Chetar Arabians ~ EQUINE COLOUR GENETICS ~ Introduction to Genetics ~

When we talk about genetic processes, we are referring to the very basis of all life - DNA, or Deoxyribonucleic Acid.
Genes are comprised of DNA, and function as a long string of repetitive elements, or processes, that together form the genetic blueprint that contains instructions for the development and functioning of all living organisms. The genetic blueprint is also referred to as an individuals' genotype, and is essentially the recipe for all life - Though in this case we'll be focusing on the genetic blueprint, or genotype, for horse colour of course!

A horses' final colour is determined by the 'strings' of genes contained within their genotype. The instructions contained within the genes essentially modify the actual colour, or the production of the actual colour. While the genes are responsible for the modification of the colour, the colour itself is the result of pigment in the hair shaft, produced by an entirely different process. This process is separate to that of the genes, though the pigment process may or may not be affected by the genotype in an individual.

Horses have only two major pigments that account for the multitude of colours we see across the breeds - Red Pigment and Black Pigment.
Pheomelanin is responsible for all shades of Red pigmentation, while Eumelanin is responsible for the shades of Black pigmentation.
Pheomelanin produces the shades ranging from a light brown with reddish tones through to the yellow and/or tan colouring.
Many horses with pheomelanin pigmentation have more than the one pheomelanin produced shade across different areas of the body.
Eumelanin produces the shades ranging from the deep purple black through to a medium flat brown colour.
In contrast to the pheomelanin produced shades, there is only one eumelanic shade possibility in each individual - A horse with eumelanin pigmentation will have only the one shade from the range of possibilities.
While both pheomelanin and eumelanin can result in the production of brown toned pigmentation, the flat brown colour produced by eumelanin, which is a chocolate type colour, is extremely rare in horses. Most of the brown colouring we perceive in horses is the result of pheomelanin.
Pigmentation resulting from pheomelanin almost always retains some degree of reddish tinge, even when very dark. This, along with the fact that pheomelanin can produce various shades across the body while eumelanin can only produce a single shade across the body, helps to distinguish pheomelanic areas from eumelanic areas.

There is what can be thought of as a third pigmentation in horses, though rather than being an actual pigment similar to that of pheomelanin or eumelanin, its' actually a complete lack of pigmentation - The colour that we perceive in these areas completely lacking in pigmentation is white.
White coloured areas are in fact hair shafts without any colour. The skin underlying areas of hair shafts with no pigmentation will also have no pigment, though rather than appearing white as in the hair shaft, the underlying skin is characteristically pink due to subcutaneous blood vessels.

Genes occur on chromosomes, which can be thought of as a 'string' of genes. The commonly used term "DNA Strand" is a reference to this string.
This entire string of genes on chromosomes together form the horses' genotype for colour.
Chromosomes always appear in pairs [and therefore so do genes always occur in pairs]. Each gene occupies a specific location on a specific chromosome - All individual horses have a specific sequence of chromosomes, or string of genes, with the same specific genes occurring on those chromosomes. Each gene always appears at the same location, on the same chromosome, with all chromosomes occurring in the same sequence, in all individuals.
The location of the gene pair is known as the genes' locus [singular] or gene loci [plural]. A genes' locus can be viewed simply as the location, or address even, of the gene - It is the physical place a gene is located.

The genes that form a pairing [and the chromosomes that they occur on], always have identical loci - Both of the pairing always occur at the same place in the string in all individuals - So we can essentially view the genetic blueprint - the genotype for horse colour - as a set series of genes lined up in a specific sequence, with two identical sets of strings lying side by side, with the identical genes [and their chromosomes] lined up parallel to one another.

When genes appear in more than one form [as is the case with horse colour] the various gene forms are called alleles. The various alleles of a gene all occur at the same place on the same chromosome, though each chromosome is limited to just the one allele. The result is that each individual horse can only have at most two different alleles due to this limitation. In horse colour, every gene has at least two allele possibilities, with some having three or possibly more. It is these various allelic forms and combinations that result in the wide variety of horse colours that we perceive.

All horse colours are resultant from the interaction of eleven generally independant processes. There processes are quite extensive and convoluted to explain. The easiest way to grasp the process of determining horse colour is to view the genes as a sequence of "Building Blocks", a series of switches containing specific instructions that build upon one another to eventually result in the end colour that we see in an individual horse.
That is - Each gene contains a specific instruction that affects the final colour, with the different allele possibilities at the gene locus forming a switch for that genes' specific instruction - Each genes' instruction can be bypassed [switched off] or implemented [switched on] depending on the allele pair that appears at the gene locus. Some genes also present further options, most often this is an instruction that lies in between the on and off switches or above the on switch, resulting in a three way switch with the possibilities of "off", "half-on" and "on" [for the former], and "off", "on" and "locked on" [for the latter], all of which will be further elaborated upon later on as I go into detail with each of the genes' that contribute to the colour.
As we travel along the specific sequencing of colour genotype, each genes' instruction is determined by the alleles therein, resulting in a gradual build up of various instructions, all of which contribute individually to the whole product of genotype that gives the horse its' final end colour we see.

The pigment cells in horses are called melanocytes. When a horse is still an embryo, melanocytes migrate throughout the body and release pigment granules into the cells that will eventually become skin and hair shafts. Melanocytes can produce either Pheomelanin or Eumelanin.
Whether a melanocyte produces pheomelanin or eumelanin is determind by a surface receptor and a hormone produced in the brain called melanocyte-stimulating hormone. The surface receptor is activated by the melanocyte-stimulating hormone.

Remember the 'Building Blocks' for horse colour mentioned above, where the genes can be viewed as switches in the 'on' or 'off' position - This surface receptor is such a switch, while the melanocyte stimulating hormone is what activates that switch.

If the receptor is activated by the presence of melanocyte-stimulating hormone and the switch is turned "on", the result is the production of eumelanin.
If the receptor is not activated, there is an absence of melanocyte-stimulating hormone and the switch is turned "off", and pheomelanin is produced.

This fundamental process of which pigmentation is produced and where is the first Building Block for a horses' colour. The first Building Block for colour occurs at the Extension Locus and the Agouti Locus, which work together to determine the Base Colour of a horse.
This process of determining the horses' Base Colour and the Extension and Agouti Locus' role in such is discussed in detail on the BASE COLOURS page.

There are multiple ways in which the surface receptor and the melanocyte-stimulating hormone are manipulated by the genotype.

Understanding the internal workings of the melanocytes and the way they relate to the receptor and the hormone are important in that all horse colours are produced by various gene mutations [alleles] modifying how the receptor, hormone and melanocytes work and/or relate to each other.

Some genes block the receptor and/or hormone completely, some produce proteins that inhibit the receptor and/or hormone, whilst still others will modify the melanocytes themselves and will affect the amount of pigment granules placed in cells, or even dilute the pigmentation. Some allelic mutations will modify either the production of pheomelanin or eumelanin whilst others will effect changes to both pigments. And then there are yet others, such as the white spotting patters, that affect the migration pattern, survival and/or function of the melanocytes.