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Genetics - learning about equine genetics

This page will surely be an ongoing work in progress as we learn and glean information / research some genetic aspects within the equine industry.
Which horse color do you prefer? (Vote below!)

Even though specific colors catch my eye, I never really thought much about what causes horses to be different colors... But when I DID start trying to figure it out, it was absolutely facinating to me! To see those stunning coat colors like Perlino... oh my I know that is a matter of opinion, but they are gorgeous. That creamy, shimmering coat and those dreamy blue eyes. (Those blue eyes don't have the same look that a "paint" that's blue eyed has.) Well, it is just beautiful... to me... as are some of the Champagne colors like Classic, Classic Dun, Classic Cream Dun, Sable, Sable Cream Dun, Amber, Amber Cream Dun... just breathtaking!

Also, I got very interested in why some horses seem to 'stamp' their offspring with certain characteristics (not color). Some with many characteristics, some with few, some with seemingly no noticable characteristics... Some term that as "prepotency" and it is more often heard when referring to stallions.  This intrigued me as I read that it too, as with the color genetics, relates to homozygousity. So trying to get that information to soak into my mind has been interesting and is relevant to trying to preserve the old "foundation bloodlines" that I prefer.

I am not an authority on the subjects/info contained on this page... the writing is here for reference only - mine mainly :)

Color Genetics - some basics and info on homozygousity of color.  

The two base coat colors in horses are SORREL and BLACK. (Sorrel is designated "ee" and Black is designated "Ee", for heterozygous black, or "EE", for homozygous black.) There are also many different modifying genes which can alter these base coats. (Agouti, cream, dun, roan, sabino, champagne, rabicano, pearl, pangare, silver etc... let's look at some here...)

AGOUTI - Agouti is a modifier that affects BLACK, not SORREL (but note that Sorrels can carry Agouti even though it can not be seen visually). Agouti restricts the black on a black horse to the points, mane and tail; thus making the horse a BAY. (Agouti is designated "Aa", for heterozygous agouti and is designated "AA", for homozygous agouti / dominant agouti. No agouti is designated "aa".)

CREAM (Creme) - The cream gene is a dilution and is designated "Cr". (A horse carrying one cream gene is heterozygous for the cream gene. A horse carrying two cream genes is homozygous for the cream gene and will therefore pass one cream gene to each offspring.) Some refer to it as 'creme'.

A sorrel horse with one cream gene is a palomino. (Heterozygous cream.)  A sorrel horse with two cream genes is a cremello. (Homozygous cream.)

A black horse with one cream gene is a smoky black. (Heterozygous cream.) A black horse with two cream genes is a smoky cream / smoky creme. (Homozygous cream.) *Note: smokey black is not necessarily visibly different than black.

A bay is a black horse that carries agouti. A bay horse with one cream gene is a buckskin. (Heterozygous cream.) If that same horse carried two cream genes, it is a perlino. (Homozygous cream.)

Cream is dominant. One parent must be carry cream for the offspring to have cream. *NOTE: Differing from other dilutions, Cream appears very noticably different depending on whether the horse is heterozygous (1 gene) or homozygous (2 genes).

DUN - Dun is a dilution gene. Even though dun is a dilution gene, it is visually different than cream. Commonly known dun colors are dun (bay dun), grullo/grulla (black dun), red dun (sorrel dun).

Dunalino (palomino dun) and dunskin (buckskin dun) are also well known (but un-officially recognized by the AQHA) dun colors which also carry the cream gene.

Dun is dominant, so your horse will visibly show dun if it carries the dun gene.  (However on double dilutes - horses with 2 cream genes - it seems that sometimes the dun markings are harder to see.) If a horse is homozygous for the dun gene, it will pass a dun gene to every foal. *Currently there is no dun gene test available, but from my understanding, it is in the process. :)

CHAMPAGNE - Champagne is a dilution gene. Even though champagne is a dilution gene, it is visually different than cream or dun. (Note a horse can have one or more dilution genes.) Champagne horses are said to have an iridescent sheen to their coat (some do but others may not).

A black horse with a champagne gene is called a Classic Champagne. (Naturally there are various shades of Classic. They may be registered as brown, dun, buckskin since they are not allowed registry under their actual color-name.)

Bay plus champagne is called Amber Champagne. (Amber Champagne horses vary in shade and may be commonly registered in the AQHA as buckskin or dun since they do resemble those colors... however Amber Champagnes commonly have brown/amber eyes (hazel eyes on occasion), freckling around the eyes and muzzle and genitals and have brown points, mane and tail instead of black.)

Sorrel plus champagne is called Gold Champagne. (Gold Champagne horses also vary in shade and may be registered as sorrel, red dun or palomino depending upon the shade/hue of color. They appear distinctly different though due to the freckling as stated above.)

