The Sooty Factor

As the name of this Basic Modifying Factor suggests, the Shade Factor is responsible for the various shades found within a certain colour catergory. Shade is a complex polygenic process under multifactoral control - The Shade Factor is anything but straightforward. An [almost] unlimited range in the tone and depth of coat colour is achievable by the Shade factor, with the shades it is responsible for being a continuous array of colours with [almost] imperceptible differences and no abrupt border between them.

The depth of colour resulting from the Shade Factor is also subject to environmental influences. The majority of the various shades of horse colour alter to some degree depending upon the season of the year, lightening a few shades during winter, and darkening during the warmer months. Other environmental influences include the quality of the feed available, the general health and wellbeing of the horse, the quality and consistency of the general care being given [eg. rugged full time and groomed daily vs unrugged and groomed once a week], the horses' age and in some cases the purpose for which the horse is kept [eg. show horse vs recreational mount]. So while the colour is affected by the Shade Factor at the genetic level by the gene[s] responsible, the phenotypical outcome can also vary greatly in depth and shade of colour due to these environmental factors.
The Shade Factor can affect all coat colours, though is most noticable on red pigmentation, and the least so on black. The genetic affect of Shade is uniform throughout the coat. It essentially alters the "tint" of the pigmentation of the hair shaft, and will change all hairs of the original colour. When environmental factors influence the Shade Factor outcome though, this uniformity can become uncertain. For example, a sunbleached coat will have lighter areas along the topline and darker on the underside of the body due to where the sunlight falls on the coat and bleaches the most.


While the complexity and variations of Shade are innumerable, we can understand the basic process of Shade by catergorizing the array of colours the Shade Factor is responsible for - It is important to remember, though, that these simplified catergories actually represent innumerable colours that blend imperceptibly into one another, and that the Shade Factor is a genetic process involving multiple loci.
As when we simplify other genes for ease of understanding, Shade can also be considered as a switch, though in this case we have a three way optional switch rather than the usual "on" and "off" instructional switch as with [most] other gene loci. The three switch options at the Shade Factor locus are "Light", "Medium" or "Dark". All colour shades can be largely grouped into one of these three catergories to differentiate the degree of modification resulting from the Shade Factor.


The following table outlines the method of catergorization by grouping some of the more commonly used Base Colour identifiers.

The Basic Modifying Factors

The Mealy Factor

Just about all coat colours have a wide range of variable shades and features. These shades and features of colour are achieved by the Basic Modifying Factors. Modifying Factors affect the colour that has already been predetermined by the interaction of the Extension and Agouti Genes, by altering the shade or tone of a certain colour, or highlighting certain attributes of a colour. Modifying Factors may also be followed by Modifying Genes in the genotype, with the end result being a completely altered colour as well as altered shade/tone/highlight, so even though a Modifying Factor technically affects only the Base Colour, they may also be seen in the phenotype of horse that does not have a Base end colour.


We are able to add further definition to a horses' colour, whether one of the three Base Colours or not, by Indentifying the Basic Modifying Factors that are at work in the horses' genotype. It is important to remember though, that most basic modifiers, generally speaking, are used only in the more exact descriptions of a horses' colour. You may find a certain colour described without the Basic Modifier[s] identified just as often [if not more often] as they are described with the Basic Modifier[s] identified. This applies to most horse registries as well, with individual registrations more likely than not lacking in these additional colour descriptive terms. Some colour registries may use some of the Basic Modifiers description[s] in a horses' registration, though this is generally quite rare. Breed registries [almost] never identify a horse using these further descriptive terms.

However, understanding the cause and affect of the Basic Modifying Factors can be extremely useful, and not only in being able to more accurately and comprehensively identify and describe coat colours, but also in more general cicumstances. For example, a breeding program aimed at achieveing the much sought after clear, golden shade of Palomino should only include Medium Shade Chestnuts and not Dark Shade Chestnuts as the dark shade can result in the "burnt" or "dirty" shade sometimes seen on Palominos, that is unwanted as a colour characteristic, and so Palomino breeders benefit greatly from the ability to differentiate between Basic Modifying Factor affects when choosing their breeding stock.

