"Shorthand" for Genetics

Geneticists use a special kind of written "shorthand", or annotation, to clearly express what they mean in terms of loci, alleles and genotypes. It is important to know the basic annotation conventions, to better understand discussions regarding various genes and alleles. It should be noted that this "shorthand" can vary between authors and particular areas of study.

For the purposes of the discussion on this site, an abbreviated version of genetic shorthand will be used for easier visualization and understanding.

A locus is denoted by a letter, or series of letters that refer to the general action of that locus.
Examples would be:

"A" for the Agouti locus

"Ch" for the Champagne locus

"G" for the Grey locus

A Dominant allele is noted by a Capital, or Upper Case letter or the first character of a series. Lower case denotes a recessive allele.

A=Agouti, Dominant Bay allele
a=Agouti, Recessive Black allele

Since each animal has two alleles at a locus, the genotypes at the Agouti locus can be shown as:

AA= Homozygous for Dominant Bay
Aa=Heterozygous (one Dominant allele, one Recessive allele)
aa=Homozygous for Recessive Black

When there are more than two alleles at a locus, or alleles that are not simple Dominant/Recessive counterparts, a ^superscript character (or series) may be used next to the Locus notation.
Examples:

E^D indicates Extension Locus/Dominant Black allele.
C^Cr indicates Cream locus/the partially dominant Cream allele.

A possible, or probable "wild-type" allele is often noted with a ⁺ character.

Example:

E⁺ indicates Extension locus/"wild-type"⁺ allele.

When generating probability charts to assess the possible colors of offspring, it is often easier to work with only the informal Allele designations (as above) to more clearly recognize the genotype visually. However, a more "formalized" version of genetic nomenclature is often used that may be more accurate.

Designation of the Locus
Each Locus is given a letter or short series of letters to indicate which locus is being discussed. In horse coat colors:

A = Agouti
Ch = Champagne
G = Grey

The first letter of a locus is always presented in upper-case letters.

Designation of Alleles
The various Alleles that may be present at a particular locus are noted in ^superscript. Also, the first letter denoting a dominant allele is presented in upper case, while a recessive allele is presented in lowercase letters.

For example, at the Agouti locus, the proper notation of the Dominant allele would be:

A^A

The proper notation for the Recessive allele at the Agouti Locus is:

A^a

Thus, with this more formalized notation, the main combinations at the Agouti locus will appear as below:

A^AA^A = Homozygous Dominant Bay
A^AA^a = Heterozygous
A^a A^a = Homozygous Recessive Black

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Views expressed herein are those of the writers and compilers of the various information. Reference sources are cited where applicable. Copyrights are the property of the respective authors.