Talk:Equine coat color genetics

message: the following link has the most informative and easy-to-understand explanation of equine color genetics that I have come across:
http://www.equinecolor.com/color.html
: I would in turn suggest to include the following link because it is very easy to understand for beginners and gives a feel for how genetics work: http://www.jenniferhoffman.net/horse/equinegenetics.html --Xaya 13:04, 14 September 2011 (UTC)
replies: text: It's a for-profit site, is slow to load, and is just pictures.  Cute, but not really a RS by WP standards.  Montanabw(talk) 18:18, 14 September 2011 (UTC)
thread_title:  Comment 

message: I have recently been researching the genetics of horses, and have found this article to be one of the least accurate I have come across. Although much of it is correct, it still states many theories that have been disproven for as long as a decade in some cases. I am currently writing an article on current horse genetics, and will post it here once it is complete. In the meantime, anyone researching horse genetics is recommended looking elsewhere. Bill Killed The Unicorns 08:01, 16 September 2006 (UTC)
replies: text: Don't just slam, provide some basic evidence and recommend an alternative link, then.  If you are so very knowledgable, you can surely do this in about 30 seconds.  Best to be positive. Montanabw 05:57, 1 November 2006 (UTC)
replies: text: WP:CIVIL, please. riana_dzasta 02:59, 2 November 2006 (UTC)
thread_title:  Accuracy of article (Comment recently restored) 

message: Noted earlier comment since removed by poster (See 'Accuracy of Article'), though it worth resurrecting for comment.
Suggest that it might be useful to explain what and how various theories are "outdated by 10 years" in the article and provide some links to current research so that those of us who care can take a look and see what kind of consensus can be reached.  My point is merely that we float test balloons before diving in with wholesale edits of what clearly was an article that someone took a LOT of work to create.  
I find the genetics of color quite interesting and a field that has changed beyond recognition since I took a class that discussed genetics during the 1980's.  I am not surprised that even now there are still changes and debates going on...but I have also seen some head in the sand attitudes amongst people who dislike the revelations of modern genetics and attack the science itself. (Thinking here of the early days of HYPP being linked to Impressive as an example.)
I am not a geneticist, I am just a horse person with a penchant for wordsmithing and my (warning: bad pun coming) horse in this race is to try and separate what is POV from what is flat-out inaccurate (amazing how often people confuse the two).  If I am convinced that something is the consensus of modern science, I am happy.  If not, I like to see the various points of view presented so that people can look into the issue for themselves.  (Like the eternal debate over on the wild horse article over whether equus ferus is or is not the same as equus caballus...sigh...everyone argues, no one cites to research.  How can we laypeople decide if we can't review the research others have done?  Arrgh!) 
Personally, I have yet to see a good research citation on the question of dominant white (WW) as a lethal, as contrasted with Lethal White Syndrome (OO).  At this point, it is my understanding that both exist, but I have also seen (though am not yet convinced) some arguments that there is no such thing as the W gene at all, that all "white" horses are so-called fully-expressed Pintos...curious to hear what folks think? Montanabw 00:17, 17 September 2006 (UTC)
thread_title:  Research issues 

message: ::I have no problem with someone adding Pearl to the chart.  If there isn't a wikipedia article on it, maybe that needs to be done too.  There is an article on Silver dapple gene, but I don't think data is in the chart yet here. I also am OK with creating some consistency with the gene symbols.  But, I  haven't the time to do it. Someone else sure can.  Best not to start a nomenclature fight, whatever is the "majority" view probably best (maybe a paragraph explaining other terminology would help.) Montanabw 16:31, 19 April 2007 (UTC)
thread_title: Pearl and Silver Dapple

message: The best article I have seen on the white gene issue is Overton, Rebecca.  "By a Hair" Paint Horse Journal March 2004.  It explains LWS and how that test works, it mentions W as a gene that really does exist and says that WW foals are actually reabsorbed as embryos, it discusses the way the LWS gene cannot be determined by coat pattern, as it can be masked by many colors, it has even cropped up in the offspring of solid-colored horses.  This one may be the most useful in practical terms.  Now, can we end this discussion?  It's getting redundant. User:Montanabw
:Found the site for it: http://www.painthorsejournal.com/archives/index.html The article referred to here is the 3rd one from the top. Bill Killed The Unicorns 12:29, 6 November 2006 (UTC)
thread_title:  End of White discussion? 

