# Brown - Just a Phenotype?



## QtrBel (May 31, 2012)

This is the explanation given by Pet DNA:
*Evidence for a new Agouti allele combining features of ‘a’ and ‘At’*

In May 2014 our testing of a group of miniature horses revealed unexpected results indicating a co-segregation of At with the non-functional allele ‘a’. In other words, a horse testing a/a in the ‘a’-specific test would also test positive for one At allele. Without any additional data available at this point, there are currently two possible explanations of this finding:
1) a potential recombination (exchange of DNA) occurred within the gene, joining the ‘a’ defect with the At mutation, thus creating a novel arrangement (haplotype) combining the features of both alleles; or
2) a new At-like DNA mutation occurred in conjunction with ‘a’.
Regardless of which of these possibilities may be true, joining the At mutation with the ‘a’ allele is not expected to have any biological consequence for the animal and its color, as the ‘a’ allele is non-functional to begin with. However, it can certainly affect the correct interpretation of our tests, and possibly complicate plans for color breeding.
Obviously, we are dealing with a natural biological system, and genetic events like this can occur. At PetDNA – founded in 2004 – we take pride in providing scientifically sound and accurate services, and it is our most sincere intention to be transparent about any new findings relevant for our customers. Thus we feel compelled to follow up on this finding and explore the situation as soon as possible, and modify and upgrade our At test as necessary.
In our experience, the next step should involve a detailed DNA analysis of the Agouti gene structure from one or more animals carrying this novel combination. Such approach will necessitate to perform simultaneous analyses of contiguous stretches of DNA encompassing in one piece the entire area responsible for the ‘a’ allele and the At mutation. This approach will require the use of DNA prepared from blood, because DNA from hair follicles used in routine lab tests is too fragmented to be informative.
Future relevant information and updates will be periodically posted at this website.
A BIG THANK YOU to our loyal clients and supporters!!!


----------



## Chiilaa (Aug 12, 2010)

Basically what has happened is that PetDNA has fallen into a bit of disrepute, and as a result, they have pulled the test. This has been a combination of things. First is the horses testing At_ when they have already tested aa, which is a huge red flag. The stuff the QtrBel linked is only part of the story - other horses outside that miniature group have tested the same way, but they are only publicising that particular family group, making a lot of people wonder why. Then you have the same story that has been causing people to doubt the At test since it was available - the research paper has never been published by PetDNA, so no one can see the science of it. 

I do think there is two separate colours going on, but don't trust PetDNA either.


----------



## QtrBel (May 31, 2012)

Thanks for the added info. There is always more than what you see or as Paul Harvey used to say "Now for the rest of the story..."


----------



## verona1016 (Jul 3, 2011)

Any insight into whether the horses who tested aa and also At_ are visually black or not? (Those that aren't chestnut that is!)
_Posted via Mobile Device_


----------



## FrostedLilly (Nov 4, 2012)

Interesting. I didn't have a lot of information, other than there was some question over the brown test. I would be eager to find out what comes out of this.


----------



## MyBayQHFilly (May 13, 2014)

Glynnis said:


> Interesting. I didn't have a lot of information, other than there was some question over the brown test. I would be eager to find out what comes out of this.


Me too. I am going to continue to call my Aa filly from a black sire and out of a cremello dam a dark buckskin until there is a reputable test from Animal Genetics or UC Davis. :biggrin:


----------



## DraftyAiresMum (Jun 1, 2011)

Never mind this post. Typed out a whole thing, posted it, then read again what I had responded to and went "Doh!!"


----------



## KigerQueen (Jun 16, 2013)

im curious to see whats going on as well. my mare is black with bright almost buckskin light points. I would not classify this color as bay more of a fadeing black with light points. i hope they figure it out soon.


----------



## SunnyDraco (Dec 8, 2011)

KigerQueen said:


> im curious to see whats going on as well. my mare is black with bright almost buckskin light points. I would not classify this color as bay more of a fadeing black with light points. i hope they figure it out soon.


Seal brown. Still an agouti modifier at work. If you test for agouti at UC Davis, it will come back as having at least one agouti as UC Davis's agouti test lets you know if agouti is present just not which agouti mutation/s is there. Let me post a picture on photobucket (so I can share it here) of a black that has lighter color in the flank and you will see the difference.

Edit: here is a black with a lighter coloring on flank. He is a yearling and the black is still maturing. His sire is tested EE aa, his dam is tested Ee aa. Notice that his whole face is completely black and all black around his muzzle?


----------



## KigerQueen (Jun 16, 2013)

i know she is brown . its more how the color translates. as in she is not dark brown/bay like a fadded black looks but she looks BLACK allover her body except for her light points.


----------



## SunnyDraco (Dec 8, 2011)

KigerQueen said:


> i know she is brown . its more how the color translates. as in she is not dark brown/bay like a fadded black looks but she looks BLACK allover her body except for her light points.


Actually, the black all over with the lighter spots around muzzle, flank, elbow is what is considered seal brown and is readily accepted by most as brown. The brown horses who look bay is where most get confused. My sisters still refuse to call a horse brown when it is a brown who looks bay (black legs, ear tips, mane, tail, reddish body) because they learned long ago that a brown was black all over except for the light points all year long. They even reference the seal brown mare that was at the big barn next door (we were paid to do feedings/barn cleaning/stall cleaning) and how she was always black with the light points and even her foal was the same coloring of black with the light points. 

We do know that there are different agouti mutations that control the black pigment, we can observe the simularities of how it is controlling the black and that there are horses who look like a traditional bay but get light cinnamon color in the same places as a seal brown, even if it only shows up in a mimic bay's winter coat.


----------



## chl1234 (Jul 10, 2015)

How the genetic plays out and what the color is called depends a little bit on the registry. The Arabian Registry ignores the modifier genes that alter the color and goes strictly with the primary genes. Quarter Horses throughbreds, etc. have more primary color genes therefor more colors before we start on the modifying genes, which are may also be included. 

In general, a non-Arabian with a dark brown or black body and light flank, muzzle, etc. is called a brown. For an Arabian, if the points are black and the body is not 100% black = bay. I have seen registered black Arabians with 'roaning' around the flank and withers.

Sorry. It's been years since I've dealt with this so don't remember everything.


----------