Black + Champagne = Classic
Bay + Champagne = Amber
Sorrel + Champagne = Gold
Brown + Champagne = Sable

Those are the basic color but some more champagne colors (which include other modifying genes) are:

Smoky Black (Black + Cream) + Champagne = Classic Cream (Classic Creme)
Buckskin (Black + Agouti + Cream) + Champagne = Amber Cream (Amber Creme)
Palomino (Sorrel + Cream) + Champagne = Gold Cream (Gold Creme)
Smokey Brown (Brown + Cream) + Champagne = Sable Cream (Sable Creme)

Grulla (Black + Dun) + Champagne = Classic Dun
Dun (Bay + Dun) + Champagne = Amber Dun
Red Dun (Sorrel + Dun) + Champagne = Gold Dun
Brown + Dun + Champagne - Sable Dun

Smoky Grulla (Grulla + Cream) + Champagne = Classic Cream Dun (Classic Creme Dun)
Dunskin (Buckskin + Dun) + Champagne = Amber Cream Dun (Amber Creme Dun)
Dunalino (Palomino + Dun) + Champagne = Gold Cream Dun (Gold Creme Dun)
Smokey Brown + Dun + Champagne = Sable Cream Dun (Sable Creme Dun)

Smokey Cream (Black + 2 Cream) + Champagne = Classic Double Cream (Classic Double Creme)
Perlino (Black + Agouti + 2 Cream) + Champagne = Amber Double Cream (Amber Double Creme)
Cremello (Sorrel + 2 Cream) + Champagne = Gold Double Cream (Gold Double Creme)
Brown + 2 Cream + Champagne = Sable Double Cream (Sable Double Creme)

Smokey Cream + Dun + Champagne = Classic Double Cream Dun (Classic Double Creme Dun)
Perlino + Dun + Champagne = Amber Double Cream Dun (Amber Double Creme Dun)
Cremello + Dun + Champagne = Gold Double Cream Dun (Gold Double Creme Dun)
Brown + 2 Cream + Dun + Champagne = Sable Double Cream Dun (Sable Double Creme Dun)

Sometimes when a horse has a cream dilution and a champagne dilution, they are confused with Cremellos, Perlinos and Smoky Creams (commonly known as "Double Dilutes"), however they do not mature to have blue eyes as do the Cremellos/Perlinos/Smoky Creams (Cremes)... their eyes may be hazel / amber / brown.

Champagne is dominant and therefore your horse will visibly appear champagne when carrying the gene. If a horse is homozygous champagne then it will pass one champagne gene to every foal, Champagne colors are not yet officially recognized by the AQHA and therefore more confusion about the 'description' is spread.    We have a page showing champagne characteristics of our champagne horses.

PEARL - A new dilution. "Pearl", when first identified in the American Quarter Horse, was referred to as "Barlink" since he seemed to be the carrier. There has been some confusion in regards to this modifier as well, especially when combined with the cream gene. ***Will be adding more after I have read up more on this one. :) Currently "Pearl" is thought to be a mutation of cream.

ROAN - Roan is a modifier in which white hair dispersed throughout the torso is seen. The horse's head, points, mane and tail are not usually affected. The degree of roaning can vary. A Sorrel horse carrying the roan gene is a Red Roan. Bay with roan is Bay Roan and Black with roan is Blue Roan. roan is dominant. A horse must have at least one roan parent to be roan. Foals will normally be their actual base color at birth and then roan as they age/shed. A horse carrying one roan gene is heterozygous roan; two roan genes is homozygous roan. (I read there is a theory that the roan gene is thought to be color linked to "e" or "E".) Horses that carry "rabicano" and "sabino" are many times referred to as "Roan" even though the three modifiers are different.  ***Hope to study this a bit more.

GRAY - Gray is a dominant modifier, meaning a horse must have at least one gray parent to be gray. Gray foals will normally be born their base color and then gray out as they shed. Gray is known to continually change in shade from dark charcoal black/gray to an almost white looking gray as the horse ages. A horse carrying one gray gene is heterozygous gray. If a horse has two gray parents and gets one gray gene from each parent then the horse would be homozygous gray, meaning it would give one copy of gray to each foal. If used in a breeding program that would mean all resulting foals from that horse would be gray.

RABICANO - Rabicano is a modifier which is often confused with Roan and/or Sabino Overo since all involve white hair dispersed on the horse. The difference is where and how... Rabicano is most often recognized by its characteristic 'coon tail' or 'skunk tail' which means there is white hair at the top of the horse's tail. The degree or amount of white can vary from unmistakable to hardly noticeable. Rabicano also sometimes carries with it a bit of white hair dispersed throughout an area (commonly reffered to as 'roaning' and frequently in the flank area or underside - which is much like 'sabino') which can also vary in degree/intensity. (Could also favor the Appaloosa coat at times.) Thought to be dominant.    ***Hope to study this a bit more.

SABINO - Sabino is a coat modifier of the overo pattern. Sabino characteristics include white hair dispersed in areas of the horse's body. Typically the flank and underside... Many horses that exhibit the sabino gene have a seemingly higher degree of 'white markings' (high stockings on the legs that may go past the hocks and into the gaskins and/or blaze or bald faces). Sabino could be compared to the Appaloosa coat in that it can be splotchy looking - the hair dispersed is in certain areas and not all over, like roan.   ***Hope to study this a bit more. We have a stallion that carries sabino.

SILVER - Silver acts on black (remember... so does agouti) and is not visible on red base coats therefore red based horses can carry silver without us being able to see it.   ***Hope to study this more - silver buckskin is beautiful.