Research in this area of colour genetics is still somewhat lacking unfortunately, though continuous developments are being made and more is discovered with each study geneticists undertake. Currently, we're able to determine the general affect that most of the basic modifiers have on the end phenotype. While some of these are a certainty, others are theorised based on those certainties. There is currently a lack of information on the genetic control process[es] of some of the genes due to most of the basic modifiers being relatively complex as well as under multifactoral control. Also, it is more than likely that there may be additional Basic Modifying Factors that remain as yet undiscovered.

There are three Basic Modifiers that have an affect on all coat colours - "The Shade Factor" aka "Shade", "The Sooty Factor" aka "Sooty", and "The Mealy Factor" aka "Mealy" aka "Pangare". Other Basic Modifiers are more colour subjective and only affect one or a few colours, or in some cases only partially affect aspects of colour[s], rather than all colours.

It should also be noted that, as with many genes and resultant colour, various Environmental Factors can also play a large part in altering the end colour phenotype. Two horses with identical genotypes, for example Golden Palominos, that are subjected to different environmental influences will have very different colour phenotypes even though they are geneticall the same. For instance, if one is rugged and groomed often and the other is turned out and fed lucerne, the formers' colour will be a richer, clearer golden shade while the latters' will deepen and darken. Environmental influences affect the Modifying Factors more than any other genes, so I have specifically mentioned Environmental Factors on this page where they have the most significant impact on Modifying Factors

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The Sooty Factor is responsible for the colour modification that results in black hairs intermingled amongst the body coloured hairs. The appearance of these black hairs can be minimal and limited to certain areas on a horses' body, or may be so extensive as to result in the horse appearing "almost black" in colour. As such, the Sooty Factor is an important modification to understand and be able to identify as, depending on how intensive the distribution of intermingled black hairs, dramatic changes to end colour as well as the colours' name often results.

The Sooty Factor is most commonly expressed over the topline and shoulder. The shoulder, back and croup of the horse will appear almost black, and this "shading" affect may extend along the upper regions of the neck, and along the sides of the barrel and hindquarter. The lower sides, belly and upper legs of the horse remain lighter [the original/unmodified coat colour], so the coat colour is essentially given a 'darker on top and lighter beneath' appearance. This common combination of Sooty Factor modification is often termed Countershading and/or Black Countershading .
The Sooty Factor goes by a few different names, though the same gene is responsible for all of these colour modifications. These names are not subject to locality and can commonly be found being used by the same people for the same affect/gene, but on different basic [unmodified] colours. As with many other gene[s], this tendancy has given/can give rise to much confusion as there is a serious lack of terminology that can considered universal [This same problem occurs with many end result colour names as well as genotypical outcome descriptions].
The more commonly used names that the Sooty Factor is also known by are "Smutty", "Countershading" and/or "Black Countershading".['Sooty Factor' or 'Sooty' may or may not be mentioned in conjunction with these descriptions, however, almost all cases of Countershading and/or Black Countershading can be attributed to the Sooty Factor, the only real exception being the Dun Dilution - See Dilution Genes Section for more].


The following table outlines the resultant modifications from the Sooty Factor on some of the colours derived from a Base Colour + Shade Factor.

While the Basic Modifying Factors discussed throughout this page [and site] are in fact genes, and so a genetic control, they are generally very complex and involve multiple genes interacting to give the end result. In addition, all genes bar the Extension and Agouti Genes which are responsible for determining the Base Colour, are technically modifying genes - All horse colours being acheived by a series of genetic "Building Blocks", with the Base Colour determined at the Extension and Agouti loci essentially being the "Foundation Blocks" that all colours are built from. Each consecutive gene that comes into play further modifies the colour achieved by the previous genes by issuing a specific instruction.

