The genetics of bay, black and chestnut

[chev]

Struck me that it might be an idea to explain how the base colours work too! :D

These are a lot simpler than you'd think. To start with, all horses are genetically either black or chestnut as a starting point. It works like this....

Strictly speaking, a gene isn't dominant or recessive. A gene contains codes for development, nothing more. Each gene, however, contains what's called 'alleles' - these can be dominant or reccessive. There is no separate gene for red and black - they're both caused by the same gene. It depends on whether the horse carries 2 reccessive alleles of that gene (e) or a dominant allele of the gene (E). Put very simply - it depends whether the gene is 'switched on' for black or not.

If a horse carries the dominant allele - E - he'll be black. If not, and he has instead two reccessive alleles - e - he'll be red (or chestnut). Dominant means he only needs one E allele to show that colour - in order to show red he must have two copies of the reccessive form e.

So, there's the start - if a horse has ee, he'll have a red base. This horse can only ever contribute e (red) to a foal.

If a horse has Ee, he'll have a black base - but if he bred, he could contribute either E (black) or e (red) to the foal. This is why black can throw non-black foals.

If a horse is EE, he's homozygous for black. This mean that he can only contribute E to a foal - breed two EE blacks and you'll only ever get black foals.

And onto bay....

Bay is caused by a gene called Agouti. Again, whether a horse carries bay depends on whether the allele for this gene is dominant (A) or reccessive (a) - whether bay is 'switched on', in other words.

A horse with the switched on copy of bay (A) will carry bay. A horse without (a) won't.

Agouti works by restricting black pigment to the points - legs, mane and tail. Because it only works on black, a chestnut horse can carry bay without showing it. A black will always be bay if it carries bay.

This is how a bay foal can be born to a black parent and a chestnut parent - the black passes on E for black, the chestnut (carrying an 'invisible' A) passes on e, which doesn't show on the coat colour, and A, which causes the black pigment to be restricted to legs, mane and tail - so there's your bay foal.

A horse that carries two A alleles will only ever throw bay or chestnut foals, never black, even to a homozygous black - because they will always pass on A that causes black to become bay.

All other coat colours are caused by genes and their alleles that modify these base colours. For example, cream on a red base to give palomino; tobiano on a black base to give piebald; roan on a red base to give strawberry roan.

[larri]

I daren't even open the other colour threads...my poor mind is boggling at this one.....waaaaay over my head :o

[casey]

Woah....Ok.

I understand, that Black and Chestnut are the only true colours.

I bred my black mare to a chestnut stallion and got a dark bay colt:confused: Now, i know NOTHING about genitics, but thought maybe, he would come out either or.

How has his colour been influenced? I genuinely am interested.

My mare's dam was chestnut, and her sire black.

My colts Sire Luidam's dad was also chestnut.:)

[casey]

Here is my colt.

Also, if I bred my colt to my chestnut mare, what colour would the foals be?:)

[Mossy]

Fascinating Chev must open the other thread. Explains why my carrot head came from a black and a bay.

[casey]

Sorry Chev, just re-read your 1st post and you explain my bay colt clearly.:o :)

[chev]

casey - my dark bay colt came from a black sire and chestnut dam... :D Works like this.

The black parent (the dam in your colt's case) is E - one allele for black - possibly two, we don't know, and it doesn't honestly matter. The black allele is dominant to the chestnut anyway so the horse appears black regardless of whether it's Ee or EE.

The chestnut parent is ee - has to be in order to appear chestnut. In this case (and in the case of my colt too) the chestnut also carries a switched on allele for bay - that is, A. It's not visible on the chestnut because there's no black pigment to restrict.

So; your colt got e from his sire, and E from his dam - making him black. He also got A from his sire, which restricts the black to the points.... and hey presto you get bay from black x chestnut.

The genetics of dark bay are a bit murkier - we don't honestly know what causes dark bay as opposed to bright bay, for example.

Your colt is genetically EeAa - this means he can throw bay, black or chestnut (depending obviously on the mare he's put to).

[Arabmare]

Brilliant thread!

