Some Terms and Notes

Starting from the bottom,

The building blocks of DNA are the Base Pairs:

Adenine and Thymine (A-T)

Guanine and Cytosine (G-C)

All DNA patterns are based on different orderings of these pairs (barring the substitution for Thymine for Uracil [U] in RNA) this simple code is what dictates the order in which the amino acids are placed making up every single protein in the body - enzymes, pigments, cell walls - everything.

A length of Base Pairs is known as either an Exon or and Intron - Exons are the pieces of DNA that code, Introns separate Exons and are thought to 'prepare' the functions the Exons execute.

Groups of Exons and Introns form Genes these genes code for a specific protein or set of proteins that have a defined function, these are given names such as KIT or MAPT. A location on this gene where a specific mutation takes place is known as a Locus (plural Loci) so for example the Cream Locus is on the MAPT gene.

These Genes are parts of Chromosomes, chromosomes are numbered, in the horse ECA1 (Equine Chromosome 1) - ECA31 plus the sex Chromosomes which are Labeled ECAX and ECAY. For example, the Cream Locus is a Mutation point on the MAPT gene which is on ECA21.

Mutation - mutations are changes in the DNA, most of these occur in 'Junk' or non-coding DNA but when they occur in the coding DNA a protein is altered. This alteration can be catastrophic preventing the resulting zygote from even being viable, can be so minimal it passes unnoticed, it can be negative - a shining albino tiger in the grasslands can't blend in to well and is consequently rare as very few survive to breed - or beneficial - the same white tiger in the northern area of Siberia where it is snowy much of the year is at an advantage in terms of camouflage. This is the basis of evolution. Humans also make use of these differing traits in 'unnatural' selection, those cows with a mutation causing them to grow faster and heavier may not live long in the wild where their increased requirement for food is a disadvantage but on the farm will be prized and bred from as they provide more meat faster.

These mutations are what provide the huge array of possible horse colours that I am trying to define and explain here.

There are several types of mutation:

Frameshift Mutation - A frameshift mutation is caused by either an insertion or a deletion in the gene’s coding From the point of the insertion or deletion, the translation is completely different from the original

Nonsense Mutation - Nonsense mutations cause a “stop” in the reading sequence, similar to a faulty computer program. the “stop”is an inability to continue reading the sequence, results in a loss of function of the protein.

Missense Mutation - This type of mutation is the result of one amino acid being replaced by another. The result is generallythat the protein is no longer functional.

Splice Site Mutation - Splice site mutations are insertions or deletions of intron coding as it is being translated into the mature genetic coding of the exon. Some of the intron code is spliced into the exon

Splice Variant - Certain exons are spliced out, altering the expression of the protein

Duplication - A duplication mutation is reasonably self-explanatory, a section of DNA is duplicated.

Inversion Mutation - an Inversion mutation is where a section of DNA code has been inverted - it is still present but back to front.

I have been pretty useless about updating as I have been waiting for replies on requests to use pictures. Unfortunately people are not getting back to me one way or another and much as I hate the idea of stealing photos I think I need to get on with it. The use is purely non-profit and (hopefully) educational so I am pretty sure it comes under fair use and I will link back to the source of any picture I use so I hope no-one will be upset by me using pictures to illustrate the colours.

Sources for this page include:

http://www.thehorse.com/ViewArticle.aspx?ID=4354 - an article from The Horse.com - A Horse of A Different Colour - Stephanie J. Corum

http://www.thesciencedictionary.com/ - A useful on-line dictionary of scientific terms. I use this a lot for when I know something but cannot work out how to say it.

Introduction to Horse Colour Genetics

First I am going to list the various colour genes with a very basic description then over the next few weeks I will go into detail on each one. I have split the colours into sections, there are not gospel and simply how it makes sense to me, others will split things up differently. I am using the XX , Xx , xx format to record zygosity as I prefer it, often one will also see it written X/X , N/X , N/N with X representing the relevant allele's code.

It is important to note a couple of things,

1 - all horses have all of these Loci (Locus'es) when someone refers to there being 'no Dun in arabs' what they mean is that all arabs are dd negative for Dun not that the locus does not exist. Like a set of filing cabinets - the loci are the drawers, all horses have all the drawers, in each drawer are two pieces of paper, some will say Yes (D) some will say No (d), is all horses in a closed stud book have No(d) in the Dun Drawer then there is no dun, the drawer is still there though.

2 - Dominance is only relevant within a locus, the A allele is dominant over the a allele because Aa has the same phenotype or appearance as AA, chestnut is a recessive trait because ee is required for it to show. Loci are not dominant to recessive to each-other, chestnut is not dominant over agouti because agouti does not show on chestnut, agouti is still there doing its' thing the fact that there is no black pigment to restrict does not stop is sending the order.

Some genes are expressed minimally to maximally, a minimal expression will show very little of the typical phenotype but still carry the gene and be capable of passing it on. A maximal expression is a very strong expression of the phenotype. The terms are most commonly used when referring to the different effects of the white patterns.

Base Colours

Extension - This is the locus that controls whether the horse is black based or red (chestnut) based, black is dominant and red is recessive. EE - Black, Ee - Black, ee - Red

Modifyers

Agouti - this is the locus that controls bay and brown, on a black base AA and Aa restrict the black pigment resulting in bay, aa does not restrict black so the horse is black. There is a test for an At allele at the agouti locus as well which causes a brown colour and it is suspected that 'wild bay' is another mutation at agouti.