Due to the complex nature and interaction of the genes discussed here, as well as the confusion that can result when the term 'modifiers' is used, the genes that modify shades and features of a predetermined colour are [generally] termed Modifying Factors, while the genes responsible for the modification of an entire coat colour by further "building upon" the instructions of another/previous gene, are [generally] termed Modifying Genes. I have used this technique throughout this site in an attempt to simplify the easy identification of each gene - Throughout this site you will find "Modifying Factor" indicative of a gene altering an already determined colour, and "Modifying Gene" indicative of a gene altering an entire colour.

Introduction

Affect of Shade On Base Colours

The Mealy Factor is responsible for a partial coat colour modification that causes the appearance of pale yellow through to pale red [or any shade in between] hairs on specific, limited areas of the body/coat. The coat areas that the Mealy Factor modifies are collectively termed the "soft parts" of the body. Specifically, these areas are the belly/underside of the barrel, the flanks, behind the elbows, on the inside of the legs, on the muzzle, over the eyes, and in some cases, the hair of the inner and possibly outer edge of the ears. The Mealy Factor can occur on all coat colours [ie. background colours], and varies from being so minimal that its' easily missed as having contributed to the outcome colour of the horse, right through to so extensive and intensive that the result is a dramatic paleness to all of the ventral areas of the body.

The Mealy Factor is yet another gene that is commonly known by many names. Along with the English terms "Mealy", "Mealy Mouth", "Mealy Muzzle" and "Toad Eye", the South American and Spanish term for the Mealy Factor is "Pangare". Those localities using Pangare as the descriptive term for this unique colour modification are generally more consistent in the terms' use as a specific colour identifier and/or description.

The following table outlines some of the various colour modifications resulting from the Mealy Factor affecting Base Colours.

 

Dapples, or dappling, is the term attributed to a pattern-like network of dark and light areas on the coat. The indiviual dapples will usually be somewhat circular in appearance, with lighter shaded areas in the centre and darker shaded peripheries. In rare circumstances this is reversed, and the centre of the dapples will be darker than the outer peripheries - This phenomenon is termed "Reverse Dappling/Dapples".

Dapples can occur on any colour, though are more commonly seen on those individuals who express the Sooty Factor due to the contrasting black/dark vs light hairs. It is an extremely common occurence, with most horses receiving good nutritional feed, in good health and condition displaying various degrees of dappling. The degree and depth of dappling expressions can also be seasonal, though this is not always necessarily so.

The genetic control of dapples as yet remains undetermined.

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What Is A Basic Modifying Factor?

The Shade Factor

Affect of Sooty On Base Colours

The Shade Factor gives tone & depth to a specific colour - Light, Medium & Dark Shades

The Sooty Factor is responsible for almost all of the colours falling into the colour classification "Brown"

The Sooty Factor is also commonly referred to as "Smutty" or "Smut", "Countershading" and "Black Countershading"

Affect Of Mealy On Base Colours

Mane & Tail Colour On Chestnuts

The mane and tail colour on Chestnuts has a wide range of variabilities. Just as often as not, the mane and tail colour on a Chestnut individual will be visibly quite different to the shade of the body. This section deals with those individuals whose manes and tails are not the same, or similar in, shade across their entire coat, mane and tail included [the uniform body, mane and tail coloured individual being controlled by/at the Extension Locus].

The individuals possessing the altered mane and tail traits may have a uniformity in shade to both their mane and tail, or they may have a number of colours, or shades of one or more colour/s, throughout their mane and tail. The darkest of manes and tails on Chestnuts are almost black, with the other end of the spectrum having the palest of yellowish through to white manes and tails. Generally the colour[s] and/or shade[s] that appear in the mane will be the same colour[s] and/or shade[s] that appear in the tail, and vice versa, though this is not always the case.
Though the darker shades are just as prevalent as the lighter ones, the darker mane and tailed Chestnuts are often misidentified as another colour altogether, and so there is a common misconception that the lighter shaded individuals are much more prevalent than those of the darker shades and/or colours.
The wide variety of possible colours and colour combinations in the manes and tails of Chestnuts, and identifying the cause, has confounded geneticists performing the studies for a long time. There have been widely publicized reports that claim specific genes to be responsible for [some of] the altered mane and tail colour of Chestnuts, but to date, none of these have actually been proven - Though they haven't been disproven either. So the result is that we have many theories as to the genetic control of this trait, but no definitive evidence to support any of the theories.

