Chetar Arabians ~ EQUINE COLOUR GENETICS ~ Genetic Terminology ~

The terms Polygenic and/or Simple are used in conjunction with the genes' name to essentially indicate the complexity of the set of 'instructions' for that particular gene.
The term Polygenic is defined as being 'of many genes'. As the term suggests, a Polygenic Colour is the result of a combination of more than one gene. All of the instructions from the combination of genes come together to give the described genes' resultant colour.
The term Simple, used in the same context as above in conjunction with a genes' name, indicates that that colour is the result of the process of a single genes' instructions affecting the phenotype.

An allele can be either dominant or recessive. When paired with a recessive allele, the dominant allele will suppress the affect of the recessive allele it is paired with. The dominant of the allele pairing will influene the instructions of the specific gene on the genotype only. The relationship between the dominant vs recessive alleles, however, is limited to the pair of alleles that form the specific gene in question only though. The relationship of the two alleles that make up a specific gene has no bearing on the alleles that make up the other genes of the genotype. In addition, the dominant vs recessive allele pairing relationship has no bearing on whether the gene itself is dominant or recessive - See directly below on this page for further explanation.

The relationship between dominant genes and recessive genes is similar to that of dominant and recessive alleles in that a dominant gene will supress a recessive gene. However, the dominant vs recessive gene relationship extends across the entire colour genotype rather than having limitations as with the allele relationship. The dominant vs recessive gene is, as a result, rather more difficult to comprehend.
A gene is either dominant or recessive. A dominant gene will suppress the expression of a recessive gene in the phenotype.

When a recessive gene is suppressed by a dominant gene, the horse will carry the genotype for a certain colour characteristic, and be able to pass this trait onto its' progeny as a result, but this trait will not actually be expressed by the horse itself. This mode of inheritance may carry for generations, and is the cause of what is termed "Crop Out" [See Below on this page for definition of Crop Out].

A dominant gene, on the other hand, will always be expressed in the phenotype of a horse. The gene may manifest in the most minimal of expressions, but a dominant gene will always be expressed in the phenotype of the horse. The same rule applies to inheritance, with any progeny inheriting the dominant gene always having some degree of expression present in the phenotype - There are no exceptions to this rule.

It is important to remember that an individual genes' dominance or recessive form is not dependant on the dominant/recessive form of the alleles that make up that specific gene. A dominant gene can contain recessive alleles. There is a distinct difference between the gene and allele relationships.

Heterozygous genes are those that consist of one dominant and one recessive allele. A horse heterozygous for a specifc gene always has a 'hidden' characteristic that can not be determined simply by looking at the horse. When progeny inherit an allele from a heterozygous gened parent, it may inherit either the dominant or recessive allele. A heterozygous gene represents various possibilities in regards to progeny inheritance.
The simplest way of understanding a heterozygous gene to see the gene as having a "single copy" of the instructions affecting phenotype contained within that specific gene. The term "single copy" is often used in this way universally, though to actually be technically correct, a heterozygous gene is one that contains a 'half' or 'partial' copy of the specific genes' instructions.

Homozygous genes are those that consist of two identical alleles - That is, either two dominant alleles or two recessive alleles. The additional reference of dominant or recessive is used as a suffix to indicate the relative homozygosity of the alleles involved. That is, 'Homozygous Dominant' for genes consisting of two dominant alleles and 'Homozygous Recessive' for genes consisting of two recessive alleles.
A homozygous gene not only indicates the presence of specific characteristics in the horses' phenotype, but in addition represents 100% certainties in regards to progeny inheritance. For this reason, those homozygous for certain colour and/or pattern genes are looked upon with much favour in coloured breeding programs. A horse homozygous for a certain gene can be relied upon to produce progeny with a certain allele at that genes' locus 100% of the time [as the parent has two identical alleles at that genes' loci it is impossible for the progeny to inherit anything other than that same allele possessed by the parent].
[As with the heterozygous 'single copy'] The homozygous gene is simplest to understand when the gene is viewed as being a "double copy" of the genetic instructions contained within the specific gene. Once again, this is the commonly used term, with the true technically correct respresentation being that a homozygous gene carries the 'full' or 'complete' set of instructions of the gene.

The terms Primary Coat Markers and Secondary Coat Markers are used throughout this site, predominantly when describing how to indentify various modified colours and the gene[s] responsible for the end colour. Please note that while these terms are commonly used, they are not considered universal terms in colour/gene identification. I use these terms to describe the group[s] of coat marking/pattern identifiers manifested by each gene.

For each colour, and the underlying gene controlling it, there are specific coat markings visible in the phenotype resulting from the genes' instructions.
By evaluating each coat marking individually as well as in conjunction with eachother, we are able to correctly identify the underlying gene responsible.

Primary Coat Markers are the coat markings that are prerequisites for an individual colour. The Primary Coat Markers for a specific colour will always be visible in the phenotype of a horse carrying that specific gene. If a horse does not possess all of the Primary Coat Markers for a specific gene, then the horse does not carry the genotype for that specific colour, therefore cannot be the indicated colour.

Primary Coat Markers are most useful in identifying the potential genes carried by individuals, as well as ruling out those not the base cause of phenotypical markings expressed by the individual.

Secondary Coat Markers are the coat markings that, in addition to the Primary Coat Markers, are also attributed to being caused by a specific gene. Secondary Coat Markers, however, are not required to be present in the phenotype to be indicative of a certain colour. An individual possessing a specific colour gene may have all, most, one, or maybe none, of the Secondary Coat Markers for a specific gene but provided the presence of all of that genes Primary Coat Markers are visible in the phenotype, the individual can still be confirmed as possessing that gene and being the genes' resultant colour.