message: There are inconsistencies in the abbreviations used.  I do not know which is correct, but this is confusing to a newbie like me.  I hope someone who knows what is right will get them consistent.
Formulas table uses C and CC often; I did not find a C in the Alleles table. (??C for chestnut??)  Formulas also uses Ccr and CCr, which may be a combination of the unknown C and Cream.  Alleles table did not seem to combine the abbreviations that way.
Alleles table mostly uses lower-case for second letter, as in Cr and Rn.  However, TO is also used.
Formulas table uses RN for roan, not Rn.  Uses TO for tobiano, which is consistent with Alleles table. but confusing.
Signupslls 13:42, 19 October 2007 (UTC)
replies: text: Good point, C seems to be related to the cream gene, which should be Cr, I think.  Chestnut is designated by "e" (indicating lack of the "E" Extension gene which creates black coloring.)  TO, however, is correct for Tobiano, I believe.  UC Davis Veterinary Genetics lab is the leader on this stuff, I suggest that anyone who wants to work on this use their material.  Not sure how much time I will have to look into this, but I agree consistency is needed. Montanabw(talk) 03:26, 20 October 2007 (UTC)

text: Works for me.  Also check in with User:Countercanter, though, she's the main genetics guru around the horse articles.   Montanabw(talk) 04:38, 26 March 2008 (UTC)
thread_title:  Consistency within and between tables for Alleles and Formulas 

