From: tracy@scoraz.resp-sci.arizona.edu (Tracy Scheinkman)
Newsgroups: rec.equestrian
Subject: re: horse color genetics program
Date: 22 Jan 93 20:35:43 GMT
Organization: University of Arizona, Tucson, AZ


	Since this subject has come up again I thought I'd post the info
that I have.
	First, color inheritance in horses is NOT governed by a single gene.
Hair color of horses like hair color of humans and other mammals is governed
by many genes interacting with each other.  
	To a certain extent it can be thought of as a series of transparent 
overlays with a figure of a horse underneath, what color the horse is 
depends on which overlay is uppermost and how much of the underlying colors 
it allows to show through.  For example in the case of a horse which has
both a gene for roan R and a gene for grey G, both of which are dominant
genes, you will not be able to tell that the horse has a roan gene because
the greying covers it up.  The only hint you would have would be when the
foal is just born if their coat is about half white hairs mixed evenly with
the backround color, except at the head where roans do not have as many
white hairs as greys, then you would know that the foal carried roan coloring
but shortly thereafter the foal's coat would begin to grey out as the grey
gene is a progressive whitener of the coat.  Thus as an adult the horse could
conceivably carry a roan gene and yet look perfectly white.
	Now on to the next lesson.  Genes always come in pairs.  Geneticists
label them with a capital letter if the gene is dominant or a small letter
if recessive thus G represents grey color and is dominant, g represents non-
grey and is recessive.  In order to see a recessive color both genes in a
pair must be recessive thus a bay horse would have gg at the grey gene 
location (called a locus) and a grey horse would either be GG or Gg.  Got it?
	Next, not all books use the same lettering system for different
genes a gene called A in one book might be B in another.  Just look for
consistency within the book or article itself.  The book I will be referring
to is called Horse Color and was written by D. Phillip Sponenberg,Phd.,DVM and
Bonnie V. Beaver, DVM.  Sponenberg is a researcher with a university in 
Virginia, I believe, and is still doing research into horse color.  This is a 
wonderfully complete book which includes over a hundred color photographs 
of the various coat colors and patterns they discuss.  The appaloosa 
information which is in the book is incorrect and Sponenberg has recently
published new information on appaloosa inheritance which I have tried to 
include here (see Equus, April 1990 issue).

	Horses have the possibility of two different color pigments, eumelanin,
which is responsible for black and chocolate brown horses and the black in a
bay's mane and tail, and phaeomelanin, which is responsible for the red or
yellow color of sorrels, chestnuts, palominos, and the red body on clear
bays.  Now we're ready for the genes themselves.
	A	a dominant gene is responsible for bay horses by restricting
		eumelanin to the points meaning the mane, tail, and legs of the
		horse, the rest of the horse has red, phaeomelanin, pigment
		(note the exception: dark mahogany bays and seal browns
		have other genetic elements at work, mahogany bays have an
		additional gene allowing some eumelanin, seal browns are
		actually genetically black with another gene P causing 
		light areas on muzzle and flanks)
	a	this recessive gene is responsible for black and uniform
		chocolate brown horses, a common color for Morgans and
		some Quarter Horses, this gene allows eumelanin over the
		whole horse uniformly (as compared with A which restricts
		eumelanin to the points)
	B	this gene is for the black variety of eumelanin
	b	this recessive gene is for the brown variety of eumelanin, the
		difference apparently is in the microscopic arrangement
		of pigment molecules, these horses also tend to have
		amber or light brown eyes and pinkish brown skin, in order
		to have a uniform chocolate brown horse then the horse must
		be aabb, if it is A-bb then it is a bay with brown points
		instead of black points(red body, brown mane tail and legs)
		this gene is only a factor in a few breeds most notably
		Morgan and Quarter Horse
	C	this gene means that the horse's color is fully expressed,
	 	non-dilute
	 cr
	c  	this recessive gene is the cremello gene it dilutes phaeo-
		melanin markedly, eumelanin a little, it is responsible
		for blue-eyed light cream or white horses that some
		call Albinos (true name is cremello if chestnut is diluted,
		perlino if bay is diluted), however there is no true Albino 
		gene for horses, this gene is also incompletely recessive so 
		when big C and little c-cr are present in one gene pair a horse
		that would otherwise have been chestnut or bay would be
		instead palomino or buckskin respectively.  Fascinating, huh!
