Glossary

This is a list of terms we use regularly. We explain them in laymen's terms but feel free to google these for more precise and scientific explanations! We will continue to update this glossary as necessary.

Allele: Alleles are different versions of the same gene or marker at the same locus. Different alleles at the same locus can control whether two dogs differ in size, color or specific health status.

Base Pair: Base pairs form the rungs of the DNA double helix and the sequence of base pairs in DNA determines genetic traits. All DNA consists of 4 chemical compounds called bases. The four bases in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T). These bases form specific pairs (A with T, and G with C). These tiny units, strung one after the other, form the essential code for life. The sequence of these base pairs determines various outcomes. Sperm and eggs each contain a random half of the parent's DNA.

Dogs have nearly 3 BILLION base pairs!

When eggs and sperm are created, tiny differences can occur, such as repeats of base pairs, missing base pairs, or changes in their order. Some of these changes are harmless, some are harmful, and some can benefit a dog. The variations in the order of these base pairs explain the different traits in individual dogs and breeds.

Carrier: This is what we call a dog with one recessive allele at a locus and one dominant allele at the same locus. In such cases, the recessive allele cannot be detected from looking at the dog.

Complex Genetic Disease or Trait: Complex genetic diseases or traits involve multiple genes (often at different loci) and may be influenced by environmental factors. These traits and diseases are harder to breed away from or toward, and developing genetic tests is far more difficult. Some genes are also "incompletely" dominant or recessive, or penetrant, so not all dogs with the genes have the trait or disease, or have it in varying degrees.

Dominant Allele: This kind of allele overrides any other kind of allele that is inherited, and is represented by a capital letter. That means that if a dog inherits just one dominant B allele from either parent at the B locus, it will be a black based dog, usually with a black coat and/or nose. If a dog inherits a dominant B allele from both parents, it is homozygous BB, and it can only have black based puppies, as they will always inherit a dominant B allele from their homozygous BB parent, no matter what their other parent has.

Gene: A gene is a specific section of DNA that determines a trait in a dog. It can be a long sequence of base pairs or just a small number, but a gene instructs the body on how to make the proteins that cause traits, like coat color, coat quality, body size, organ functions, disease susceptibility, and much more.

Gene Pair: A dog inherits two alleles of each gene—one from its dam and one from its sire. These alleles may be the same (homozygous) or different (heterozygous).

Genetic Diversity: This is a very general term meaning the variation in all genes across individuals within a breed. It is influenced by historical breeding practices, the number of founders, geographical isolation, and events like population bottlenecks. Some breeds have a lot of genetic variation from one dog to another, or from one line to another. Some breeds have very little genetic diversity, meaning most of the dogs have many of the same genes across the genome.

The amount of genetic diversity in a breed is determined by a few different things. They are:

• What were the breeding practices of breeders in the last century or two? Did they inbreed heavily to get specific traits, or did they usually look for outcrosses with similar desirable attributes?
• How many dogs were the original ancestors or "founders" of a breed? How related were those dogs?
• How geographically isolated was the breed originally and did it stay that way?
• How much was the breed affected by historical events like wars and famines that might have reduced the population of the breed, or sudden popularity that might have increased the population of the breed?

Genetic Marker: Markers are specific sequences of base pairs consistent enough to serve as "tags" for geneticists. There are different kinds of markers, some in regions of DNA more likely to control traits, which are useful for genetic research and some in regions that are not known to control traits, and these are better for studying ancestral lineages and conservation genetics. Markers can vary from dog to dog or breed to breed.

Genotype: Genotype refers to the genetic makeup of an individual, specifically the alleles present at one or more loci. For example, a dog with a dominant B on the B locus and a recessive b on the B locus will have a heterozygous genotype of Bb at the B locus. Dogs can, for example, be called homozygous dominant, homozygous recessive, or heterozygous. Some markers are only called homozygous (same) or heterozygous (different) and some genes are more complicated than being simply recessive or dominant.

Genome: This is the whole set of DNA found in a dog, including all the coding DNA  (genes) and "non-coding" DNA, which has an unknown function.

Haplotype: A haplotype is an identifiable set of genes or markers that are passed on as an intact block. A haplotype can be large or small, and can have many genes, markers, or base pairs, or few. It is usually used as a descriptive word for any section of DNA that is inherited. Like genes, every dog inherits one haplotype from each parent.

Heterozygous: This is when a dog has inherited the different alleles or markers from both parents.

Homozygous: This is when a dog has inherited the exact same allele or marker from both parents.

Inbred: An inbred dog has inherited many of the exact same genes or markers from both parents. The more ancestors each parent has in common, the more likely their puppy will inherit the exact same genes throughout their DNA. This can be due to recent ancestors being closely related, or a great many distant ancestors being the same. All purebred dogs will have some of the same ancestors on both sides of the pedigree. This is what makes purebred dogs consistently recognizable. However, some species and breeds have many of the same genes in all individuals that control visible phenotype, while the rest of the genome is largely heterozygous. Inbred populations and breeds are more homozygous throughout all of the DNA. Inbreeding is relative—no pun intended. While all purebred dogs experience some level of inbreeding, it is more pronounced in breeds with smaller gene pools

Incomplete penetrance: This is when a dog has the genotype required to create a disease or trait, but may or may not have the disease or trait. In some dos there is no expression of the trait at all, or the trait is only somewhat expressed. There are usually unknown factors that cause that variability. 

Locus/Loci:  A locus is a specific location on a chromosome where a gene or genetic marker is found. More than one locus are called loci. When DNA in dogs is compared, geneticists have to compare precisely the same loci in each dog for the comparison to be meaningful. 

Outbred or outcrossed: An outbred dog has inherited many different genes or markers from both parents. Crossbred dogs are always outbred, at least for the first generation. If a crossbred dog is bred back to a purebred dog like one of its parents, it can produce somewhat inbred puppies again. Outbreeding is also relative. All dogs are a single species, so they all have some genes in common. Any two purebred dogs of the same breed will have many more genes in common than two random dogs. Some breeds have so much genetic variation in the breed that some breedings can truly be considered outbreeding. However, this will not likely be as outbred as when crossing two purebred dogs from different breeds. Some breeds have very little genetic diversity, so all the dogs are more genetically similar and any breeding within the breed considered an outcross will not likely be as outbred compared to what is possible in more diverse breeds.

Phenotype: This is the term for what a dog looks like, acts like, or how their body functions. This, however, may not reveal the dog's actual genotype. The phenotype may be black in a black dog, but that doesn't necessarily determine the genotype. A black-based dog may have a genotype of Bb or BB at the B locus.

Recessive Allele: This kind of allele can only determine a trait if it is inherited along with the same recessive allele from the other parent. It is represented by a lowercase letter. Therefore, if a dog inherits a recessive b allele at the B locus from both parents, it is homozygous bb, and it will be a brown-based dog, not a black-based dog. It will be recognizable from its brown nose. (Some breeds call this color red or chocolate!) Any dog that is homozygous bb will only have puppies that have at least one b allele.