message: The known, not proposed, genes to date with all the mind-numbing information...(more coming, interrupted)
COAT COLOR...
Locus: Extension (E)
Gene/protein: Melanocortin-1-receptor (MC1R)
Mutation: C901T (basepair format) single nucleotide polymorphism
Notation: Wildtype = E, C901T polymorphism = e
Phenotypes
* E/E and E/e unaffected
* e/e loss of function of MC1R protein in the hair; aeumelanistic coat, unaffected skin and eyes
Locus: Agouti (A)
Gene/protein: Agouti Signalling Protein (ASIP)
Mutations: 11 basepair deletion in Exon 2 (Positions 2174-2184); another as yet undescribed in peer reviewed journal
Notation: Wildtype = A, ADEx2 = a; unpublished = At
Phenotypes:
* A/A and A/a unaffected
* a/a modified agouti signaling protein; loss of eumelanistic colorpointing in the coat, unaffected skin and eyes
Locus: Dun (D)
Gene/protein: unknown (I believe "they" know where it is...but not tellin!)
Mutations: unknown
Notation: Wildtype = D, non-dun = d
Phenotypes:
* D/D and D/d unaffected
* d/d unrestrained, intense pigment deposition in the coat and loss of primitive markings, unaffected skin and eyes
Locus: Cream (C)
Gene/protein: Solute carrier family 45, member 2 (SLC45A2) aka Membrane associated transporter (MATP)
Mutations: N153D single nucleotide polymorphism, exon 2
Notation: Wildtype = C, N153D = CCr
* C = unaffected
* C/CCr = hypophaeomelanism (dilute red pigment), skin and eyes superficially affected
* CCr/CCr = hypomelanism (dilute pigment) coat, skin and eyes only faintly pigmented
Locus: Champagne (Ch)
Gene/protein: Solute Carrier 36 family A1 (SLC36A1)
Mutations: C188G single nucleotide polymorphism
Notation: Wildtype = ch, C188G = CH
Phenotypes:
* CH/CH and CH/ch = blue eyes and pink skin at birth, changing to amber/green and mottled pink/pumpkin tones at adulthood, respectively; hypomelanism in coat
* ch/ch unaffected
Locus: Silver (Z)
Gene/protein: Silver homolog (SILV) or Premelanosomal protein 17 (PMEL17)
Mutations: Arg618Cys single nucleotide polymorphism
Notation: Wildtype = z, Arg618Cys = Z
Phenotypes:
* Z/Z and Z/z = hypoeumelanistic coat, unaffected skin and eyes
* z/z = unaffected
Locus: Pearl (Prl)
Gene/protein: Unknown (no paper)
Mutations: unknown
Notation: Wildtype = prl, unknown mutation = PRL
Phenotypes:
* PRL/PRL = hypophaeomelanism: apricot-colored coat, light tan eyes, pinkish-purple skin.
* PRL/prl = unaffected, unless accompanied by other hypopigmentation genes
* prl/prl = unaffected
COAT PATTERN...
Locus: Leopard (Lp)
Gene/protein: Transient receptor potential cation channel, subfamily M, member 1 (TRPM1)
Mutations: unknown
Notation: Wildtype = lp, unknown mutation/leopard complex = LP
Phenotypes:
* LP/LP = striped hooves, mottled skin, white sclera, leopard-associated dense white regions; dense white regions may have a few small spots of pigment; predisposed to congenital stationary night blindness
* LP/lp = striped hooves, mottled skin, white sclera, leopard-associated dense white regions; dense white regions have a multitude of large, round spots of pigment.
* lp/lp = unaffected
Locus: Gray (G)
Gene/protein: Syntaxin 17 (STX17)
Mutations: 4.6kb duplication in intron 6; cis-acting regulatory mutation
Notation: Wildtype = g, cis-acting regulatory mutation = G
Phenotypes:
* G/G and G/g = coat progressively loses pigment, turning gray; predisposed to melanoma and vitiligo
* g/g = unaffected
Locus: Frame Overo (O)
Gene/protein: EDNRB
Mutation: Ile118Lys
Notation: Wildtype = N, Ile118Lys = O
Phenotypes:
* O/O = ileocolonic agangliosis, 90%+ unpigmented/white, sometimes deafness, blue eyes, death within 72 hours of birth.
* N/O = healthy; frame overo white spotting pattern, eyes often blue
* N/N = unaffected
Locus: Sabino 1 (SB1)
Gene/protein: KIT
Mutation: KI16+1037A or r.2350_2472del or c.2350-13T>A or g.166003T>A, resulting in exon skipping
Notation: Wildtype = sb1, KI16+1037A polymorphism = SB1
Phenotypes:
* SB1/SB1 = typically 90%+ unpigmented/white; eyes unaffected
* SB1/sb1 = typically jagged/roan-edged markings concentrated on the head and legs and midventral line; eyes unaffected
* sb1/sb1 = unaffected
Locus: Roan (RN)
Gene/protein: KIT
Mutation: Unknown
Notation: Wildtype = rn, unknown polymorphim = RN
Phenotypes:
* RN/RN and RN/rn = interspersed, non-progressive white hairs except on head and legs
* rn/rn = unaffected
Locus: Tobiano (TO)
