular alleles than is the case for the population as a whole.

Free radical

Highly reactive oxygen molecules that occur naturally in the body because of metabolic processes which can damage DNA.


Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes.


The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule). See expression.

Gene frequency

Percentages of the different alleles of a particular gene that are found in a population. Also referred to as "allele frequency".

Genetic diversity

Percentage of genes that are polymorphic in a population; sometimes refers to the proportion of genes that are heterozygous.

Genetic drift

Changes in gene frequency due to random chance (as opposed to selection or mutation.)


The complete nuclear DNA sequence of a species, including all variations.


The genetic constitution of an organism. See phenotype.


A single set of chromosomes (half the full set of genetic material), present in the egg and sperm cells of animals.


Set of linked genes on a single chromosome, usually inherited as a unit.


Portion of phenotypic variation possible due to genetic inheritance as opposed to environmental influence.


Bunched segments of a chromosome which are transcriptinally inactive.


Containing two different alleles of the same gene. See homozygous.

Homologous pairs

A pair of chromosomes containing the same linear gene sequences, each derived from one parent.


Containing two copies of the same allele. See heterozygous


The crossing of two distinct strains, sometimes across species lines (i.e. a mule.)


The expression of a gene determined by which parent it has been inherited from.

Inbred line

A line of animals produced by mating related animals.


The mating of related individuals; also includes what dog breeders term "linebreeding." The technical definition is the breeding of animals which results in progeny having a greater coefficient of inbreeding than is the average for the breeding population.


The progeny resulting from the mating of animals from different inbred lines within a breed.

Incomplete dominance

Alleles that, when heterozygous, result in a phenotype intermediate between those of the homozygotes of those alleles.


Reaction between genes, as in epistasis.


Reaction between alleles of a particular gene.


The expansion of the gene pool of a population via the introduction of unrelated individuals from another population (i.e. through imports or cross-breeding.)


The DNA base sequences interrupting the protein- coding sequences of a gene; these sequences are transcribed into RNA but are cut out of the message before it is translated into protein. See exons.


A type of enzyme that that catalyzes the conversion of proenzymes to active enzymes.


An individual's chromosome complement; also the arrangement of chromosomes at metaphase into a sequence ordered by length and location of the centromere.

Lamda phag

A bacterial virus used as a cloning vector.

Line breeding

The mating of later generations back to some ancestor or its descendents. Line breeding is a form of inbreeding. A poular use of the term related to a form of inbreeding in which animals mated are related to some supposedly outstanding individual.


A measure of the frequency at which two genes on the same chromosome will pass together to gametes.

Linkage disequilibrium

The tendency of alleles of closely linked genes to be inherited together.

Locus (pl. loci)

The position on a chromosome of a gene or other chromosome marker; also, the DNA at that position. The use of locus is sometimes restricted to mean regions of DNA that are expressed.

Major Histocompatability Complex (MHC)

A group of genes that govern immune system function, all closely linked on a single chromosome.


The process by which germ-line cells produce gametes.

Messenger RNA (mRNA)

RNA that serves as a template for protein synthesis.


Chromosomes in which the centromeres are located mid-way down their length.


The addition of the functional group -CH3. This plays a role in gene expression and in post-transcriptional modification.


Highly repetitive segments of non-coding DNA, often used for parentage verification or as markers in indirect gene tests.


The process by which cells divide.


Occurs when an individual has inherited only one copy of a chromosome; in mammals this is lethal not long after fertilization.


The phenotypic effect of the random deactivation of one copy of the X chromosome.


A permanent transmissible change in the genetic material, usually in a single gene. Also, an individual exhibiting such a change.

Natural selection

Process that results in adaptation of an organism to its environment by means of selectively reproducing changes in its genotype. Variations that increase an organism's chances of survival and procreation are preserved and multiplied from generation to generation at the expense of less advantageous variations. As proposed by Charles Darwin, natural selection is the mechanism by which evolution occurs. It may arise from differences in survival, fertility, rate of development, mating success, or any other aspect of the life cycle. Mutation, gene flow, and genetic drift, all of which are random processes, also alter gene abundance. Natural selection moderates the effects of these processes because it multiplies the incidence of beneficial mutations over generations and eliminates harmful ones, since the organisms that carry them leave few or no descendants.


