Color and Genetics Discussion This discussion, question and answer series were presented during recent discussion on color and genetics between Peruvian Horse owners and breeders and is placed here for your enjoyment and with the hope you may find the answer to a color question you have Submitted by Jann Bach, Rancho Arista, Colorado Springs, CO. Check out Jann's website which features her beautiful sculpture and show award designs. Enjoy!

Welcome to Color Genetics 101. Today's topic will be base colors. Those who already know this stuff, can skip forward. Those who don't, read on because unless you understand this part, the rest won't make any sense. DISCLAIMER: I am not a genetics book nor have I ever written one. The schooling I've had in genetics was thirty-some years ago and I admit may be outdated. I do not own nor have I read any of the current books on the subject, so what you are getting from me is only MY understanding of the subject. My information may be wrong, outdated, or simply incorrect. I don't mind being corrected. I am just giving you what I know ... or thought I knew.

Base Colors 101	The "B"'s	Dun/Grulla
Cremelo/Perlino	Palomino	Detail on Dun
Manes and Tails	Sticky genes	Lethal Gene Factor
Base Color registration	Gray & Roan	Cremelo/Albino
Roan Patches	More Gray	Dominant Color Q&A
More Roan Patches	Gray Q&A	More Discussion
Buckskin	Color, Markings & Gait	References for your reading

Base Colors There are only two base colors in horses. Those colors are chestnut and bay. Chestnut is a horse whose "points," (mane, tail, legs and ears) are at least approximately the same color as his body. A bay is a horse whose points are black. All other colors come from color-altering "factors" being applied to these base colors. I need to explain a couple of terms at this point. I will explain them rather simply which I think for our purposes will suffice. If we were going to be extremely accurate, this explanation wouldn't do, but I hope those of you who know this more intimately will forgive me. "Genotype" refers to the color a horse is genetically, i.e. what color genes he carries. Genotype is what we need to know when we look to what a horse might be able to produce. "Phenotype" refers to the color a horse is by appearance. A bay horse is phenotypically bay even though he may carry chestnut genes. "Dominance" refers to the aspect of a gene that means that if that gene is present, it will show up. It "dominates " other genes. A "recessive" gene is one that is dominated by another gene. Dominant genes require only one gene to show up. Recessive genes require that the horse have two of them in order for it to show up. A recessive gene can remain hidden in a horse's genotype and may not be present in his phenotype. In other words, it is a gene that he can "carry" without it being apparent when you look at him. A horse gets two or more genes for every trait from its parents, one set from its sire and one from its dam. Of the base colors, chestnut is recessive and bay is dominant. That means that for a horse to be chestnut he cannot have a bay gene (since bay is dominant, if he had a bay gene it would dominate the chestnut gene and he would appear bay.) So a chestnut horse can only have two chestnut genes, one from each of its parents. A bay horse can have either one chestnut gene and one bay gene, or two bay genes. In either case the bay gene will dominate and the horse will appear to be bay. It is customary in genetics to denote genes by a letter. The letter chosen usually is the first letter of the dominant gene, in this case B for bay, and to assign the capital letter to the dominant gene and the lower case letter to the recessive gene. So in our notation we will use B for bay and b for chestnut. Using this notation, a chestnut will be bb (two recessive chestnut genes) and a bay can be either Bb or BB. In the case of the bay, you can see the difference between a horse's phenotype and his genotype. Both Bb and BB appear to be bay horses. But as parents, they will produce different colored offspring. Let's take the case of a cross between a chestnut horse and a bay who we know carries the chestnut gene (Bb). There are two ways we can know that a bay carries the chestnut gene. One is if the bay horse has a chestnut parent. (Remember that a chestnut can only have chestnut genes. Therefore he can only give his offspring a chestnut gene. If his offspring is bay, you know by looking at him that he has one bay gene because he appears bay, and one chestnut gene because he has a chestnut parent.) The other way we can tell is if he has produced a chestnut offspring (In order for that offspring to be chestnut he must have two chestnut genes, one from each parent, so the bay parent must have had a chestnut gene to give him.) The easiest way to demonstrate the crossing of genes is with a square. I hope this will come out okay on-line. Draw what looks like a tic-tac-toe board, with three rows of three boxes, one row on top of the next. Let's put the chestnut parent (bb) across the top and the bay parent (Bb) down the side. Put a big X in the upper left box. Put the chestnut's genotype, bb, in the rest of the top row, i.e., the top row will read "X/b/b." Now put the bay's genotype below the big x in the left side boxes, i.e., the left side will read "X/B/b going from top to bottom. Are you totally confused? If not good, 'cause you're probably going to be if you haven't used this square before. Now you have both genes from both parents (four genes) represented in the boxes. If you take one gene from each parent and put it in the open boxes you will see the possible offspring's genotypes. In the center box you bring over the B from the bay, and bring down the little b from the chestnut, so you have Bb in the center box. Do the same for the other three open boxes. The next box to the right will be Bb also. In the bottom row, you take the b from the bay (it is the gene next to that row of boxes) and the next b over on the top row from the chestnut and you have bb in both of the remaining bottom boxes. The foals represented by Bb will be bay because they have the dominant bay gene from the bay. The foals represented by bb in the bottom row will be chestnut because they only have the recessive chestnut gene, one from each parent.