	D	a dominant dilution gene is responsible for all dun horses 
		except claybank duns which are mostly c-cr horses, this gene
		dilutes body color but not point color, duns have 
		dorsal stripes, some also have leg striping, black becomes
		grullo when D is present, chestnut becomes red dun, bays
		become line-backed buckskins, other examples of dun colors are 
		lilac dun, olive grullo, line-backed palomino, zebra dun, 
		yellow dun, etc. the dun gene D can act in concert with 
		other dilution genes, for example with Cc-cr in the case of 
		a chestnut D- would produce a line-backed palomino
	d	non-dun
	E	this dominant gene allows eumelanin at the points meaning
		it allows bay and black this allowance of black color
		becomes important because of the next gene
	e	this recessive gene causes phaeomelanin red or yellow
		over the WHOLE body and points of the horse in other words 
		chestnut, sorrel, or palomino, this gene is said to be 
		epistatic to the A locus this means that if two e genes are 
		present they cover up the effects of A or a, think of it as 
		opaque plastic overlays the horse might have been black, bay, 
		or chocolate brown according to its other genes but because of 
		ee it's red (note: sorrel and chestnut both generally refer to 
		the same color genetically, red, however different breed 
		associations refer to the lighter phases of the color 
		differently than the darker phases of the color, to further 
		complicate things different breed associations do not agree as 
		to what term shall cover what shade of color)
	 d
	E 	the proof for this gene is incomplete, this is a dominant
		gene at the E locus that causes the color called jet black
		which is a non-sun-fading black color mostly seen on
		Clydesdales and a very few other large breeds it is not
		present for example in Arabians whose black color when
		present comes solely from the normal recessive mechanism
	F	normal red mane and tail on ee, chestnut or sorrel horses
	f	flaxen mane and tail on chestnut or sorrel horses
	G	grey, this dominant gene is like a transparent plastic
		overlay, when the foal is born whatever color it would
		have been without the G shows through, thus it is black,
		or chestnut or bay or whatever, then as it grows older
		it progressively whitens as each new coat gets more and
		more white hairs mixed into it
	g	non-grey
	P	pangare (pronounced pan-gar-ray), this causes light areas
		on muzzle, over eyes, on flanks, stomach, it causes
		black to become seal brown and chestnut with flaxen mane
		to become blond	sorrel
	p	non-pangare
	Sty	smutty, causes some black to become mixed into body coat
		clear sorrel becomes chestnut or liver chestnut, clear bay
		becomes mahogany bay, palomino becomes smutty palomino, etc.
	sty	recessive causes clear pure color, a clear pure red is 
		often called sorrel among Thoroughbreds and Quarter Horses
		other breeds call this chestnut
	Z	silver dapple, causes eumelanin to be diluted to flaxen usually
		a little eumelanin remains in the coat, silver dapple bays are
		possible when the eumelanin in the mane and tail are diluted
		causing the mane and tail to have a silvery color to them
		because of some of the remaining black hairs, this gene is 
		really only a factor for breeds such as Shetlands, Icelandics, 
		Dutch Warmbloods, and Norwegian Fjords, Norwegian Fjords may 
		have a combination of silver dapple and dun genes
	z	non-silver-dapple 
	R	roan, causes white hairs to be mixed with base coat color,
		this color is non-progressive as opposed to grey which
		is a progressive whitener, though it does change a little
		with the seasons, roans often have fewer white hairs mixed in
		to the base coat on the face and legs than on the body, also 
		this gene is thought to be a dominant lethal meaning that RR 
		horses die during development, most roans are Rr and throw 
		solid colored foals as well as roans, Dutch and Brabant draft 
		horses may be an exception to this rule and if so roans in 
		those breeds are probably due to some other mechanism
	r	non-roan
	T	tobiano paint spotting, this paint color has bold sharp edges
		and has white in a vertical pattern that often crosses the spine
		the face and legs are usually dark the amount of white is 
		governed by independent modifiers and can be selected for, 
		thus a tobiano with a lot of white will tend to have foals with
		a lot of white, homozygous tobianos, meaning TT horses, will 
		throw 100% tobiano color
	t	non-tobiano
	O	non-overo
	o	overo paint spotting, also called frame overo, there is some 
		argument over whether this gene is recessive or dominant, the
		color tends to splash in a horizontal pattern with sharp edges
		that rarely crosses the spine, the legs and face are often 
		white, blue eyes are common, overos that are mostly or all 
		white die within a few days of birth because of a malfunction 
		of the colon, there may be another gene at this locus that is 
		responsible for these lethal white overos, the amount of white 
		caused by this recessive gene is governed by an unknown 
		mechanism possibly womb temperature maybe independent genes 
		but cannot be selected for, overos often throw solid or nearly 
		solid foals 