There are basicially two main leading theories behind the genetic control at the moment. There are supporters of each theory of course, and each has its' own "pros and cons" to back them up, but both are essentially an educated guess by those in the know at the moment. There are currently a number of studies being undertaken to determine the cause of alternate colouration of Chestnuts' manes and tails, and there have been quite a few studies also performed over recent years. The more recent studies do suggest that the genetic control of this trait is a result of the first theory. This evidence though is only a tentative indication in that direction and it has not been proven as factual as yet.
At this stage there is actually no factual evidence that confirms or excludes either theory at this point.

 

The first theory claims that the genetic control for these altered mane and tail colours on Chestnuts is a polygenic trait [meaning that it is controlled by multiple genes at multiple loci], that is identifiably separate [though may or may not work in conjunction with], and epistatic to [meaning it will suppress the phenotypical expression of the mane and tail "instructions" located at the Extension Gene when the genes and alleles appear in the correct/appropriate combination] the Extension Gene .

The second main theory is that of a singular gene occurring at a singular locus is responsible for these altered mane and tail colours on Chestnuts - The gene behind this theory has been named the "Flaxen Gene" after the term that has been commonly attributed to lighter mane and tailed Chestnuts for many decades. It is suggested that the Flaxen Gene occurs at the Flaxen Locus. The theory claims that the Flaxen Gene is a simple [meaning the colour is controlled by only the one gene at a single locus] recessive gene that is only expressed in the phenotype when it exists in homozygous recessive form and therefore can remain hidden in the genotype for generations.
The Flaxen Gene theory is currently widely accepted by the majority of equine colour enthusiast populations across the globe as being responsible for the alternate mane and tail colour trait of Chestnuts due to this theory being extensively publicized as being factual and evidenced when, to date, it has not actually been proven at all. That this theory is proven fact is a very common misconception.

The are groups in support of each theory, each with their own 'problems' with the alternative theory. The issue that seems to be debated the most though, is what appears to be a fault that lies with the Flaxen Gene theory. The Flaxen theory essentially suggests that there is a "switch" at the Flaxen locus, with the options being "on" or "off" and as with all genetic 'switches', the instructions, which are in this case the alteration of the colour of the mane and/or tail, are either implemented [switch in on position] or bypassed [switch in off position]. The 'problem' with this theory arises because the basic principles of colour genetics and the associated 'rules' of such that would apply to the Flaxen theory, would result in there being only two options at the single controlling Flaxen Loci - Option A is 'switched off', the gene is bypassed and the Chestnut horse has a uniform colour across the body, mane and tail ie. a 'normal' Chestnut colour. Option B is 'switched on' and the 'instructions' of the Flaxen Gene suppress the uniform colour [of Option A] and implement the alteration of the mane and tail colour. The problem is that for only these two options, and therefore the Flaxen theory itself, to be correct, Option B would have to result in an altered mane and tail colour that has very little variation in shade, and almost no variation in colour. For example, the mane and tail would/should be altered to a yellowish colour. It may possibly be a few shades darker or lighter in other individuals, but would/could not be a completely different colour, ie. could not be black, brown, red or a mixture of those etc. And as we have just as many Chestnuts with these completely different, dark coloured manes and tails as we do Flaxen Chestnuts [lighter coloured manes and tails], the Flaxen Theory vs the Polygenic Theory remains in debate.
It has been put forward that the Flaxen theory is correct and that there are other gene loci that are responsible for the darker shaded manes and tail, but this is considered a long shot as it is quite common for a Flaxen Chestnut bred to a Flaxen Chestnut to produce progeny with a mane and tail of a darker colour, or a mixture of colours and/or shades.
Either way, we don't know at this stage which, if either, theory is accurate, and only time will tell us the true source of this colour trait!
Regardless, there is factual information that exists now that can be attributed to this classification of equine colour.