Gene/protein: KIT
Mutation: Downstream chromosomal inversion
Notation: Wildtype = to, chromosomal inversion = TO
Phenotypes:
* TO/TO and TO/to = unique depigmentation pattern, typically smooth, vertically-oriented, crosses the dorsal midline
* to/to = unaffected
Locus: White 1 (W1)
Gene/protein: KIT
Mutation: c.2151C.G or g.164267C>G or p.Tyr717X, nonsense mutation from SNP in exon 15
Notation: Wildtype = W+, p.Tyr717X = W1
Phenotypes:
* W1/W1 = presumed embryonic lethal
* W+/W1 = lack of melanocytes in part of skin and coat; typically 90%+ white/unpigmented, with pigmented areas along the topline that lose pigmentation with age; eyes unaffected. Franches Montagnes breed.
* W+/W+ = unaffected
Locus: White 2 (W2)
Gene/protein: KIT
Mutation: c.1960G>A or g.160670G>A or p.Gly654Arg, missense mutation from SNP in exon 17
Notation: Wildtype = W+, p.Gly654Arg = W2
Phenotypes:
* W2/W2 = presumed embryonic lethal
* W+/W2 = lack of melanocytes in part of skin and coat skin and coat; typically 90%+ white/unpigmented; eyes unaffected. Thoroughbred.
* W+/W+ = unaffected
Locus: White 3 (W3)
Gene/protein: KIT
Mutation: c.706A>T or g.131675A>T or p.Lys236X, nonsense mutation from SNP in exon 4
Notation: Wildtype = W+, p.Gly654Arg = W2
Phenotypes:
* W3/W3 = presumed embryonic lethal
* W+/W3 = lack of melanocytes in part of skin and coat skin and coat; typically 90%+ white/unpigmented; eyes unaffected. Arabian.
* W+/W+ = unaffected
Locus: White 4 (W4)
Gene/protein: KIT
Mutation: c.1805C>T or g.160429C>T or p.Ala602Val, missense mutation in Exon 12
Notation: Wildtype = W+, p.Ala602Val = W4
Phenotypes:
* W4/W4 = presumed embryonic lethal
* W+/W4 = lack of melanocytes in part of skin and coat skin and coat; typically 90%+ white/unpigmented; eyes unaffected. Camarillo White Horse.
* W+/W+ = unaffected
Locus: White 5 (W5)
Gene/protein: KIT
Mutation: c.2193delG or g.164309delG or p.Thr732GlnfsX9, Deletion in Exon 15 produces frameshift, premature stop codon
Notation: Wildtype = W+, p.Thr732GlnfsX9 = W5
Phenotypes:
* W5/W5 = presumed embryonic lethal
* W+/W5 = lack of melanocytes in part of skin and coat skin and coat; typically 90%+ white/unpigmented; eyes unaffected. 6 white, 2 near-white, 4 sabino-type. Puchilingui family. 3/4 sabino-type = W+/W5
* W+/W+ = unaffected
Locus: White 6 (W6)
Gene/protein: KIT
Mutation: c.856G>A or g.136456G>A or p.Gly286Arg, missense mutation in Exon 5
Notation: Wildtype = W+, p.Gly286Arg = W6
Phenotypes:
* W6/W6 = presumed embryonic lethal
* W+/W6 = 1 almost pure white Thoroughbred.
* W+/W+ = unaffected
Locus: White 7 (W7)
Gene/protein: KIT
Mutation: c.338-1G>C or g.130210G>C or r.spl?, Splice site mutation at 3' of Intron 2, alters reading of Exon 2-21
Notation: Wildtype = W+, r.spl = W7
Phenotypes:
* W7/W7 = presumed embryonic lethal
* W+/W7 = solid dam and nearly all-white filly, some pigmentation around her ears, topline. Thoroughbreds.
* W+/W+ = unaffected
Locus: White 8 (W8)
Gene/protein: KIT
Mutation: c.2222-1G>A or g.164835G>A or r.spl?, Splice site mutation at 5' of Intron 15, alters reading of exon 15-21
Notation: Wildtype = W+, r.spl = W8
Phenotypes:
* W8/W8 = presumed embryonic lethal
* W+/W8 = partially-white Icelandic Horse, solid-colored parents and 4 solid maternal half-siblings. Spontaneous mutation.
* W+/W+ = unaffected
Locus: White 9 (W9)
Gene/protein: KIT
Mutation: c.1789G>A or g.160413G>A or p.Gly597Arg, missense mutation at Exon 12
Notation: Wildtype = W+, p.Gly597Arg = W9
Phenotypes:
* W9/W9 = presumed embryonic lethal
* W+/W9 = all-white Holsteiner, no family members
* W+/W+ = unaffected
Locus: White 10 (W10)
Gene/protein: KIT
Mutation: c.1126_1129delGAAC or g.143284_143287delGAAC or p.Glu376PhefsX3, frameshift mutation at Exon 7
Notation: Wildtype = W+, p.Glu376PhefsX3 = W10
Phenotypes:
* W7/W7 = presumed embryonic lethal
* W+/W7 = 27 family members: 5 white, 5 spotted, all heterozygous. Wide range of phenotypes; apron blaze, four white legs, belly spots.
* W+/W+ = unaffected
Locus: White 11 (W11)
Gene/protein: KIT
Mutation: c.2684+1G>A or g.169780G>A or r.spl?, Splice site mutation at 5' of intron 20
Notation: Wildtype = W+, r.spl = W11
Phenotypes:
* W11/W11 = presumed embryonic lethal
* W+/W11 = One all-white South German Draft Horse stallion + 3 white offspring.
* W+/W+ = unaffected
Countercanter (talk) 00:51, 27 May 2009 (UTC)
thread_title:  Refresher and updates 