Below is how your square should look: X/ b /b B/ Bb /Bb  b/   bb   /bb

A cross of two chestnut horses would look like this: X b b b bb bb b bb bb All chestnut offspring.

A cross between two bays who both carry chestnut genes would look like this: X B b B BB Bb b Bb bb This cross will produce three bays, two of which carry chestnut genes, one which carries only bay genes, and a chestnut.

Now you try it crossing a BB bay with a chestnut. Those who carry only one type of a particular color gene are referred to as being homozygous, and those who carry more than one are heterozygous. If you cross two homozygous horses, you will ONLY get offspring with that trait. This is the case with crossing two chestnuts - they are homozygous (only chestnut genes) and can produce only chestnuts. The same would be true if you crossed two homozygous bays - they would produce only bays. But the incidence of homozygous genotypes in horses with dominant phenotypes (bays) is relatively rare. In other words, most bay horses carry chestnut genes. We've already established how to define a horse by his genotype and phenotype as to his base color. Remember that these two colors, chestnut and bay are the only two base colors. EVERY other color is the result of some altering or modifying factor acting on those base colors. For my purposes I am going to ignore the theory that gray is a base color because to consider it one means that prediction of color from a gray is impossible, and I just don't believe it is true. The first and perhaps the easiest "modifier" we'll consider is the Dilution factor, which produces palominos and buckskins, cremellos and perlinos. (We'll do this first because I was asked specifically to do it first.) The dilution factor is pure dominant, meaning that if it is present you will see the results of it. A chestnut base color with one dilution gene produces a palomino. A bay base color with one dilution gene produces buckskin. Here I need to clarify something. Buckskin and dun are two different factors, though the terms are often used interchangeably. Buckskins can have or not have a dun factor. Those with it are the buckskins we see with a dorsal stripe, shoulder and leg stripes. Dun can also be seen with any other color, but it most associated with buckskins as its appearance is most dramatic in a light colored horse. Since the dilution factor is dominant, if it is present, you will see it. There is one exception to this in apparently black or extremely dark liver horses, but I'll go into that at some other time. A horse cannot "carry" a dilution factor and not show it, with the above exceptions. It doesn't matter how many palominos a chestnut horse has in it's background, if the individual is chestnut, he has NO palomino genes. I can't stress this enough. Even if a horse has a pedigree where every single ancestor is a palomino, if he is a normal chestnut color, he has, carries, etc. no, none, zilch, nada palomino genes. Palomino is pure dominant, if it is there, it shows. So, given that, we can describe the dilution factor as P. A palomino is Pbb (a chestnut base color with the dilution factor.) A buckskin is PBb (or PBB). The lack of the gene can be described either as p or just left out. For our purposes, I will just leave it out to indicate the absence of the gene. So a chestnut horse can either have one dilution gene Pbb, no dilution genes bb, or two dilution genes (one from each parent) PPbb. Where a horse gets two dilution genes, it will be either cremello (chestnut) or perlino(bay). In some breeds, BUT APPARENTLY NOT IN PERUVIANS, the double dilution genes carry a lethal gene along with them, resulting in the deaths of most double dilution foals. Again, this does not appear to be the case in Peruvians. If you use these designations in our "Punit Square" we can visualize the crossing of horses with the dilution factor and their possible offspring.

A cross of a chestnut and a palomino will look like this in its simplest form: X Pb b b Pbb bb b Pbb bb The offspring of this cross are 50% palomino and 50% chestnut.

The cross of a palomino and a heterozygous buckskin might look like this in its simplest form: X PB B Pb b Pb PPBb PBb PPbb Pbb b PBb Bb Pbb bb

PPBb = perlino PBb = buckskin PPbb = cremello Pbb = palomino Bb = bay bb = chestnut

Try the other crosses; chestnut to buckskin, bay to buckskin or palomino, perlino to chestnut or bay, and cremello to bay or chestnut, cremello or buckskin to each other. The dilution factor is one of the simplest of the modifiers as it is pure dominant, and the results of a double dose can be readily seen. There should be no question as to whether a horse has one, two or none of the dilution gene.

Question #1:	In a cremello or perlino does every base color gene have a dilution gene attached to it, or can the base color genes be transmitted separately from the dilution factor? Does it matter? Can a horse who is homozygous for the dilution factor ever throw a solid colored offspring? (solid colored for our purposes means one without any apparent modifiers)
Answer to Question #1	Each set of genes are normally transmitted separately from any other set of genes. There are exceptions, such as sex-linked genes, but these do not normally apply to color genes. Base color genes are transmitted with or without altering factors and altering factors are transmitted independant of the base color. But every offspring must inherit one of each set of genes from each parent. In the case of, say a palomino, the set of genes to choose from is either a dilution gene or the absence of it. In other words, regardless of the base color transmitted, a palomino or buckskin can give the dilution gene or not give it to its offspring. We'll discuss what I call "sticky genes" later. (These are genes that tend to attach thenmselves to other genes when the chromosomes divide and appear to occur together.)