Weve always wondered (and been asked) If AH Mahal is homozygous black. His breeding is almost all black all the way through! How would we find out if he has that dominant gene? Does that mean if he is he can only produce black (all the time) if the mare is proven Homozygous too? Hes had 2 foals out of bay mares and the foals were bay does that mean he is not Homozygous black or it was the mares genes making the foal bay? Confuzzled!:o

[chev]

Honozygous black will only breed black every time when put to another black, or a chestnut that doesn't carry bay. On a bay, or a chestnut with the bay gene, there's a chance of a bay foal - if put to a homozygous bay, the foal will always be bay no matter how many black genes the parents carry!

There is a test available to ascertain whether a horse is homozygous for black - but it's important to remember that even a homozygous black won't throw black every time unless they're used on another black.

So - if AH Mahal is homozygous for black, he'd be EE. He can only pass on the allele for black, not red. On a chestnut mare that's ee (two red alleles) and aa (no switched on bay allele) you're guaranteed a heterozygous black foal (Ee).

On a chestnut mare that carries one bay allele (eeAa) there's a 50/50 chance she'll pass the A on - so although you're guaranteed the base colour will be black, there's also a 50% chance the foal will get A, and be bay.

On a chestnut mare with two A genes, the foal will only ever be bay - it'll get E from AH Mahal, and eA from mum - no blacks at all from this pair.

If AH Mahal is Ee (and it is possible, even with generations of black breeding. Both parents would have to pass on e for baby to be chestnut) then there's only ever a 50/50 chance he'll pass E for black on - so the chances of a black foal are reduced again. If he is Ee, and put to another black that's also Ee, there's even a 25% chance that the foal would be chestnut!

[ruthncallie]

Ok i think i understand. But i have a piebald, how does that one work?

[horseygal90]

Hm... Intereesting! Makes good reading that.

If I've read right, then a piebald would be EE and then tobiano, so would throw either a black, or piebald? Gah. Confusing. (But I'm pretty sure, not a chestnut or bay)

I'm probably wrong.

[chev]

That's one possible black tobiano. It could also be Ee and T (tobiano). They have the same chances of throwing black as a black with no tobiano, but there's also a 50/50 chance they'll throw tobiano (or, if they're homozygous, the foals will always be tobiano patterned).

A piebald is a black horse (so Ee, or EE) with a Tobiano gene on top of that.

[Alle]

I've been reading all your color threads with interst! Very confusing and facinating.

My mare is a red bay and has a faint dorsel stripe which actually shows much darker in the winter. Does she have a dunning gene somewhere to cause the dorsel do you think?

What a great subject!

Alle

[chev]

Dorsal stripes are not just a dun thing - they can occur in any colour. They are usually very sharply defined in a dun though - as if someone's drawn a line down the back in felt pen. On non-duns, they do tend to be a bit more blurry and indistinct - this type of dorsal marking is known as countershading.

I'd say your mare is probably a bay - certain red duns can have a very red body, but their legs, manes and tails won't be black, as dun also dilutes black pigment.

Dun is a simple gene - a horse either has dun, or it doesn't. If it does, it'll be dun in colour - with at least two of the dun charcateristics.

[virtuallyhorses]

You're forgetting brown ;) which is also EE or eE or Ee and black\brown horses may also be aaeE (from Bay)

Strictly speaking there is only one base colour - red or black (whether that is e or E is irrelevent as that nomenclature simply defines whether the gene is dominant or recessive so the red and black 'gene' is identical) depending on whether you believe that red is washed out black or black is very undiluted red :)

[WelshJumper]

How do the geans {sp}work? As we have had the family of Duns,

Dam was a Dark Golden dun, her foal Golden dun, her foal Dark dun {mouse} and agane from the same mare {golden} a Chestnut Dun {almost creem} so would the next be lighter or does it depend on the sires col?

[Alle]

Originally posted by chev
Dorsal stripes are not just a dun thing - they can occur in any colour. They are usually very sharply defined in a dun though - as if someone's drawn a line down the back in felt pen. On non-duns, they do tend to be a bit more blurry and indistinct - this type of dorsal marking is known as countershading.

I'd say your mare is probably a bay - certain red duns can have a very red body, but their legs, manes and tails won't be black, as dun also dilutes black pigment.

Dun is a simple gene - a horse either has dun, or it doesn't. If it does, it'll be dun in colour - with at least two of the dun charcateristics.