message: Plopping them here for now. Countercanter (talk) 02:05, 26 May 2009 (UTC)
thread_title:  Proposed genes 

message: For future reference, the diff on the theoretical colors that was tossed from the main article;  http://en.wikipedia.org/w/index.php?title=Equine_coat_color_genetics&diff=292343431&oldid=286149520  
I know that there is a contingent amongst the Haflinger crowd that is big on proving that there is a flaxen gene, and the Friesian folks as well as some other color breeders are bound and determined to prove there is a non-fading black.   Just FYI.  Montanabw(talk) 06:22, 26 May 2009 (UTC)
replies: text:  I absolutely believe that there is a gene for flaxen, and a gene for non-fading black. However, a very thorough search of the MC1R gene failed to produce ANY other notable polymorphisms, so to annotate "non-fading black" as an allele of Extension is inaccurate. Countercanter (talk) 13:06, 26 May 2009 (UTC)
thread_title:  Tucking in the theoretical stuff 

message: ...let's make it a TABLE.
Phenotype              	Potential Genotype	Potential Genotype	Potential Genotype	Potential Genotype	Potential Genotype	Potential Genotype	Potential Genotype
                       	Extension         	Agouti            	Dun               	Champagne         	Silver            	Cream             	Pearl
Bay                    	E/-               	A/-               	d/d               	ch/ch             	z/z               	cr/cr             	prl/prl
Bay dun                	E/-               	A/-               	D/-               	ch/ch             	z/z               	cr/cr             	prl/prl
Amber champagne        	E/-               	A/-               	d/d               	CH/-              	z/z               	cr/cr             	prl/prl
Silver bay             	E/-               	A/-               	d/d               	ch/ch             	Z/-               	cr/cr             	prl/prl
Buckskin               	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/cr             	prl/prl
Perlino                	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/CR             	prl/prl
Bay pearl              	E/-               	A/-               	d/d               	ch/ch             	z/z               	cr/cr             	PRL/prl
Bay double pearl       	E/-               	A/-               	d/d               	ch/ch             	z/z               	cr/cr             	PRL/PRL
Amber dun              	E/-               	A/-               	D/-               	CH/-              	z/z               	cr/cr             	prl/prl
Silver bay dun         	E/-               	A/-               	D/-               	ch/ch             	Z/-               	cr/cr             	prl/prl
Buckskin dun           	E/-               	A/-               	D/-               	ch/ch             	z/z               	CR/cr             	prl/prl
Perlino dun            	E/-               	A/-               	D/-               	ch/ch             	z/z               	CR/CR             	prl/prl
Bay dun pearl?         	E/-               	A/-               	D/-               	ch/ch             	z/z               	cr/cr             	PRL/prl
Bay dun double pearl?  	E/-               	A/-               	D/-               	ch/ch             	z/z               	cr/cr             	PRL/PRL
Amber silver           	E/-               	A/-               	d/d               	CH/-              	Z/-               	cr/cr             	prl/prl
Amber cream            	E/-               	A/-               	d/d               	CH/-              	z/z               	CR/cr             	prl/prl
Double cream champagne 	E/-               	A/-               	d/d               	CH/-              	z/z               	CR/CR             	prl/prl
Amber pearl            	E/-               	A/-               	d/d               	CH/-              	z/z               	cr/cr             	PRL/prl
Amber double pearl     	E/-               	A/-               	d/d               	CH/-              	z/z               	cr/cr             	PRL/PRL