Dilution and Dun Factor Responses	ANSWERS TO SPECIFIC QUESTIONS
Buckskin	As for your buckskin, the only way you can get a buckskin from your chestnut mare is to breed her to a buckskin. You statistically have a one in four chance of getting a buckskin. Like you said, though, you have a 100 percent chance if you go out and buy a buckskin!!!!!
Dun/Grulla	I love a good dark brown-cast buckskin with strong dun factor (dorsal, shoulder and leg stripes.) I also love grullas. As for describing grulla (my very favorite color in all the world) it is the diluted form of black, where the hairs in the body are actually a uniform mousy gray color ( not a combination of dark and white hairs as in gray or roan, but each hair is a true gray color.) The diluted form of bay is buckskin and the diluted form of black is grulla. In our breed these horses are often so dark because of the darkening factor that produces black, that they appear black and not grulla, and produce buckskins and palominos much to everyone's surprise.
Dun Factor	It sounds like Sahara's line has a very strong dun factor in it. The shoulder and leg stripes are often hard to see in chestnut horses as it blends well with the coat color. Your foal is probably still a red dun, but his darkened coat is hiding most of it except the dorsal stripe. The dun factor can affect any coat color, but the only ones that seem to mind are the "palomino people" (The dun factor on a palomino gives you a gray or silver mane and tail instead of white.) If your colt has a palomino dam, he can have the dilution gene from her. But since in our breed we often see a black cast over the diluted color, we have apparently black horses throwing colored ones ( colored meaning palomino or buckskin. If it throws diluted babies, it is a diluted horse (one form of palomino or buckskin) even if it doesn't look it. Many black babies are born frosty black, but some grullas (a form of buckskin) are so dark that they look black, but will still produce as a buckskin would. Your baby with the white tail with the stripe is probably some form of dilution. The dark stripe in his tail is from the dun gene which produces a dorsal stripe that goes into the tail. I can't tell you whether he is a base bay or a base chestnut. Most bay bases don't have light tails (a black is genetically a bay and all bays should have black tails), but most chestnuts aren't dark enough to be considered true blacks. Without seeing him, and perhaps even if I did see him, I don't know what he is. You will know a little more when he produces offspring. Until then I guess he is a horse of a different color, so just enjoy the view.
"Carrying" the dilution gene	I'm afraid that your bay mare does not and cannot carry "golden genes." The "golden gene" or dilution factor is dominant and is not "carried" by a horse that doesn't show it. The only exception is the case of a very very dark buckskin color that appears to be black. (Remember that this color can also have an additional roan or gray factor and appear to be either a roan or a gray horse that produces color when it is in fact a dark buckskin roan or gray if it were properly identified.) Your mare being bay in appearance does not , by definition, have these factors ( she would be buckskin if she had the dilution factor, and would appear black or dark brown if she had the darkening factor. So I believe you are incorrect in thinking that she contributed any golden genes to her offspring. As for those foals she produced, I'll address the palomino first. He got the dilution factor from his sire, the buckskin, and a chestnut gene from each of his parents. Assuming that he does not have a gray mane and tail, he is simply, and happily, a palomino (Pbb - P for the dilution factor and bb for the chestnut genes) and can throw any color depending on what he is bred to. As for the black filly, unless she is one of those black-cast buckskins who make liars out of those of us who think we know everything, she could only have inherited a chestnut gene and the darkening gene (since she is black) from her sire. If she had inherited the dilution factor, she would be a buckskin, with the above exception. She inherited either a chestnut or a bay gene from her dam. The gene that made your palomino chocolate rather than golden is the same gene that makes the filly black rather than bay. The square for the breeding of these two horses (the choc. pal sire and bay dam) looks like this, with P=dilution, d=darkening, B=bay and b=chestnut. (this is simplified as the darkening factor can also be transmitted independently.) sire (choc palomino) X Pdb  Pb db b dam (bay) B PdBb PBb dBb Bb b Pdbb Pbb dbb bb   in this square, the possible offspring are: top row - PdBb=black cast buckskin, appears black, PBb=buckskin, dBb=black, Bb=bay; second row - Pdbb= chocolate palomino, Pbb=palomino, dbb= dark liver chestnut, bb=chestnut. Your black filly is either PdBb or dBb. You won't know which she is until you breed her and she produces a colored foal. If she does, you will know she is PdBb.
	Buckskin, palomino, gray or roan, none of these are dominant over the other, they are a toss of the die as to which comes up genotypically. The dilution factor and the roan or gray factor are completely independent of each other and one or both of them can show up separately or together. A good friend of mine had a lovely roan buckskin. Neither the buckskin nor the roan was dominant over the other, they acted in combination to alter the horse's bay base color.
	I have no idea what your champagne horse is. Maybe it is one of the Isabellas. Like I said earlier about the bay with chestnut legs, or was he a chestnut with a dun factor, some colors defy our description. The only way to identify what they truly are genetically is by breeding them and seeing what they produce. The laws of genetics are sufficiently well described that you can tell what a horse is genetically if you breed it enough times to the right horses and see what it produces, even if you can't tell by that horse's phenotype.