The tendency of a species to retain infantile or juvenile characteristics.


An error of cell division that allows two copies of a chromosome to wind up in a single daughter cell or gamete, ultimately causing trisomy or monosomy.

Nucleic Acid

Linear polymers of nucleotides. Nucleotides form the basic building blocks of nucleic acids. They are made up of a nitrogen-containing purine or pyrimidine base linked to a sugar (ribose or deoxyribose) and a phosphate group.


A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked to form a DNA or RNA molecule.


The major organelle of eukaryotic cells, where the chromosomes are separated from the rest of the cell by the nuclear envelope


A term generally taken to be the opposite of inbreeding. It can be applied to outcrossing or cross breeding and is the mating of animals less closely related to each other than the average relationship within the breed or population concerned.


The progeny resulting from the mating of unrelated animals within a breed.


Breeding from totally unrelated animals of which one is or both are inbred (or linebred) within a given breed.


The short arm of a chromosome.


The frequency with which a genotype will produce a phenotype.


Viruses which infect bacteria.


Different genes which produce similar phenotypes.


The physical appearance/observable characteristics of an organism. See genotype.


The ability of a single mutation affect several traits.


A trait resulting from the action of multiple genes.


A gene which has multiple alleles. It also applies to non-coding regions.


A peptide containing more than two amino acids and that are named according to the number of amino acids they contain.

Posttranscriptional modifications

Changes in the RNA after DNA transcription.

Primary transcript

RNA transcript immediately after transcription in the nucleus, before RNA splicing to form the mature mRNA.


Regulatory section of DNA to which RNA polymerase binds prior to transcription.


A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene coding for the protein. Proteins are required for the structure, function, and regulation of the bodys cells, tissues, and organs, and each protein has unique functions. Examples are hormones, enzymes, and antibodies.


the long arm of a chromosome.

Reading frame

A contiguous, non-overlapping set of triplet codoms in RNA or DNA that begin from a specific nucleotide.

Recombination (homologous)

The exchange of DNA fragments between two DNA molecules or chromatids of paired chromosomes (during crossing over) at the site of identical nucleotide sequences.


A gene that is expressed only when it is present in two copies or if the other copy is missing. See dominant.


Process by which like segments of homologous chromosomes will exchange places during meiosis.

Regulatory gene

One that is involved in the control of other genes.


Any virus in the family Retroviridae that has RNA as its nucleic acid and uses the enzyme reverse transcriptase to copy its genome into the DNA of the host cells chromosomes. Many cancers in vertebrates are caused by retroviruses.

RNA (ribonucleic acid)

A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.

RNA polymeras

RNA enzyme involved in the transcription of DNA.

Sex linkag

Inheritance patterns resulting from genes located on the sex chromosomes.

Simple dominance

See [[#complete_dominant|complete dominant]]

Structural gene

One that encodes amino acids that ultimately lead to formation of tissues or the regulation of body functions.


Chromosome in which one arm is slightly longer than the other.


An allele that causes slightly reduced function.

Syntenic groups

Genes on the same chromosome.


Section of the DNA that is copied by RNA.

Transcribed (transcription)

The synthesis of a RNA copy from a sequence of DNA (a gene); the first step in gene expression. See translation.


The process in which the genetic code carried by messenger RNA directs the synthesis of proteins from amino acids. See transcription.


A condition in which a cell or individual has three copies of a chromosome.


Occurs when an individual has inherited three copies of a chromosome; in mammals this is lethal before or shortly after birth.

Uniparental disomy

condition in which an individual inherits two copies of a chromosome from one parent and none from the other.