PANGARE - Pangare (oftentimes spelled pangre) is a modifier that is also referred to as "Mealy" by some. It apparently lightens the hair around the muzzle and eyes, inside of lower legs, on the lower rear of buttock, behind the elbows, in the flank and along the underside of the belly.   ***Hope to study this more as there is a question in my mind that we might have a mare with pangare.

We hope to explore "silver" more, "pangare" and "agouti", especially as it relates to brown in the future as well as "sooty" / "smutty", "mottling", "dappling", "flaxen" and other color genes! Hope to learn about "brindle" too.  WHAT FUN!!! 
(Let's don't forget chimeric / chimerism - not that it's a color thing but 'tis mind boggling :) And I love some of the brindle cattle - I would love to have a beautiful brindle quarter horse!)


Which official AQHA color do you like best?


Other Equine Genetics - some things to glean from when choosing breeding stock.

More on Genetics

LINEBREEDING Is a form of inbreeding, an attempt to concentrate genes of a specific family line while maintaining the percentage of inbreeding where performance is not adversely affected. Linebreeding is a horse with common ancestors with a coefficient greater than 1.80% but less than 3.33%, which would give the animal less than 1 matched pair of chromosomes. A coefficient less than 1.80% is considered a hybrid.

INBREEDING Relates to the number of times one or more common ancestor(s) appear in a pedigree. (And that doesn't mean just on the three generations of the AQHA papers. It means, you go back as far as you can go and use all the information you have available.) The more times those specific ancestors appear on both the sire and the dam's side of the pedigree, the higher the inbreeding percentage can be however this can depend also on how "close up" the common ancestor(s) are as well. Inbreeding is defined as an animal having an inbreeding coefficient of 3.33% or higher which gives the subject animal one or more matched pairs of chromosomes. (Inbreeding reduces the gene pool and therefore lends to homozygousity and prepotency; the ability to consistently reproduce.)

DOUBLE BRED - The term "double bred' means that the horse referenced has a specific bloodline on the top and bottom of its pedigree. (Both the sire and the dam carry that bloodline.)

Crossing individuals from two different breeds, such as Quarter Horses and Thoroughbreds.

Hybrid Vigor is the extra vitality observed when no defective genes are expressed and allows an individual to exhibit added vigor, size, speed, over that of the parents. It is attained by lack of inbreeding. (When hybridization is practiced without inbreeding or linebreeding, athleticism may be present although the ability to reproduce is not consistent.)

The number of matched chromosome pairs out of (32). The higher this number, the more likely the animal will be able to reproduce itself (prepotency).

It has been said that the RULE OF THUMB is: Hybrids run and breed down, Inbreds breed up!

Careful attention to quality selection is crucial to optimal hybrid vigor as well as inbreeding / linebreeding. The end result is maximum prepotency / homozygousity and athleticism.

The ability of a stallion to consistently stamp or mark foals with desirable traits. 

It has been said that 10% of a horse's genes is the minimum needed of a particular line to affect race performance and 20% of a horse's genes is needed to produce a major significant influence in offspring's performance.

Inbreeding should be practiced with selection as should linebreeding. Since inbreeding increases the ability to consistently reproduce, make sure you are reproducing desireable and not undesireable.

Outcrossing of inbred horses to produce Hybrid runners is a method used by some. Outcrossing should also be practiced with selection (some crosses are better than others).

Make sure you make breeding decisions based on your goals. (Example: To produce quality.) Basing your decisions upon the trend of the times is not necessarily the right thing to do ;)

One last note... We have also seen from history that some not so pretty ones have foaled/sired some legends. Guess that's where the 'mind' comes in :)

Have you heard of X-Factor?

I've heard of it and became interested in it when looking at my Dad's mare's pedigree. (That mare's name is Kinda Rosey and I'm pondering the potential of her offspring. She's also the one that started me thinking on the pre-potency of stallions and mares. ... so I'm glad my dad bought that mare LOL Since, I have noted things in my mind from other horses.)

This is still not all settled in my mind (the color genetics part I'm more comfortable with) but from what I have read, this seems to be the jest of it...

Sex of the foal is based on the chromosomes in the sperm.  A stallion can pass either an X or a Y chromosome, while a mare can only pass an X chromosome.  Two X chromosomes (one from each parent) result in a filly, but an X and a Y chromosome (the X coming from the mare - since that's all she can give :) and the Y coming from the stallion) can only result in a colt.

It is believed that the female chromosome (X) has particular recessive genes which can produce physical characteristics that result in exceptional performance. 
Recessive genes are "realized" when they are inherited from both the sire AND the dam (read more on recessive / dominant and homozygousity in the color section). 
X Chromosomes can not be passed from father to son... they are passed from father to daughter, mother to daughter or mother to son. 
One can, at times, trace athletic talent and ability through mare line (female X chromosome - known as the "X Factor").  This is why the "tail female line" in a horse's pedigree is so important.  A broodmare's sire is of great importance in successful breeding programs - both paternal and maternal bloodlines play a part and maternal lineage should not be under-estimated - as is sometimes the case.