Dun Factor: Another question	Dun is a factor, not a base color, and can appear with any base color. With chestnuts it is called a red dun; with palominos it shows up as a gray mane and tail, and often a noticeable but faint dorsal stripe; in bays and buckskins, it shows up as dorsal, shoulder, and leg stripes; and in browns and blacks, it is usually not visible due to their dark color. The dun factor is prized in the buckskin world, they even have a class called dun factor, the winner showing the most prominent of the aforementioned traits. Dun in our breed usually refers to a bay horse with the dilution factor, i.e. a buckskin. Since you were in effect breeding a buckskin to a buckskin in your Perulero breeding, it stands to reason that you could get a cremelo. Going back to the good old square, it would look like this:  x  PB  B  Pb   b  PB  PPBB  PBB  PPBb  Pbb  B  PBB  BB  PBb  Bb  Pb  PPBb  PBb  PPbb   Pbb  b  PBb   Bb  Pbb   bb   I've represented the possible gene combinations as follows: PB is a bay gene and a dilution gene (buckskin), B without the dilution gene is the bay gene, Pb is the chestnut gene with the dilution gene (palomino), and b is a chestnut gene, no dilution factor. A buckskin has all these possible genes to give to his or her offspring (assuming he is not homozygous for bay.) Neither of the horses you are talking about is homozygous for bay (they had in effect, a chestnut foal). So, the possible offspring will inherit one of the four possibilities from each parent. In the chart, the first space is PPBB. This is a double dilution factor homozygous bay - a perlino. The second across the top is PBB - a homozygous bay buckskin. Next is a heterozygous, double dilution bay - another perlino. The final horse in that row is a palomino. You guys still with me???? Next row down we have a buckskin, bay, buckskin, bay. Next row is Perlino, buckskin, CREMELO, palomino. And the final row is buckskin, bay, palomino, chestnut. While Perulero's cremelo offspring isn't statistically common, it is entirely predictable and not at all unexpected. Breeding Perulero to a gray or a roan would give you unpredictable results only because we have no idea what their base colors are. If you knew their base colors, it would be predictable. The fact that neither foal grayed or roaned out is also totally predictable, you have a heterozygous gray parent who can either give the foal their gray or roan gene or not give it to them. If they did, you'd have colored foals, if not, solids. As to the Medallion x bay mare breeding, the black filly could be either. If she inherited the dilution factor from Medallion, she may be a case of black masking the dilution factor. You won't know until you breed her. If she produces palominos or buckskins, then she did inherit it. Those are relatively rare, but since she has an ancestor who was a black masked buckskin, she could. The second foal, the palomino is a result of Medallion's dilution factor acting on the chestnut gene it inherited from both parents (I'll bet you the bay mare has a chestnut ancestor and has or will produce chestnut foals - she already has in your palomino.)
Roan and The Dilution Factor	Your cross of a black roan with a palomino is an interesting one in that it can produce almost any color horses come in. Basically there are only two coat colors in horses. All other colors result from factors acting on those base colors. The two base colors are chestnut, with self-colored (meaning some shade of the body color) points (mane, tail legs and ear tips), and bay, with black points. Chestnut is pure recessive, meaning it requires two chestnut genes to produce a chestnut, and bay is pure dominant, meaning that if the gene is present from one or both parents, the offspring will appear bay. Chestnut base coats can be altered into colors from cremelo to deep liver chestnut, and bay alters from perlino to black. Roan and gray factors can turn any base color nearly white. You can visualize these base colors as B for bay and b for chestnut (dominant colors are usually represented by capitals.) Your black roan, I'm going to assume that this is the sire, is a bay horse with two altering factors, one for a dark coat, and one for roaning. Since he has produced a chestnut foal, he must carry a chestnut gene (remember, chestnut is recessive and you have to have two genes, one from each parent to produce it.) One of his ancesters has to have been chestnut. Your palomino, I'm assuming it is the dam, is really a chestnut with a dilution factor (this factor causes chestnuts to be palominos and bays to be buckskins.) We can represent your two horses' base colors as Bb for the black roan, he has a B (bay) gene and a (b) chestnut gene, and bb for the palomino, she has only (b) chestnut base coat genes. Bb can give his offspring either a B or a b; bb can give only b's. Now we're going to combine each of Bb's genes with each of bb's genes to see what potential base colors you can get and in what proportion. First, combine Bb's B gene with each of bb's, and you get two Bbs, or two bay colored foals (remember that B is dominant, and if it is present, it shows as the base color). Next combine Bb's b with each of bb's and you get two bb or chestnut foals. You have already gotten one of the Bbs and two of the bbs. The Bb you got also inherited the roan and darkening factors from its sire. The three altering factors you have in your two parents are (D) darkening, causing the black color, (R) roaning, and (P) a dilution factor causing the chestnut base color to become palomino. Any of these factors can combine with either of the base colors to produce just about any color. From a breeding of your two horses you could get chestnut, bay, black, brown, palomino, buckskin, liver chestnut, chocolate palomino, or any of these colors in roan or even gray. If your black roan has a palomino or buckskin ancestor, and is really a buckskin underneath, you can also get cremelo or perlino, which require two P genes.