Heh, so her color is nothing very special then? ;) I was wondering about the stripe, b/c I have seen the faint, indistinct dorsels on several horses, so this clears it up. Thanks!

[chev]

Originally posted by virtuallyhorses
You're forgetting brown ;) which is also EE or eE or Ee and black\brown horses may also be aaeE (from Bay)

Strictly speaking there is only one base colour - red or black (whether that is e or E is irrelevent as that nomenclature simply defines whether the gene is dominant or recessive so the red and black 'gene' is identical) depending on whether you believe that red is washed out black or black is very undiluted red :)

How could I forget brown! :o

Or seal... thought to possibly be a variety of bay modified to some extent (a large extent in the case of brown) by the sooty gene.

And yes - strictly speaking there is only one base gene - but I didn't fancy explaining how a horse is only one base colour - red or black....

I stand corrected Viv! ;) :D

[chev]

Welshjumper - it depends on the base colour. Remember that dun is only a modifier - it dilutes whatever base colour a horse is.

So, if you take dun out of the equation, your family of duns would be a family of bays, black and chestnut. Add the dun gene that's obviously been passed down from the mare, and you have your family of duns.

As an example;

Bay mare has bay foal

Bay mare has chestnut foal

Bay mare has bay foal

Bay foal has black foal

Now add dun -

Golden dun mare has golden dun foal

Golden dun mare has red dun foal

Golden dun mare has golden dun foal

Golden dun foal has mouse dun foal

See how it works?

[virtuallyhorses]

Originally posted by chev

And yes - strictly speaking there is only one base gene - but I didn't fancy explaining how a horse is only one base colour - red or black....


:D I understand completely, its often so much easier to give the half answer when on a subject where a reasonable amount of background info is required - I was only teasing ;) :D

I would correct the person who said that dorsal stripes are not a dun thing - indeed they are! when you see them in other colours they are the evidence (usually) of a recessive dun gene for instance EeAaCCDnndDnnd would be a bay horse and may or may not show any traits of the recessive Dun gene. The exception is a foal which starts out with a dorsal stripe which then fades.

The dorsal stripe (and dun colouring) are known as 'primitive' because they tend to appear on those older breeds such as tarpans which still show coat colourings that help them blend in to the steppes and grasslands from which horses evolved and also to reappear on horses when they are bred back to those roots. Sort of the equine equivalent of the 'little yellow dog' to which most mongrels revert.

[Shiny McShine]

Great topic!

I have always been fascinated by colour genetics. There has always been one aspect however that my mind has stumbled over, perhaps someone can clarify for me...

It is the definition of a bay vs. the definition of a brown and where you draw the line between the two? I know some geneticists consider brown to be a type of bay. I tend to feel that the seal browns are separate from bay, but that some "brown" horses with black points are just shades of bay. What do you think?

Also does the agouti series influence chestnut colour? I know that chestnut horses carry agouti and in one of my books it says that the shades of chestnut are caused by agouti, ie. liver, standard orange/brown, red, and sandy chestnut. Has anyone else heard/read this?

[chev]

Originally posted by virtuallyhorses
I would correct the person who said that dorsal stripes are not a dun thing - indeed they are! when you see them in other colours they are the evidence (usually) of a recessive dun gene for instance EeAaCCDnndDnnd would be a bay horse and may or may not show any traits of the recessive Dun gene. The exception is a foal which starts out with a dorsal stripe which then fades.

But then we are faced with all the duns who are genetically dun, but show no dorsal stripe, along with the 'layman's' dorsal stripe on non-duns, which is in fact a form of counter-shading caused by the sooty gene (probably among others).

A clear, sharp, true dorsal stripe is certainly a dun characteristic - but there are also 'pseudo' dorsal stripes that really just confuse the whole issue.

One of the things that really fascinates me is the dun gene. In spite of the fact that there is, almost without doubt, a simple dominant dun gene, it's also been shown that horses left to breed for several generations without human intervention 'develop' dun colouring. That would support the theory of a reccessive form of dun. Dun as described here is described in the simple dominant form though - mainly to try and keep it simple. In order to register a horse as dun it must show the characteristics of the dominant form of dun - including the need for at least one dun parent.