Grey - This locus carries a dominant trait - GG or Gg cause the foal to be born whatever colour it's other genes dictate but over time more and more white hair appear in the coat giving a grey effect until the horse is white all over.

True Roan - This locus carries a dominant trait - RnRn or Rnrn cause the horse to show white hairs mixed in with the coat fairly uniformly across the body and less so on the face and lower legs. It is often seasonal in variation as to the proportion of white in the coat.

Sooty - causes a dark dappled effect on the coat, often seen in Morgans and in the extreme in the Para farms Arabian lines. Cause and inheritance unknown.

Rabicano - Causes roaning in the tail arranged in bars that are referred to as a 'skunk' tail, often with barred stripes of roaning on the barrel. Thought to be related to 'sabino'.

Frosted Roan - Roaning along the topline only, possibly a minimal expression of true roan.

Dilutions

Silver - A dominant trait, ZZ or Zz causes black pigment to be diluted, blacks will look brownish often dappled, bays may look chestnut, the mane and tail are usually more dilute showing a silver or blonde colour.

Champaign - A dominant trait, ChCh or Chch will result in a dilute coat and 'pumpkin' dilute skin and often dilute 'amber' eyes. Foals are often born with blue/green eyes and darker coats. Champaign can be mistaken for palomino on chestnut and buckskin on bay, it also often displays an unusually high gloss on the coat.

Cream - An Incomplete Dominant trait, when heterozygous CrC it dilutes only red pigmented hair giving a palomino on chestnut and a buckskin with bay, it has little to no effect on black. When Homozygous CrCr is causes a much stronger dilution of skin, hair and eyes, giving a cremello on chestnut, a perlino on bay and a smoky cream on black, typically doubly dilutes as they are often referred to have pink skin, light hooves, blue eyes and creamy to white hair.

Pearl - also known as the barlink factor. and incomplete dominant which dilutes only the skin when heterozygous and mimics champaign when homozygous. When paired with cream it will mimic a double dilute. It is theorised to be another allele at the cream locus of closely linked however despite offering a test UC Davis have not yet published their work so this cannot be confirmed.

Dun - A dominant trait DD and Dd dilute the hair causing a lighter coat with 'primitive markings' - dorsal stripe, leg barring, cobwebbing and face masks.

Flaxen - Causes a creamy or blonde mane on a chestnut base. Cause and inheritance unknown.

Pangare - Causes a mealy muzzle and creamy areas around the belly, the stifle and the elbows, sometimes expressed more strongly than others. Cause and inheritance unknown..

White Patterns

Tobiano - Causes pink skinned white patches on the base colour, ToTo or Toto seem to cause a similar amount of white though 'ink spots' or 'cats paws', little spots in the white patches, seem to be related more (though not exclusively) to homozygous horses. Tobiano seems to 'like' to leave the face, chest and flank shields coloured.

Frame - Also known as LWO or OLW, overo lethal white, OO causes lethal white foals, the homozygote will be born white and with an incomplete colon, they do not survive beyond 48 hours or so. Oo horses display pink skinned white patches that rarely cross the ventral or dorsal line and can often leave a single leg coloured, blue eyes are common.

Sb1 - When homozygous causes white, pink skinned, dark eyed horses sometimes will a little colour along the topline, heterozygous horses tend to show socks, blazes, sometimes belly spots, messy markings and roaned patches. Expression can vary and not all horses showing these traits test positive hence the theory that there are more Sb genes to find.

Dominant White - there are at the time of writing at least 7 dominant white genes out there, they all seem to cause a range of effects from pure white, pinks skinned, dark eyed horses to long socks, roaned patches and messy white. They are all in a similar area of the KIT gene and are all homozygous lethal. They seem to be restricted to particular families and have been found in TB's, Drafts, Arabs, Icelandics and Holsteiners.

Splash - The cause and inheritance of this is uncertain but it is a distinct pattern causing smooth edged white patches with pink skin, long socks, belly spots, bald faces and a 'paint dipped' look are indicative. Blue eyes are common.

'Sabino' - Sabino is in italics as bar the Sb1 gene it tends to be used to refer to any roaning, spots or white patterns not covered elsewhere.

Spots - Spots are insanely complicated with leopards, near leopards, blankets, snowcaps, fewspots and 'appy roans' all to be accounted for. The theory takes up far to much space to go into great detail here but I will at some point I promise.

Misc

Odd spots and effects - tetrach spots, bircatcher spots, brindling, bloody shoulders, cobwebbing ect ect. I will do a post covering these at some point.

The information on here has come from my own knowledge which has been gained over the last 7 years or so of interest which started with me trying to list all the colours that horses came in during a biology lecture on mendelian genetics. I have read so many books, websites and papers since then I cannot hope to list them all here but I will list a few that were particularly useful.

http://equine.colorgenetics.info/ - Good coverage of basic genetics as well as equine colour specifics, now being extended to cover donkeys, dogs and various other species. A good set of information and an attached forum that is friendly and informative.

http://www.duncentralstation.com/ - Shows some lovely examples of duns and how to differentiate dun from, among other things, buckskin. Also - http://duncentralstation.com/PDF/KITGeneMutations-Castle.pdf is one of the best descriptions of KIT mutations I have ever seen.

Google scholar is my friend when it comes to finding papers on various things and the equine-colorgenetics forum is another good place to look for links.

Dr. Ann T. Bowling of the University of California and Dr. Phillip Sponenberg of Virginia Polytechnic Institute have both written extensively on the topic and are definitely worth reading though I would urge anyone reading them to remember that the field moves on at a terrifying pace so anything published more than a year ago is pretty much out of date.