Gray and Roan Question	Q: Now, I want to clarify something in reference to your answer about the gray horse's base color... QUOTE from JB: "As to the gray question, you are a little backwards. The base color, i.e. chestnut or bay, is still the important color of the horse. Gray is a factor, just like dun or dilution, that alters the appearance of the base color. Unfortunately, the registries don't classify horses by their base color, which is the only way you can accurately describe or predict color. Your gray horses sound like bays with a graying factor. Bay is dominant to chestnut, but either can be altered by a graying factor. The horse's base color isn't "dominated" by a factor such as graying, it is altered by it. As far as heredity, though, the base color is the most critical in determining what color offspring will be." end quote. Q:Your answer that gray is not a base color but more like a dilution, etc., does make sense... and would in a way answer my original question about foal color and recessive genes of gray babies... which, is to say, that my theory was correct... But... I don't know about any other registries, etc., but I do know for certain that gray coloring is considered a "base color" by the Arabian Horse Registry of America, and also has been proven to follow the inhertance patterns typical of the other 2 color genes, bay and chestnet, with gray being the dominant gene... in other words, thru consistant breeding it is determined that gray inheritance patterns follow the same inhertance patterns as the other two, with gray dominant over bay and bay dominant over chestnut. There are also the rules such as a chestnut bred to a chestnut shall always result in a chestnut, as well as a gray foal must have at least 1 gray parent. Also, the Arabian breeders (since we only have 4 recognized colors, gray, bay, chestnut, and black many breeders try to find the genetic color patterns of their breeding stock) have studied color inheritance patterns in Arabians enough to know that the gray color pattern is the sole color passed from the gray parent... IOW, a gray parent bred to a chestnut parent can produce all 3 (or 4) colors in a foal, but in the case where the foal is a gray foal, the foal will ALWAYS have the configuration of a gray gene and a chestnut gene (chestnut recessive)... therefore, when there is a gray foal out of a gray parent and a non-gray parent, the only color gene given to the foal by the gray parent is a gray gene... and one parent must be gray in order for the foal to be gray, as the gray gene is dominant over the bay and chestnut... at least, this is the way that the AHRA defines the color genes in Arabians, and from everything I can tell, it definately stands true in the Arabian breed, anyhow. It would seem to me that if the gray color was a result of a similar thing to say, the dilution gene, that it wouldn't breed as true as it does... as, with a gray to chestnut breeding, the results are rather consistant... 50% chestnut, 50% grays in the case of a heterozygous gray parent, and 100% gray in the case of a homozygous gray parent (Yuck! Lots of those in Arabians!!)... and it has never been the case that a gray foal out of the gray/chestnut breeding has shown to posess any other recessive color gene besides a chestnut... IOW, breed the resultant gray foal from the gray to chestnut breeding to a chestnut and you will either get a gray foal or a chestnut foal, never a bay or black.
Answer and Response	JB: Genetics is a wonderful science for predicting statistical results in a general population. It sometimes falls short when trying to predict individual members of that population, though there are some things that are close to predictable. "IOW a gray parent bred to a chestnut parent can produce all 3 (or 4) colors in a foal, but in the case where the foal is a gray foal, the foal will ALWAYS have the configuration of a gray gene and a chestnut gene... therefore, when there is a gray foal out of a gray parent and a non-gray parent, the only color gene given to the foal by the gray parent is a gray gene..." If you look at the actualities, I think you will find that this is not true. I'll give you an example that I think disproves your theory. Sindical+ is a gray stallion who is the product of a chestnut (Cortesano+) and a gray (Soledad). He should therefore carry only a chestnut gene from Cortesano and by your theory, a gray gene from Soledad. He was crossed with Perla Concha. She is a gray who also is the product of a chestnut (Principe de la Solana) and a gray (Francesca Cielamente) and by your theory should likewise carry only a chestnut and a gray gene. They produced a black offspring, Perla Blanca. If gray is a base coat color, and the only color gene Sindical and Perla Concha inherited from their gray parents, as evidenced by their gray color, where did the black or bay gene come from? A black or bay HAS to inherit at least one bay gene to be either bay or black. That gene can't be passed down from the chestnut parent because chestnut is recessive to bay and if there was a bay gene it would cause a bay phenotype (appearance.)The only way this could have happened is if gray is an altering factor and one or both of the grays'(Sindical and Perla Concha) base coat is bay. If you view gray as a factor and not a base color, you still get them to breed true. If there are two versions of the factor, gray(G) which is dominant, and non-gray(g) which would actually be the absence of the gray factor, you get the following results. A heterozygous parent can transmit either G or g, and the offspring will be gray in the fist case and non-gray in the second. If the parent is homozygous, it can only transmit a gray gene G to its offspring and since gray is dominant to non-gray, the foal will be gray 100% of the time. The dilution factor that produces palominos and buckskins works the same way, except that a homozygous horse is cremello or perlino. I still believe that in order to predict what offspring a gray parent will produce, you have to know what else is in there, i.e. the base colors that are hidden by the gray factor. I have seen nothing yet to dissuade me from feeling that gray is a factor and not a base color. Your statement that a gray/chestnut cross that produces a gray will always produce a Gc (gray/chestnut) genotype is not born out by the facts as indicated in the above real-life example, at least not in Peruvians. I know nothing of Arabians, and can't speak to their definitions or their inheritance. But I sure have enjoyed the conversation.