Generally the darkest of colours, the almost blacks and mixtures of black and dark reddish pigmented hairs, will usually appear in conjunction with one [or more] Basic Modifying Factors, resulting in the body shade tending towards the dark side as well. The mane and tail will likely be a similar colour to most of the body colour/shade. The darkest of these horses, those with black or almost black across the whole body, are often mistakenly classified as Blacks, Black-Brown or Sooty/Mahogany bays. Upon closer inspection though, the horse will be seen to have the 'normal' Chestnut shade on the lower extremeties rather than the dark hairs required for these colour classifications. Sometimes this normal chestnut colouring will be limited to the coronet, pastern, fetlock and/or feathers only, but it will still most definitely be present. The individuals of these darker shaded colours are usually termed "Black Chestnuts" or "Liver Chestnuts" depending upon the shade and depth of colour.

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Bend Or Spots

This phenomenon of horse colour was named for the Thoroughbred "Ben d'Or" who displayed these unusual markings. Most commonly seen on Chestnuts and its' Base derivatives, yet still seen at times on all colours though just not as visibly identifiable nor as common, Bend Or Spots are the appearance of random dark spots, or darker patches, [usually] on the Chestnut background colour. Most chestnuts have one or more of these dark spots. Depending on the Chestnut shade of the horse they appear on, they are sometimes dark red, sometimes dark brown or black. They may occur singularly or in a small number through to that many that they are misidentified as Dapples [See Above]. They can be small and inconspicuous right through to large and unmistakable, and scattered across the entire body. I've heard people complaining about a stain on their irridescent chestnuts coat, only to have found later that the stain is in fact a Bend Or spot, which support the evidence that they can be present at birth but also develop with age. They occur in most, or all, breeds with Chestnut horses, and the genetic control of these spots remains undetermined.

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Dapples

There are two basic theories of the genetic control of the altered colour of chestnuts' manes & tails

Basic Colours

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Please Note: Some of the terms used above are universal while some are locality specific - See Introduction page for more information.

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The Sooty Factor & the Colour Classifcation "Brown"

The Mealy Factor causes the appearance of pale yellow through to pale red hairs on the ventral areas of the body

The Sooty Factor causes the appearance of Black hairs to be intermingled with the Base/background body colour

The Mealy Factor is also known as "Pangare", "Mealy", "Mealy Mouth, "Mealy Muzzle" & "Toad Eye"

The affect that results from the Mealy Factor being superimposed upon the original 'background' colour of the coat will - or should - almost always result in a name change to the resultant outcome coat colour. Further problems with [more] nonclemanture of the multiple names used to describe the affect of a single gene, and the same problems already associated with the lack of universal use of terms for other Basic Modifying Factor modifications, all adds to the confusion surrounding these colours.
Sorrel vs Chestnut is a great example of the confusion the nonclementure of the past one hundred years as resulted in!
The Mealy Factor is relatively important in the Chestnut classification of colours. Sorrel is used in some localities [primarily in the Americas and Canada] instead of and along with Chestnut. In some areas the meaning is [generally] a "lighter" shade of Chestnut uniform across the entire coat [That is, a Chestnut base with the "Light" Shade modification - See 'The Shade Factor' above] that is also called Pseudo Palomino in the same localities, while in other areas the names Sorrel and Chestnut mean much the same coat colour with the use of either being more of a personal preference rather than indicating different coat colours. In addition, the term Sorrel has also been noted [in various localities] to be indicative of any Chestnut not uniform in colour shade and any Chestnut with a lighter mane and coat [this colour is/should technically be termed "Flaxen Chestnut"]. To be techinically correct, the name "Sorrel" is indicative of the colour resulting from the Mealy Factor superimposed upon a Chestnut base [Chestnut + Mealy/Pangare]. The term "Chestnut" should be reserved only for those horses with a uniform red pigmentation to the coat across the entire body, while "Sorrel" should be reserved for those with the lighter, paler ventral areas resulting from the Mealy Factor. The terms "Light Chestnut" and/or "Pseudo Palomino" should be reserved only for the Chestnut + Light Shade individuals.