Buckskin silver        	E/-               	A/-               	d/d               	ch/ch             	Z/-               	CR/cr             	prl/prl
Perlino silver         	E/-               	A/-               	d/d               	ch/ch             	Z/-               	CR/CR             	prl/prl
Silver bay pearl       	E/-               	A/-               	d/d               	ch/ch             	Z/-               	cr/cr             	PRL/prl
Silver bay double pearl	E/-               	A/-               	d/d               	ch/ch             	Z/-               	cr/cr             	PRL/PRL
Buckskin pearl         	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/cr             	PRL/prl
Buckskin double pearl  	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/cr             	PRL/PRL
Perlino pearl          	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/CR             	PRL/prl
Perlino double pearl   	E/-               	A/-               	d/d               	ch/ch             	z/z               	CR/CR             	PRL/PRL
Amber dun silver       	E/-               	A/-               	D/-               	CH/-              	Z/-               	cr/cr             	prl/prl
Amber buckskin dun     	E/-               	A/-               	D/-               	CH/-              	z/z               	CR/cr             	prl/prl
Amber perlino dun      	E/-               	A/-               	D/-               	CH/-              	z/z               	CR/CR             	prl/prl
Amber dun pearl        	E/-               	A/-               	D/-               	CH/-              	z/z               	cr/cr             	PRL/prl
Amber dun double pearl 	E/-               	A/-               	D/-               	CH/-              	z/z               	cr/cr             	PRL/PRL
dun + silver + cream = Silver buckskin dun
dun + silver + 2cream = Silver perlino dun
dun + silver + prl = Silver bay dun pearl
dun + silver + 2prl = Silver bay dun double pearl
dun + cream + prl = Buckskin dun pearl
dun + 2cream + prl = Perlino dun pearl
dun + cream + 2prl = Buckskin dun double pearl
dun + 2cream + 2prl = Perlino dun double pearl
champagne + silver + cream = Amber silver cream
champagne + silver + 2cream = Silver perlino champagne
champagne + silver + prl = Amber silver pearl
champagne + silver + 2prl = Amber silver double pearl
champagne + cream + prl = Amber cream pearl
champagne + 2cream + prl = Perlino pearl champagne
champagne + cream + 2prl = Amber cream double pearl
champagne + 2cream + 2prl = Perlino double pearl champagne
silver + cream + prl = Buckskin silver pearl
silver + 2cream + prl = Perlino silver pearl
silver + cream + 2prl = Buckskin silver double pearl
silver + 2cream + 2prl = Perlino silver double pearl
dun + silver + champagne + cream = Amber silver cream dun
dun + silver + champagne + 2cream = Silver perlino dun champagne
dun + silver + champagne + pearl = Amber dun silver pearl
dun + silver + champagne + 2pearl = Amber dun silver double pearl
dun + silver + champagne + cream + pearl = Amber silver buckskin dun pearl
dun + silver + champagne + 2cream + pearl = Silver perlino dun pearl champagne
dun + silver + champagne + cream + 2pearl = Amber silver buckskin dun double pearl
dun + silver + champagne + 2cream + 2pearl = Silver perlino dun double pearl champagne
How awful, no? 
There are ten options: black, chestnut, bay, dun, silver, champagne, heterozygous cream, homozygous cream, heterozygous pearl, and homozygous pearl. That is to say, the table that included all the potential coat COLORS in horses from KNOWN genes would be 10! Which, according to Google, equals 3,628,800. Since silver doesn't affect chestnut, it's rather fewer than that, but still... Countercanter (talk) 22:00, 26 May 2009 (UTC)
replies: text: My mind just boggled!  Montanabw(talk) 00:14, 27 May 2009 (UTC)
thread_title:  And if there's going to be a table... 