Secondary Coat Markers are most useful in determining the degree of the genes' expression in the phenotype, with the more secondary markers present the more intensive the expression [detailed on each individual genes' descriptive page].

When describing the expressions manifested by certain genes, the terms minimal, moderate, maximum, and in some cases extreme are used to indicate the degree[s] of expression. These terms are primarily used for the genes that manifest in white patterned markings [spotting as well as roaning].
Each of the terms will generally appear within the colour/gene description of an individual, as a prefix to the name of the colour/gene.

'Minimal' is used to indicate the presence of only the basic of required markings for the gene. A minimal expression of a certain gene would generally include only the Primary Coat Marker indicators, or the bare minimum of markings. In some cases, a minimally expressed gene may be easily missed as being present in the genotype of an individual.

'Moderate' is used to indicate the presence of the more than the basic prerequisite of markings, though generally will not indicate the presence of all of the possible manifestations of the gene. Generally speaking, a moderate expression would include one or two of the Secondary Coat Markers in addition to all of the Primary Coat Markers - So a moderate expression of the gene is essentially 'in the middle', not the least but neither is it the most of markings.

'Maximum' is generally used to indicate the presence of all of the possible marking manifestations of a certain gene. In most cases, a maximally expressed individual will possess all of the possible Secondary Coat Markers, in addition to the Primary Coat Markers, for the particular gene.

'Extreme' is an expression description that is only used for those genes that cause a resultant manifestation of colour that is, as the term suggests, extreme - The individual will essentially be completely phenotypically affected by the specified gene. The description of extreme should only be used for those individuals that are affected to the extent that identifying the presence of certain gene characteristics, specifically the Primary and Secondary Coat Markers, becomes so difficult as to be next to impossible due to the extent of the gene related markings. Generally speaking, when used in reference to the white spotting patterns, an extremely expressed individual will be almost completely white in colour, with very few, if any, solid coloured markings.
It should be noted that the terms 'Maximum' & 'Extreme' are often interchanged & commonly used to describe the same or similar degrees of expression.

"Crop Out" is the term used to describe the often surprising occurrence of a colour gene in progeny bred from parents &/or a family not known for possessing that certain colour gene. A Crop Out is always the result of recessive colour genetics. The colour gene in question will be recessive and as such, would be able to remain 'hidden' for generations as the recessive gene has been 'covered up' by dominant counterparts, often for multiple generations. When the time comes, the breeding of the dam and sire have provided the right genetic environment for the recessive gene to be expressed phenotypically, and a Crop Out is produced. It should be noted that once a colour is expressed phenotypically by a Crop Out, the colour gene becomes much easier to breed on in the Crop Out's progeny, and doesn't always nor often follow the previous pattern of being recessively 'hidden'.

While the genotype [discussed on the Introduction Page] is the very basis of life, giving the initial instructions for the formation, and providing an ongoing contribution to the growth and development, of a living organism, there are external factors that play a part in the formation, growth and maturation of each individual. These additional aspects are called the environmental factors. The more prominent of the environmental factors include the [but not limited to] nutrition, housing, grooming and care that the horse receives.
Environmental factors are subject to external influences, such as a change in feed nutrition levels or the weather as the seasons change, can have a resultant affect on a horses' colour. However, while these environmental factors can be, and often are, influential on an individuals' colour, the result is a relatively small alteration of colour, such as the depth of shade or the development of highlights in the coat, rather than an outright change in the colour itself - Environmental factors can be influenced resulting in superficial changes to a predetermined colour, whereas the genotype that provides the predetermined colour is set in stone at conception and is not subject to external influence.

An individuals' genotype combines with the contribution of environmental factors to result in the individuals phenotype.
The phenotype concerning equine colour genetics is the end body coat colour visible to us.

Pheomelanin and Eumelanin are the two different pigments that horses are capable of producing.
Pheomelanin is the red pigmentation, the colour we perceive as Chestnut and/or the body colour of Bays.
Eumelanin is the black pigmentation, the colour we perceive as Black, some Browns, Black/Brown and the points of Bays.

These terms will be used often throughout this site where I discuss the genetic process of how each colour is achieved by manipulation of the pigments.
The Introduction Page explains the genetics of Pigmentation and how the Pigments Cells, called melanocytes, distribute pigment to the cells of the body.
Each Gene Page will carry on with a "Genetic Process" section that will explain the way in which each individual gene operates on or interferes with the method of transportation, distribution, reception and/or survival of the melanocytes and how they alter the resulting pigment placement.

As discussed above, a gene that is recessive can remain hidden in the genotype for generations as it is 'hidden' by a dominant gene, which is the one expressed in the phenotype. This gene interaction of dominance vs recessiveness is known as "Epistasis".

The gene that is dominant and expressed in the phenotype is 'epistatic' to the recessive gene not expressed in the phenotype [ie. hidden].
For example, the colour Chestnut [homozygous recessive at the Extension Locus] is epistatic to Bay [heterozygous or homozygous dominant at the Agouti Locus] - So Chestnut is expressed in the phenotype of the horse and the Agouti genotype is hidden - not expressed - in the phenotype.

The gene that is recessive and not expressed in the phenotype [ie. hidden] is 'hypostatic' to the dominant gene that is expressed in the phenotype.
Using the same example as above - Bay [Agouti genotype] is hypostatic to Chestnut [Extension genotype].

It should be noted that the epistasis of gene loci changes with different allelic combinations - meaning that, [continuing on with the example used above], the epistatic vs hypostatic relationship noted here does not mean that the Extension Locus is epistatic to the Agouti Locus, only that those specific allelic combinations at those loci have that specific dominant vs recessive relationship.