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Mealy Factor Nonclemanture Notes

The Mealy Factor & the Colour Classifcation "Brown"

The many colours that are lumped under the classification of "Brown" can be catergorized into three groups. The main causative being the Sooty Factor superimposed upon a Bay base to varying degrees of expression - See "The Sooty Factor" section above for further information. The least responsible for the Brown outcome colour is the recently proven but long standing theory of the Dominant Black Allele [or Extension Black] residing at the Extension Locus - See Base Colours Page for more information on the Dominant Black Extension Allele.
The causative of Brown outcome colour[s] that lies between the Sooty Factor and the Dominant Black Extension Allele in prevalence of cause is that of the Mealy Factor superimposed upon a Black Base Colour. The result is a Black horse with reddish hairs on the muzzle, belly, flanks and upper legs [ie. ventral areas] etc of the horse - All of the areas that are left lighter than the main body colour when a Bay based horse carries the Sooty Factor modification are affected by the Mealy Factor superimposed upon Black, with both of these resulting in an almost identical outcome colour modification to the coat - Making these two colour modifications are a great example of how difficult it can be to determine the genotype of a horse by phenotypical evaluation alone. They are completely different in genotype, yet almost identical in phenotype, and as such can produce a very similar as well as vastly different array of colours in their progeny dependant upon the genotype and phenotype of the other parent.

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The coat colour modification resultant from the Sooty Factor is [almost exclusively] responsible for the group of colours that are lumped under the classification of "Brown". This group of colours is quite substantial, with just about every shade of colour that falls between Bay and Black generally being termed Brown by many people around the globe. Just about all of the Brown classification of colours are the result of a Bay Base Colour with a Sooty modification. However, it should be noted here that, along with the Sooty Factor modification, two other causatives have further been identified, thus far, as being behind [some] of the colours within the Brown classification[s]. See Below for Brown causatives.


The second colour modifier that results in [some] Brown coat colours is the Basic Modifying Factor known as "The Mealy Factor", or "Pangare". Further information on how this factor modifies the coat colour to give the appearance of Brown can be found directly below.

The final proven causative of Brown coat colouring is an allele that has been termed "Dominant Black", or "Extenstion Black", and resides at the Extension Locus [ie. "Dominant Black Extension Allele"]. This Dominant Black Extension Allele has been proven to be prevalent among the Arabian breed, but is to date still considered as rare amongst other breeds.
Further information on the Dominant Black Extension Allele can be found on the Base Colours page.

 

Theory 1 - Chestnut Mane & Tail Colour is Polygenic with identifiably separate genes epistatic to the Extension Locus

PLEASE NOTE: The following section is NOT in reference to the Gene known as 'Silver Dapple' [aka 'Taffy' aka 'Silver'] & refers to only with the Basic Modifying Factor 'Dappling'/'Dapples' - The 'Silver Dapple Gene' is dealt with in the Dilution Genes Section.

Reading that may assist with Understanding the Information contained on this page
~ Introduction to Genetics ~ Genetic Terminology ~ Genetic Shorthand ~

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Modifying Factors give the Base Colours their shade, tone, depth and highlights etc.

Modifying Factors further define the end colour of an individual horse but usually aren't included in the genotype

Understanding the Modifying Factors affect on colour can be beneficial for Owners & Breeders alike

Modifying Factors are under complex, multifactoral control & not all of them are understood on a genetic level yet

There are three Modifying Factors that affect all horse colours - 'Shade', 'Sooty' & 'Mealy'

PHOTOS WANTED - For all of the colours named in the table below

PHOTOS WANTED - For all of the colours named in the table below

The Sooty Factor almost always results in dramatic change in colour & name

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The external environment plays a large part in the Base Colour + Shade Factor result

PHOTOS WANTED - For all of the colour named in the table below

The Colour Classification "Brown"

The colours that are generally lumped under the catergory of Brown usually result exclusively from three different genetic interactions.
It is important to remember that there is no singular cause of the phenotypical colour we describe as Brown in horses [as aposed to other species such as canines, where the flat brown chocolate colour seen in Cocker Spaniels for example is the result of a singular locus].

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