The Y chromosome

the small chromosome that is male-determining in most mammal species. The male has one Y chromosome and one X chromosome. The Male Specific region (MSY) comprises 95% of the chromosomes length and is made up of heterochromatic areas (condensed during the interphase portion of the cell cycle) and three 3 specific euchromatic (diffuse during the interphase portion of the cell cycle) areas. So far only the euchromic areas have been found to contain transcription factors, including coding genes. One region of the euchromic region is homologous to and pairs with the X chromosome and is now called the x-transposed region. It contains 2 coding genes that are expressed in the testis. The x-degenerate region is composed of ancient remnants of autosomes (non-sex determining chromosomes) from which both the x & y chromosomes evolved. It contains 16 coding genes that are expressed widely in all the tissues of the body. (These genes have x-linked homologues) The amplionic region contains 60 coding genes that are linked to male sexual development with regard to sperm development and triggering appropriate hormonal output.

Chapter08[Previous Section]|| Chapter10[Next Section]

Articles at

Blogs Discussion Controversies in Dog Breeding

Jemima Harrison

Pedigree Dogs Exposed - The Blog

Border Wars

A Border Collie Manifesto

Desert Windhounds

A Bitter Cynoanarchist Rages On

Carol Fowler

Dog Breed Health

Interactive Genetics Tools Websites

Online COI Generator by Henk Meijers

Online COI Calculator

Academic Genetics Tutorials/Courses/Resources Online

Online Mendelian Inheritance in Animals (OMIA) OMIA

Understanding Gene Loss in successive generations An Interactive Academic Site on "Gene Dropping" at University of Montana

BIOL 4312: Genetics

GENUPComputer aided learning for quantitative genetics.
Although a Windows application Bonnie Dalzell has been able to run it under Ubuntu Linux from my desktop.

Design Of Crossbreeding Programs

A tactical approach to the design of crossbreeding programs.

Applied Animal and Plant Breeding

Cultivar Crazy - Preserving the Genetic Heritage of Plants

Applied Animal and Plant Breeding

Fitness and Viability of Small Populations
by Nina Pekkala

The Effects of Genetic Drift, Inbreeding, and Interpopulation Hybridization experimental study involving Drosophila (fruit flies)

Authoritative Inherited Diseases in Dogs Sites

Inherited Diseases in Dogs

Inherited Diseases in Dogs (IDID)

Canine Inherited Disorders Database

Canine Inherited Disorders Database

Inherited Disorders in Animals

List of Inherited Disorders in Animals (LIDA)

Canine Health Registries and Organizations

VMDB Veterinary Medical Database
The Veterinary Medical Database (VMDB) compiles patient encounter data from nearly all North American veterinary medical databases.

CERFCanine Eye Registration Foundation

CHIC) Canine Health Information Center

OFAOrthopedic Foundation for Animals

CERF Canine Eye Registration Foundation

APGAW: Associate Parliamentary Group For Animal Welfare
[Great Britain]

A Healthier Future for Pedigree Dogs

Canine Genetics Sites

The Hounds of Claybrook

Closed Registries, Genetics, and Inbreeding Depression


Canine Genetics Resources

Canine Diversity Website Homepage

Canine Diversity Homepage

A series of articles concerning the genetics of selection, inbreeding, inheritance of congenital defects.

Canine Inherited Disorders Database

CID Database

Sue Ann Bowling:

Animal Genetics Pages

To Breed or Not to Breed

All 4 essays by Susan Thorpe-Vargas Ph.D., John Cargill MA, MBA, MS, and D. Caroline Coile, Ph.D

The Genetic Cul-De-Sac

Dogs As An Endangered Species

Breed Related Sites

Borzoi Heritate Borzoi Pedigree Collection

Borzoi Pedigrees

Cesky Terriers

Cesky Terriers

The Dalmation Heritage Project

Project to breed Dalmations with normal uric acid metabolism

Author's Sites in no particular order:

John Burchard

Tepe Gawra Salukis

Jim Seltzer

Willowind Dalmations

Jeffery Bragg

Seppala Siberian Sleddogs

Dorothea Penizek

Clarmorris Parson Russell Terriers

Bonnie Dalzell

Borzoi Information Site

Academic Articles on Inbreeding, Fitness and Population Genetics

Fitness and Viability of Small Populations

by Nina Pekkala

The Effects of Genetic Drift, Inbreeding, and Interpopulation Hybridization experimental study involving Drosophila (fruit flies)