ShinyMcShine - the answer to that one really depends on which theory you subscribe to. It has been shown in research in France that seal brown actually carry Agouti, but are not considered bay because two Seal browns will never produce a bay foal. Current thinking is that there are in fact four alleles at the Agouti locus instead of simply A or a for bay or not bay.

Thsi would mean that at the Agouti locus we now have - A (bay), a (black), A+ (Wild-type bay - where the black on the legs is mixed with red, so points appear paler - may also be linked with the lightening of flanks and muzzle which may also be caused by or in part by Pangare or Mealy gene) and a^t - Seal brown, where Agouti partially restricts black.

Agouti, because it affects black pigment, doesn't influence chestnut. Chestnut can, however, be influenced by other genes - Pangare, Mealy and Sooty among them. It's possible that liver chestnuts are red base with sooty modifier - again, it doesn't satisfactorily explain all the variations. I have 3 liver mares. One is a dark reddish liver, with mane and tail the same liver colour. One has darkened over the years and now has mane and legs so dark they can easily be mistaken for black at times. The third is a gingery liver with a grey mane and tail. It would seem there is more than one gene at work to cause the variations in shade.

[virtuallyhorses]

Browns are actually quite easy to identify - by their brown noses. Take a look at the horse on the new rider logo and he has that distinctive brown nose of a brown. Many ask whether Imp is a black horse (and although I could answer yes because there is no black\brown genetic distinction) he is quite easily identifiable as brown because of the brown nose (and the red hairs in mane and tail) and of course he will fade to brown in the summer.

A 'black' horse showing the typical brown nose and red hairs of the mane that distinguishes him as a brown.

BTW One of the big things to remember with all this genetic 'science' is that many of the genes and alleles we are discussing are theoretical only! Only a few genes have been identified and the majority of modifiers have not.

Also genes are only part of the story - humans only have two genetic eye colours brown or blue but look at the diversity of eye colour! :)

[chev]

Originally posted by virtuallyhorses
BTW One of the big things to remember with all this genetic 'science' is that many of the genes and alleles we are discussing are theoretical only! Only a few genes have been identified and the majority of modifiers have not.

Also genes are only part of the story - humans only have two genetic eye colours brown or blue but look at the diversity of eye colour! :)

Very true. Genetic tests have only actually identified genes for black/red (Extension), Agouti the bay gene (A), cream (called the MATP gene) and frame overo (called the EDNRB gene). Although horses can be tested for tobiano homozygosity, the actual tobiano gene has not been identified yet - the test looks for two protein markers closely linked to the gene, in conjunction with 3 generation pedigree analysis.

All other genes are still, as Viv says, in the realms of scientific theory....

A black horse with a brown nose (like Imp) can be tested to ascertain whether or not it is black or bay, by identifying the red factor. Some horses that are genetically black can appear more brown - sunlight can fade black coats, or they may be carrying a single cream gene that causes the coat to appear a slightly browner black. Generally though if a horse has brown on its muzzle, or near the eyes, or the flank - it's not black.

It's the theory aspect that causes most confusion. Because colour genetics is by and large mostly theory, there are also more than one system of notation in use. Sponenberg, for example, theorises that flaxen is a reccessive gene (similar to chestnut) which causes red mane and tail hair to dilute to blond. He believes this accounts for the colour in the Hafflinger, where flaxen chestnut is the only colour - if both flaxen and chestnut are reccessive that would explain nicely why no other colours occur. Each horse would pass on one copy of e and one copy of f so every foal is homozygous for e (making it chestnut) and f (what Sponenberg terms ruano - flaxen) making it flaxen chestnut. It also explains why two non-flaxen horses can produce a flaxen foal - same way two blacks can produce a chestnut. But this is just theory, and notation used only by Sponenberg, not Bowling, Davis or other geneticists. Another of Sponenberg's theoretical genes is F - the Tostado gene, which causes red points on chestnut horses. Again, based on observation, the theory would seem to be sound - but it is just theory, and until these genes are identified (or the action they supposedly cause attributed to another gene or group of genes) it will remain theory.

Still very interesting though....