More Gray	As to the gray factor, I'm not sure which theory you are referring to as being shot down. I still feel that gray is a factor and not a base color. Some gray babies are born chestnut and some are born bay. These are their base colors and are far more important than the gray factor in determining what they will produce. By my theory, the two grays you speak of still have two base color genes that transmit independently of the gray factor. The stallion is chestnut, he can only give bb, chestnut genes. The grays are hard to predict because they aren't registered as to their base color. But since they produced chestnut they must be either Bb or bb along with the gray factor which we'll call G since it is dominant when present. As to the configuration of your gray mare, since she has produced a non-gray foal, she must be Gg (heterozygous) with regard to the gray factor. We don't know what her base color configuration is though because she isn't registered as to her base color. If you owned her or saw her at birth you might know. Her base color is the one she was born with, i.e. was she born chestnut and then grayed? Or was she bay, black or brown before graying? It is very difficult to predict what colors your gray mare COULD produce without knowing her base color. The fact that she has produced a chestnut and a gray only tells us that she is Gg (on the gray factor) and ?b on the base color. From PPHRNA records *Dominguito has produced 4 solid foals - 2 chestnuts, 2 bays - out of chestnut, bay and gray mares. That means his offspring are 85% gray or roan. With a dominant trait, you would expect to see a 75% rate, so he is really not very far off what you would expect if gray / roan is dominant. Add this to the fact that many of the mares he is bred to are also gray, his statistics are not surprising. The fact that the gray/chestnut, roan/bay patterns seem to follow the base color of the foals, may be due to the attraction of the genes for each other and their location on the chromosomes. *Dominguito can transmit either a chestnut gene (from his sire) or a bay gene (from his dam), and can transmit a gray gene, a roan gene, or neither (resulting in a solid colored foal.) If the gray and roan genes are closely allied with or stuck to the base color genes it is most likely that they will transmit with each breeding and you will get a predominance of grays and roans whose genes also stick together and who produce predominantly grays and roans themselves. Gray and roan inheritance is a bit more difficult to predict than chestnut /bay as it is not as easily described, and often seems to be a case of incomplete dominance and / or multi-gene determined. It is also often inaccurately recorded, making research into its inheritance problematical. If a solid foal is determined by a particular multi-gene combination, your best bet for getting a solid foal is to rebreed to a solid-colored mare who has already thrown a solid colored foal with him. *Dominguito's contribution is most likely the determining factor, though. I noticed that most of the mares who have had solid foals have also produced gray or roan foals with him, so it's really a toss up as to what you are going to get.
Roan vs Gray	First off, the difference between a gray and a roan isn't the degree of graying (how white they get). It is that a gray changes color throughout his coat. His head and legs, mane and tail gray out at least a little. Some grays keep thier dark legs, mane and tail until they are quite old, but their heads gray out approximately as much as their bodies, and sooner or later, they get at least a few gray hairs in their manes and tails. A roan, on the other hand, keeps his head, legs, mane and tail the same color as his solid colored kin, i.e. a chestnut roan keeps a chesntut colored head, legs, etc. and a bay keeps a solid bay head with black legs, mane and tail. I have seen grays who never gray out beyond the "steel gray" stage. Their color loooks like a roan, but because their heads, etc. are also steel gray and not base colored, I believe they are properly grays and not roans. There are two distinct graying patterns. One is the "dappled" gray where the horse grays into a dappled pattern primarily on his shoulders, rump and legs, which tends to lighten earlier in life, and eventually leads to a nearly white horse. This is the primary pattern seen in thoroughbreds. The second is the one that looks more like a roan throught its early years, can stay very dark for a long time, and eventually leads to a "flea-bitten gray" (the ones who look "freckled" when they are older.) This is the dominant graying pattern in Peruvians, though I have seen the other also. As far as I know, by definition, a roan has a solid head and legs, so this should be an accurate test. I have seen two mares, a mother and daughter, who I can't classify as either roan or gray. They started to gray-out early in life, all over, face and legs included, though not as heavily there. But then it stopped. They remained very dark gray, or what is a typical dark roan color, all over, including their heads and legs, and remained this way their entire lives. I saw the mother well into her 20's and she was still darker than most yearling grays. As far as I know a true gray will continue to lighten throughout its life. I don't know what you'd call these two.
Manes and Tails	I don't believe that these are governed by complete dominant and recessive genes as base body color is. There are many factors that affect the color of manes and tails, and they don't appear to affect them evenly. A dun factor will darken any mane and/or tail, but not necessarily both. A dun factor in a palomino produces gray manes and tails or white ones with black in them. But it can affect only the mane or the tail or both. I have seen palominos with with white manes and very dark tails. I have seen chestnuts with flaxen manes and extremely dark tails. I know of no way to predict mane and tail color except to say that if you have a horse of any color with a dun factor, it WILL have a darker mane and/or tail than it would have had if it did not have the dun factor.