message: Surprise! Countercanter (talk) 13:57, 27 May 2009 (UTC)
replies: text: Hm.  Indirect marker test.  They like to do these.  Seems like when they do enough, they get a large enough set of samples to isolate the actual gene(s) more closely.  I know the Tobiano test started out this way, but I think they've got it more specific now.  This is also what the CA test is now, too.  Now to get the Arabian registry to quit registering Sabinos and Rabicanos as "roan."  Sigh...Montanabw(talk) 04:03, 28 May 2009 (UTC)
replies: text: I think that indirect tests reflect the intense competitive pressure to offer a test. There are a LOT of good DNA testing services out there. But yes, I think an indirect test also helps them get a bigger sample pool. Countercanter (talk) 11:40, 28 May 2009 (UTC)
thread_title:  Roan zygosity test 

message: Okay. I can appreciate why you wrote the intro the way you did. There is a difference between "We chose this arbitrary starting point because it would be easier to synthesize this way" and "The fundamental genetic default color of all domesticated horses is "red"." In reality, the DEFAULT (that is a simple term for "wildtype") coat color is bay dun with pangare.
It seems logical to me, from the presence of grullo bred-back primitive horses, that the first event that may have altered the wildtype might have been "The Breaking of Agouti." Let me rephrase. BAY is the default. Uniform black is the result of the BREAKING of Agouti. 
Our friends researching early domesticated horse coat colors seem to feel that "The Breaking of Extension" was one of, if not the, earliest events, too. Let me rephrase again. NON-RED is the default. Chestnut is the result of the BREAKING of Extension.
I think that as the data on Dun becomes more clear, we will hear more about it, but DUN is the default state and NON-DUN is the mutation. There is precious little molecular research out there on it. Aside: The one paper I read seemed to be drawing connections between "Dun" in horses and "Dilute" in dogs, cats, and mice. Can you imagine that there is a protein whose job it is to stick to a melanin granule and drag it to a good spot in the hair? These fibers are called melanophilin, and I believe they are similar to the fibers that grab the chromosomes and drag them apart in cell division, but I am just guessing. Anyways, this review seemed to suggest that Dun and Dilute were related. I use the Horsey Genome Scan to look for the Melanophilin (MLPH) gene and it's on chromosome 6, not 8...but then I'm not sure I had an entirely good grasp of the features. It also seems like such an obvious choice, and clearly researchers have been scratching their heads over candidate genes.
The important thing I wanted to communicate is this: I think that the "base color" approach is the most digestible way to understand horse coat color genetics. However, that introduction needs to say that: we chose this method of explanation because it's easier to understand, and it has no significance beyond that. Countercanter (talk) 12:38, 28 May 2009 (UTC)
replies: text: I get it.  I think I was going on the idea of simple to complex, the "chestnut is a form of albinism" concept...not the evolutionary formula (though there is an argument for adding section on evolution of coat colors).  So to the extent I screwed up on the red/black thing, thanks for the fix, I won't argue about that one. (though I can also point to a popular horse magazine article that described it precisely that way, LOL!).  I tweaked some more, fix anything I just screwed up again!  Montanabw(talk) 01:19, 29 May 2009 (UTC)
thread_title:  Oh my! 