[White-Blazes]

Blimey Chev, where do you find all this info;)

[chev]

I read a lot! :D The really sad part is that I know most of this stuff off by heart now.... there are some good books on genetics (not just colour although there's a couple that deal with colour and nothing else too) if you want to learn more.

[Bronya]

Just a curious question (or two) is brown a dark red or light black - with reference to the base colour being either red or black.

And, why does a bay's coat get lighter and more red in the summer?

[Jaimee]

A brown is a black based horse as is a bay.

Most colours change appearance from season to season. There is no specific genetic "reason" as such known. But there are a lot of factors that will influence the appearance of a colour. Seasonal changes in hair length and diet can be contributing factors.

[chev]

Some red-based horses can appear very dark brown and even be mistaken for black-based horses, just as some black based horses wilol fade out so much they appear red. The difference is that seal brown horses will have black points; red based horses cannot produce black pigment and so will have brown points too.

There are brown horses that don't appear to have black points but who test positive for a black base. Causes vary; some are a particular shade of agouti that seems to restrict black pigment in a different way, some may have another modifier at work (like cream; cream on black usually doesn't give much visual clue to it's presence, but it can also result in a faded brown-looking horse).

As Jaimee says, seasonal variations occur in most colours; sweat and teh sun fades some colours, the diet usually changes to an extent, which will affect coat colour, and winter and summer coats do usually vary in shade anyway.

[pengapenga]

A very fascinating subject. As I am now getting ready to buy some broodmares to start the friesian warmblood breeding programme the subject is even more fascinating.

I ideally would like to breed the horses darker preferably black or as close to black as possible.

Frits is black, his nose is black the only 'red' (more of a maroon colour than red)is at the tip of his tail after summer. In the friesian breed it can cost a stallion a studbook breeding licence if he has the chestnut gene (or active chestnut gene, as I am not sure how it all works). The stallions when given the nod will be tested for this gene.

Now with that thought in mind whilst shopping for broodmares I have been looking for horses that would compliment Frits. I am looking at horses that are bay or brown in the hope that the darker colour of the mares and the black of Frits will produce dark horses. Am I on the right track?

Recently I saw a broodmare that fitted almost all of the criteria except that she was grey. I was not sure how grey to black would work - but I guess I should ask this after I read the grey sticky:)

[mayoguinness]

My head hurts, I think I'll just stick to the Natural Horsemanship and leave the colourings to you.........Mayos a chestnut, hehe, as long as I remember that I'll be fine!!

[holz]

Really confused!:confused:

My grey mare had a chestnut foal. We put the mare to a brown stallion. Dams dam chestnut dam sire grey.
Sire dam dont know sire sire brown

Im looking to put her to a chestnut stallion next time Who sire was bay. What colour am i likely to get??

[chev]

Grey mare only has one copy of grey, which she did not pass on to the foal. She did however have one copy of chestnut, which she passed on to the foal. Stallion also had one copy of chestnut which he pased on; so you get a chestnut foal.

We don't know what colour your mare is under the grey, but we do know she has at least one copy of chestnut, so put to a chestnut stallion you'd have a 50% chance of chestnut at least. There's also a chance she carries black or bay, so you might also get a bay or black foal.

[Welsh_Girl]

Wow this is so interesting:)

I'm dieing to know; I have an appaloosa mare, bred from an appaloosa dam by a bay TB stallion. If I bred her to an appaloosa stallion what are my chances of getting a spotty foal?

[maverick927]

My horse is very interesting.

Dam piebald, full feathers
Sire piebald, fulls feathers

Foal - Black! No feathers!


After a lot of research, its turns out my mare is a throw-back to her great grand sire, Ard Allez Cat, a pure black TB

[chev]

Wow this is so interesting:)

I'm dieing to know; I have an appaloosa mare, bred from an appaloosa dam by a bay TB stallion. If I bred her to an appaloosa stallion what are my chances of getting a spotty foal?

It depends really. Does your mare have spots? If so, bred to a stallion with spots there's a chance of spots, no spots, or a fewspot (fewspots are homozygous for the spotting gene Lp). There's also another aspect, which is the expression of white - frosting, blankets and so on (PATN1).

Bred to a fewspot stallion guarantees either a spotty foal or a fewspot.

That's a very basic start anyway...