Base Color Registration	The BIGGEST (IMHO) problem we have in this breed with color prediction is that our horses are not properly identified as to color. You cannot predict what color you will get if you don't really know what color you are starting off with. We register grays as grays and not by their base color, so you have no idea what color the horse really is (Gray is a factor that alters the base color, not a color.) Some duns are registered as blacks or duns, but again, dun is a factor and not a color.) The same with roans. Without knowing the base color of a horse, either bay or chestnut, you cannot accurately predict the color of their offspring. I'd love to see our horses registered as to their base color and the altering factors they demonstrate. I'll bet if this were done, you would be able to predict, with 99% accuracy the possible colors of their offspring. Granted, we have a great many variations of each color, much more than any other breed I've seen, but I think many of the "surprise" colors in Peruvians are merely the result of misidentified parental colors.
Roan Patches	I don't have any specific knowledge of the inheritance of those roan patches. I've seen them in other breeds as well and since they show up in horses whose ancesters do not seem to be roans (you are right on target with your comment that colors are not always accurately recorded) I'd guess that they are controlled by a separate gene or set of genes from that which causes general roaning. I have noticed that those who have it very often throw foals who have it, though not necesarily in the same places. It is probably a case of incomplete, if not true dominance. Roan "patches" can be found in all breeds and in any coat color. I believe it is determined by something totally unrelated to the base color or altering genes (such as graying).
"Sticky Genes"	It sound like you have a "sticky" problem. Many genes have a tendency to attach themselves to other genes (not permanently like sex-linked genes, just sort of buddy-buddy.) They occasionally are transmitted independently, but they are often located very close to each other on the chromosomes and the majority of the time they stay together during cell division and therefore tend to be transmitted together.
Color Markings and Gait	I don't know anything about the correlation between markings and gait, but leg and face markings are controlled by different genes from white body markings. When you talk about solid colored horses are you referring to body markings and / or leg and face markings? Either way, it could be that at least in some lines, the white markings genes are closely located, or "stuck" to gait genes. Get rid of the marking genes, and very often, the gait goes too.
Lethal Genes	I think it is absurd to judge our horses by their color. One possible reason why grays and roans have historically been less desirable may be that both they and palominos are associated with a fatal factor. Roans and palominos, in some breeds, carry a lethal gene.These genes usually manifest themselves in "missed" cycles or loss of embryos shortly after conception. The palomino version requires a palomino gene from each parent, which, when it lives, produces either a cremelo or perlino. I don't know what is required of the roan version. !!!! I have never seen anything to indicate that this gene exists in Peruvians, in fact, the number of live cremelos, perlinos, and roans of all colors in the breed might indicate just the opposite!!!! But even if it doesn't exist in our breed now or in the past, its existence in other breeds might explain the prejudice against it.
Darkening Factor	This deepest liver color is produced by the same darkening factor that makes a bay look black and a palomino look chocolate. Liver can be very dark, appearing nearly black, but is distinguished from bay or black in that the points ( legs, mane, tail) are liver, not black. Your chances or getting a chocolate palomino in breeding to Escorpio depends on how dark your liver chestnut mare is, and if she is dark enough, whether or not the foal inherits the darkening gene. If your mare is the usual medium dark liver, you will most likely get a liver the color of the dam or a nice golden palomino. If she is the almost black form of liver your chances or a chocolate are good, but not certain. Either way, you should get a beautiful and deep color as Escorpio (from his pictures) is a beautiful golden color.
Cremello vs Albino	I'd just like to clarify one point. Cremelo and albino are not the same thing. Cremelo and perlino are very pale versions of chestnut and bay that result when two palominos (or buckskins, or buckskin and palomino) are bred and the offspring inherits a dilution factor from each parent. In our letter jargon, it is a PP. These horses will produce 100 percent colored offspring when bred to non-colored horses, i.e. chestnut or bay. It is the result of a double dominant gene. Albinism is a pure recessive trait unrelated to the dilution factor. It does not produce palominos and buckskins. It is extremely rare, but looks very similar to cremelo. An albino has little or no pigment, not just a pale coat color.