	Sb 	sabino paint spotting, often confused with overo, this may be 
		an example of incomplete dominance such that homozygous horses 
		SbSb have more extreme patterning and markings than 
		heterozygous horses Sbsb, this pattern is typified by extremely
		ragged margins rarely crosses the spine and blue eyes are 
		common, the minimum expression seems to be high white 
		stockings and extreme facial white, this gene is common amongst
		Clydesdales where the color is sometimes erroneously called 
		roan, many sabino horses exhibit the Medicine Hat pattern 
		popular among some breeds such as the North American Spanish, 
		pure white foals develop normally in contrast with overos
	sb	non-sabino
	Note: the term tovero refers to a horse which exhibits a combination
		of overo and tobiano patterning, such horses would be 
		genetically T-oo, a horse that is genetically T-ooSb is 
		theoretically possible, either tovero or sabino horses may
		exhibit the Medicine Hat pattern
	Rb 	rabicano, which is a white hairs starting at the dock of the
		horse's tail and sometimes white hairs mixed in the flank area
	rb	non-rabicano
	W	dominant white, neither this gene nor the c-cr genes are true 
		albino genes as some pigment is still present, the skin of
		dominant white horses is pink, the eyes of such horses are 
		usually brown, this is a dominant lethal gene meaning that all 
		dominant white horses are Ww, the WW form apparently dies in
		development there are no exceptions
	w	non-white
	Apl	non-appaloosa, to be a non-appaloosa the horse must be
		Apl Apl
	apl	this is another incompletely recessive gene, apl apl horses
		are the few spot appaloosas that produce 100% appaloosa
		babies no matter who they are mated to, Apl apl horses are
		the brightly patterned appaloosas we are most familiar with,
		other modifier genes cause the different patterns -- leopard,
		blanket, varnish roan, etc. -- combination patterns are 
		common, for example I once saw a black varnish roan with a 
		white blanket over the rump and leaopard spots over the 
		whole horse, there may be other appaloosa mechanisms that 
		are unknown currently (note: the grey gene has the same affect 
		on appaloosa pattern spots and splashes that it has on solid 
		colored horses and eventually such appaloosas that carry the 
		G grey gene will become completely white just as solid grey 
		horses do, in those cases the skin under the white hairs is 
		often visible and is pink in the blanket areas and dark where 
		the spots or solid areas were, thus an all white horse with 
		pink skin and a few oval spots of dark skin may actually be a 
		few spot appaloosa that has turned grey) currently there are
		about eight different known appaloosa patterns, there may be
		a form of Appaloosa roaning (or greying) which only affects
		the backround color and does not affect the spots however
		evidence for this is not available

	Now how it works, let's take the case of a black horse, which is one
of the most difficult colors to achieve in most breeds.  Remember that
chestnut ee covers up black aa and bay A-.  So a chestnut horse with a black
ancestor is bred to a bay horse with a black ancestor, the chestnut's gene
pattern looks something like a?ee the bay's gene pattern looks something
like AaE?, now there are 16 different combinations possible of which 4 are
definitely bay, 4 are bay or chestnut depending on what genes the ? are,
4 are chestnut or black, 2 are bay or black, and only 2 are definitely black.
If we make the first ?=A and the second ?=e then, the possible offspring
are 8 chestnuts, 6 bays, and 2 blacks in other words a ratio of 4:3:1.   When
you add more color genes it becomes more complicated.
	As to the grey question, grey covers up the base color, let us say
that color is bay, well bay can hide a black gene or a chestnut gene, so
depending on what the grey is bred to you could have a chestnut, a bay, a
black, or another grey, or numerous other colors.  Remember to look at
your horse's breed and parentage, certain breeds don't have some color genes
available to them.  For example Arabians don't have Z silver dapple or E-d
jet black, or b chocolate brown so those genes are unnecessary to consider.  
My mare's line has had nothing but greys, bays, and chestnuts for many 
generations, black may have been known many generations ago but hasn't shown 
up since then so I won't need to bother checking for other colors such as 
overo genes or cremello genes when I breed her to another of her line.  Since 
I am interested in black I would want to see if the sire had a line that 
included black genes.  One more thing, the likelihood of a recessive gene 
showing up in subsequent generations decreases with each new generation that 
does not show it, but, as in the case of black coloring, it never completely 
goes away.  If on the other hand you selectively breed away from a dominant
color it can be completely lost in one generation (that actually happened
with the Crabbet Arabians in the early 1900's, it wasn't until Skowronek
was found and purchased that the grey color reappeared in the Crabbet herd.)

				Tracy and Bruce (beautiful man) and
				Cachet (7 year old Arabian mare) and
				Mithril (2 year old Arabian filly,
				daughter of Cachet) and The Cats