Maverick - your mare is not a throwback. Both her parents have one copy of tobiano, the splodgy gene. In your mare's case, neither passed it on, so she is solid. The first foal I bred from my black and white stallion, to a bay and white mare, was... solid chestnut! There's a 25% chance of a solid foal from two parents who both carry one copy of tobiano.

[titch_]

OOOOH I get it :D!!!!! thanks chev!

[Welsh_Girl]

Hi Chev

She's 12 now and still has spots, she's currently grey (white) with black leopard spots. Her dam was marked like this when I saw her at about 20 yoa.

When my horse was born she was black with a white rump and big black "splotches". Another pic i saw of her at five she was blue roan with black flecks through the coat and dark legs. When I bought her 4 years ago she was a very well covered leopard spot (white with lots of black spots of different sizes.

I'd be interested to know why all the changes of colour throughout her life, could it indicate many different appaloosa genes?

[titch_]

is it Like eye colours? that u study in Biology and the little chart for blue and brown Eyes
B - Brown
b - blue

BB Bb
Bb bb

So does black and red look like this???

BB Br
Br rr

[chev]

Sort of. The gene controlling coat colour is the Extension gene. It contains the alleles which say whether a horse can produce black pigment or not. If it can, it'll have at least one E allele. E is a simple dominant, so a horse only needs one copy of E to be black based. If both alleles within the Extension gene are e, it means the horse cannot produce black pigment, only red. Red is reccessive and is noted as ee.

A horse with two alleles that allow black to be produced (EE) will only ever pass E onto a foal, so all foals will be black based. An Ee horse can also pass on red (or, not-black, really) so can produce chestnut based foals. So possibilities are EE, Ee, and ee.

All coat colours other than black and red are down to genes that modify the black or red base. Bay is one; in black horses it restricts black pigment to the points. In chestnut horses it does nothing visually, but means a chestnut can produce a bay foal if put to a black. In black horses, it keeps black to the mane, tail and legs, and leaves the body red. Cream is another that alters the appearance and production of pigment in the coat, as do dun, champagne and silver. They are modifiers. A bay horse might be EE AA, Ee AA, EEAa, or EeAa. A buckskin might be Ee Aa Crcr, or EE Aa Crcr, or EE AA Crcr... you get the idea!

Then there are pattern genes; they control the white and spotting patterns. The KIT gene contains several of these alleles; tobiano, sabino, roan etc all at different loci.

So it's slightly more complicated than blue or brown eyes, but the theory is the same.

[lachlanandmarcu]

Following on from this, do you know if the pattern genes have any statistical liklihood like the colours do eg if I bred my pure Haflinger (chestnut with flaxen mane/tail) to a strawberry roan or chestnut roan what might I get odds wise???

[chev]

You'd have a 50/50 chance of a roan if put to a chestnut/strawberry roan.

[titch_]

Chev what would you get with a black and a bay??

[chev]

Black, bay or chestnut.

It depends on the exact genetics, but if both black and bay are hiding chestnut, you have a 25% chance of an orange baby. If neither have chestnut, or just one, you won't get chestnut.

Say neither has chestnut; if the bay has two copies of bay, baby will be bay. If the bay has only one copy of bay, you have a 50/50 chance of black or bay.

[titch_]

oooh i see thanks :D (belle is going is going to a nice black stallion in april)

[lachlanandmarcu]

many thanks for the roan/chestnut response.....food for thought,,,,:)

[Jen_e_Jen]

Heres a question for you chev, what determines the color of bay? My geldings dam was a gorgeous dark mahogany bay, and his sire is black w/a red gene(Sire's dam was dark bay as well). Jackson is a much lighter copper bay almost the color of a penny when freshly shed out, he does have some countershading but there is no dun in his lineage so I know it's not a "dorsal stripe" as w/Dun. Do both parents have something to do w/the color bay, or is it mainly just the parent that contributes the agouti gene?

[chev]

The sooty gene contributes to dark bays, and can give quite a variation from vague countershading that resembles dun stripes through to those who have countershading all the way down the ribcage to the soft parts.

But as to what causes different shades... that question hasn't been answered yet!

[Jen_e_Jen]

Lol, I didn't really think so just thought I'd give it a shot. Thanks though!