The B's	I'm sorry if all my B's are confusing you. I'll try to explain. Capital letters are usually used to represent a dominant gene, while the lower case of the same letter is used to represent the gene that is recessive to the dominant gene. Big B is used to represent the dominant bay gene. Little b is used to represent the recessive chestnut gene. Remember that when a parent sires offspring, he, or she, transmits only one of the two genes he carries to each offspring. The pairs ofchromosomes divide into two single sets and each sperm or egg gets only one set. Since chestnut is recessive it is represented as bb because it is only expressed (or seen) if the individual has two of these genes, one from each parent. Bay can be either Bb or BB. Since big B is dominant, the individual will appear bay regardless of what the second gene is. The importance of that second gene comes out when we breed that individual. If he is BB he can only transmit a big B gene (bay) so all of his offspring will have a big B from him and will appear some form of bay. If he is Bb he can transmit either a big B or a little b to each foal. If the gene from the other parent is b it will be a chestnut; if it is B it will be bay. You can determine whether a bay is BB or Bb in two ways. If one of its parents is chestnut, the second gene must be b (a chestnut can only transmit a b). If that bay has ever produced a chestnut, the second gene must be b (that offspring must have gotten a b from each parent) Now, if you aren't confused enough, we have your palomino. A palomino is a chestnut with a dilution factor. Therefore, your palomino is bbP (bb for chestnut base color, and P for the dilution factor.) The P is in capitals because the dilution factor is dominant (though it can be masked by such factors as roan and gray.) To determine your possible colors with a breeding of these two, you might want to represent the bay as Bbp (I'm assuming that your bay has a chestnut gene because most of them do, and the absence of a dilution gene, since it would be recessive, is represented by p.) Sooooooo, if you breed these two together you can get Bbp-bay, BbP-buckskin, bbP-palomino, or bbp-chestnut. This is assuming that there are no hidden factors like roan or gray in there. If your bay is BB you can only get bay or buckskin. Bay is dominant over chestnut, and palomino and buckskin are dominant over chestnut and bay. But the statistics will give you exactly equal chances for each of those colors.
More "B's"	There is a very easy way to demonstrate all this, but I don't know how it will reproduce on-line. I'll give it a try: draw what looks like a tic-tac-toe board, with three rows of three boxes, one row on top of the next. Your black mare obviously carries a chestnut gene - if you look at her background you will find a chestnut parent somewhere. So she would be represented as genotypically B for bay (black is a form of bay), and b (a recessive gene such as chestnut is usually represented by the lower case letter of the dominant gene.) She is Bb. The chestnut sire has only chestnut genes(chestnut is recessive) so he is represented as bb. Now go to your boxes. Put a big X in the upper left box. Put the sire's genotype, bb, in the rest of the top row, i.e., the top row will read "X/b/b." Now put the mare's genotype below the big x in the left side boxes, i.e., the left side will read "X/B/b going from top to bottom. Are you totally confused? If not good, 'cause you're probably going to be if you haven't used this square before. Now you have both genes from both parents (four genes) represented in the boxes. If you take one gene from each parent and put it in the open boxes you will see the possible offspring's genotypes. In the center box you bring over the B from the dam, and bring down the little b from the sire, so you have Bb in the center box. Do the same for the other three open boxes. The next box to the right will be Bb also. In the bottom row, you take the b from the mother (it is the gene next to that row of boxes) and the b from the father and you have bb in both of the remaining bottom boxes. The foals represented by Bb will be bay because they have the dominant bay gene from their mother. The foals represented by bb in the bottom row will be chestnut because they only have the recessive chestnut gene. Below is how it should look if this comes out on-line okay. X b b B Bb Bb b bb bb As for all of your babies being chestnut, it is a statistical coincidence. Statistically a Bb black and a bb chestnut should have an equal number of bay (or black) offspring, and if you bred these two together enough times, it would probably turn out that way. (NOTE: a BB black or bay will always produce a bay or black regardless of the other parent, subject to other factors such as gray or dilution.) But with only a few breedings, you can easily get only chestnut even though chestnut is recessive. (You can see by our chart that these two will produce 50% chestnut - you just happened to get those first.) If you want to get a bay or a black, or optimize your chances of your mare producing a bay or black, breed her to a bay or black that does not carry a chestnut gene. These are few and far between, and determining who they are is difficult because horses generally do not have enough babies to accurately predict or determine what their genotype truly is. But if you find a bay who has NEVER produced a chestnut when bred to a chestnut, he is probably genotypically pure.
Question "B's"	Q: I bred a Chestnut to a Black Mare and the result was a Chestnut Filly. This Chestnut Mare, was bred to two different Black Stallions and both resulted in Chestnut Babies. If the dominant color is bay why both babies chestnut? Maybe I'm not understanding this. I also bred a grey mare out of two gray parents. This grey mare was bred two times to a Chestnut Stallion, the same Stallion, and one Grey baby and one Chestnut baby was the result. This would seem to dissolve the grey theory? Is the Chestnut dominant? Just curious. The babies are all great, so the color reaslly doesn't matter. But this particular Stallion has produced Chestnuts with every baby except the grey, no matter what color the mare was. A: In getting a chestnut baby, you haven't shown that chestnut is dominant, only that it is the possibility that showed up this time. From your chart, you can see that there are a number of possible outcomes in most breedings. With your gray mare and a chestnut stallion she can produce chestnut (both her b and the sire's b) or bay IF the other base color gene is B, or either of these with the gray factor. The gray doesn't dominate the base color, it changes it. Since your mare carries Gg, half her babies, statistically, will be gray (those that get the G) and half will be non-gray (those that get the g, or the absence of the G.) Factors such as the graying factor and the dilution factor are transmitted independent of the base color (though sometimes because of their location on a chromosome factors can stick to a particular base color gene and cause a disproportionately high occurrence of a particular phenotype) and can cause any base color to show the changes they cause. All of the results you have gotten are consistent with this theory of genetic inheritance (unless I am missing something in what you are saying.)

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