message: Hmm. I understand why dun and cream are under the "dilution" heading, however, I kinda feel that dun does not belong under that heading. Dun is the wildtype, and to be categorized the same way as cream makes it look like it's a dominant mutation. Countercanter (talk) 12:41, 13 June 2009 (UTC)
replies: text: The concept here is that I think we aren't classifying the colors based on evolutionary steps from wildtype to domestic, but rather by the phenotypical effects of progressively "switched on" genes acting in a layering fashion on the "simpler" colors, to put it in layperson's terms  ... just as chestnut is a "base" coat color, though it is not a wildtype.  Genes that overlay the darker "base" colors and dilute them are dilution genes.  Dun actually IS a dominant gene... how it became un-dominant is interesting to me, just a random mutation that was a consequence of domestication??  But anyway, in terms of phenotype, we have the 2 or 3 base colors (depending on how you treat Bay/Agouti) that every single horse has no matter what, and then from there all the other genes modify those colors.  So by that standard, dun is a dilution factor.  But I also see your logic in explaining the evolutionary process.  Maybe a different section in the article describing the wildtype origins?   Montanabw(talk) 21:32, 18 June 2009 (UTC)
replies: text: Normal extension is dominant. The faulty extension that results in chestnut is a recessive loss-of-function mutation. Normal dun is dominant. The faulty dun that results in a rich coat color is likely a loss-of-function mutation. But I gotcha. Countercanter (talk) 00:35, 19 June 2009 (UTC)

text: But the terminology "faulty" oh dear, that makes it sound like chestnuts are flawed or something! LOL!  Laypeople have enough trouble with "mutation" !  (grin). We (or well, um, you, I guess)  really need to do some work on that wildtype article.  it's a confusing enough concept in these horse coat color articles, and the underlying article is pretty weak.   Montanabw(talk) 04:45, 22 June 2009 (UTC)
thread_title:  "Dilution" heading and dun 

message: * I found an image of a cross between a zebra and a pony, and it was piebald, but with the black areas zebra-patterned instead of black. Anthony Appleyard (talk) 06:35, 9 November 2015 (UTC)
thread_title:  Zebra striping 

message: Hello fellow Wikipedians,
I have just modified  on Equine coat color genetics. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
*Added archive https://web.archive.org/web/20090522151520/http://www.petdnaservicesaz.com:80/Equine.html to http://www.petdnaservicesaz.com/Equine.html
*Added archive https://web.archive.org/web/20071010003713/http://www.intl-pag.org/11/abstracts/P5n_P640_XI.html to http://www.intl-pag.org/11/abstracts/P5n_P640_XI.html
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
Cheers.—InternetArchiveBot (Report bug) 06:29, 25 December 2016 (UTC)
thread_title:  External links modified 

message: Hello fellow Wikipedians,
I have just modified 2 external links on Equine coat color genetics. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
*Corrected formatting/usage for http://www.petdnaservicesaz.com/Equine.html
*Added archive https://web.archive.org/web/20070927040626/http://www.hancockhorses.com/article-roanQHNews.pdf to http://www.hancockhorses.com/article-roanQHNews.pdf
When you have finished reviewing my changes, you may follow the instructions on the template below to fix any issues with the URLs.
Cheers.—InternetArchiveBot (Report bug) 04:56, 22 September 2017 (UTC)
thread_title:  External links modified 

message: "Horse sperm do [not] carry the color genes" and whatever follows from that, such as [the foal's color depending on the mother's genes]. It would be comparable to the human egg not carrying sex determination genes so that birth of a boy or girl depends on which human sperm fertilizes the egg.
100.15.127.199 (talk) 02:02, 17 January 2022 (UTC)
replies: text: I'm not sure what you mean by that, but a foal's color is determined both by the sperm and the egg. For instance if an E/e mare is bred to an E/e stallion, the foal can be chestnut but only if the mare's egg passes along her e and the stallion sperm also passes along his e. If the mare's egg has E or the stallion's sperm has E, then the foal will not be chestnut. Iamnotabunny (talk) 22:09, 5 January 2023 (UTC)
thread_title:  one statement I can't find