Theory: Ml and id+ cause brown eyes in chickens

[Amer]

Over the years I've been obsessed with brown eyes, especially those of my d'Anvers. I stare into the dark depths and ponder. All this pondering led me to wonder: How come no matter what breed you have, brown eyes come with quail coloring?
In my female-line d'Anvers I get brown/dark red eyes in hens and bay eyes in the cocks

But in male breeder lines dark-eyed males are achieved because they have more melanin.

(I really struggled to find a good example of this because d'Anver cock beards tend to obscure the eyes. Also the website this photo came from is completely gone)
And dark eyed quail females are the defaults in all breeds:

(Old English credited to Larson's Miniatures http://larsonsminiatures.com/old-english-game-bantams.html)
And maybe it came obvious to those are familiar with genetics and I am annoying you with my "breakthrough" that was already well known. But when I looked up causes for brown eyes it said extended black and id+. And the sexlinked brown eye gene.
https://www.backyardchickens.com/threads/eye-color-genetics-help-me-help-me.293503/
But quail-colored birds obviously aren't E and it would be weird if somehow the sexlinked brown gene happened to be involved whenever the quail pattern emerged in different breeds.
I think it is caused by the interaction of id+ and Ml. Dark eyes are found in Spangled and pencilled Hamburgs and Silver Sebrights but not in Wyandottes which lack the slate legs. Since both ER based Hamburgs and e^b based Hamburgs have dark eyes, we can extrapolate that it is the id+ gene and not the base color that affects the eye color in Sebrights vs. Wyandottes.
Interestingly, I can't think of an example of a quail chicken with light-colored legs, but if my theory is correct, it would have bay eyes. I feel like that would be the ultimate test.
@KristenG @nicalandia
@MysteryChicken
Writing this post was difficult because quail are an entirely different species of bird and I needed the language to indicate chickens, lol.

 

[MysteryChicken]

Over the years I've been obsessed with brown eyes, especially those of my d'Anvers. I stare into the dark depths and ponder. All this pondering led me to wonder: How come no matter what breed you have, brown eyes come with quail coloring?
In my female-line d'Anvers I get brown eyes in hens and bay eyes in the cocksView attachment 3578240(blue quail, the blue kinda dilutes it to a very dark red.)View attachment 3578241
But in male breeder lines dark-eyed males are achieved because they have more melanin.
View attachment 3578279(I really struggled to find a good example of this because d'Anver cock beards tend to obscure the eyes. Also the website this photo came from is completely gone)
And dark eyed quail females are the defaults in all breeds:
View attachment 3578258(Old English credited to Larson's Miniatures http://larsonsminiatures.com/old-english-game-bantams.html)
And maybe it came obvious to those are familiar with genetics and I am annoying you with my "breakthrough" that was already well known. But when I looked up causes for brown eyes it said extended black and id+. And the sexlinked brown eye gene.
https://www.backyardchickens.com/threads/eye-color-genetics-help-me-help-me.293503/
But quail-colored birds obviously aren't E and it would be weird if somehow the sexlinked brown gene happened to be involved whenever the quail pattern emerged in different breeds.
I think it is caused by the interaction of id+ and Ml. Dark eyes are found in Spangled and pencilled Hamburgs and Silver Sebrights but not in Wyandottes which lack the slate legs. Since both ER based Hamburgs and e^b based Hamburgs have dark eyes, we can extrapolate that it is the id+ gene and not the base color that affects the eye color in Sebrights vs. Wyandottes.
Interestingly, I can't think of an example of a quail chicken with light-colored legs, but if my theory is correct, it would have bay eyes. I feel like that would be the ultimate test.
@KristenG @nicalandia
@MysteryChicken
Writing this post was difficult because quail are an entirely different species of bird and I needed the language to indicate chickens, lol.

E^R, & E^E not only make Brown/Dark Brown eyes, but also Amber eyes.

Amber Eyes: Examples

Extra Melanizers also play part in creating Red Eyes. But what I see in my JungleFowls is they have Bay, Brown, & Red eyes, & Slate Shanks.

Will check, & see if I have any white/pink/yellow shanked birds with dark eyes.

Red Eyes: Example

 

[Amer]

This only spirals to more questions like: what causes the dark face and eyes on a gold or silver birchen Modern Game? I’d think they don’t have Ml because that would erase the gold lacing on the breast, right?
Is id+ and E^R enough? I mean, black copper Marans have bay eyes and they seem to lack id+.
I guess that disproves that Ml is completely responsible for the dark eyes in Sebrights.
But it doesn’t disprove the dark eyed e^b based Hamburgs.

 

[pipdzipdnreadytogo]

I just recently was reading about eye color genetics for chickens and for the life of me I cannot find where I was reading about it to refresh my memory on what it said. I do remember it mentioning that there were only like two known genes that directly affected eye color and that eye color was primarily impacted by genes that change skin and plumage coloring, but darn if the details aren't gone from my brain. I'll see if I can dig up where that was. But definitely following the conversation here in the mean time! I feel like there's just so little info out there about eye colors in chickens that I really try to pay attention whenever it's brought up.

 

[MysteryChicken]

This only spirals to more questions like: what causes the dark face and eyes on a gold or silver birchen Modern Game? I’d think they don’t have Ml because that would erase the gold lacing on the breast, right?
Is id+ and E^R enough? I mean, black copper Marans have bay eyes and they seem to lack id+.
I guess that disproves that Ml is completely responsible for the dark eyes in Sebrights.
But it doesn’t disprove the dark eyed e^b based Hamburgs.

My FBCM pullet had Amber eyes.

 

[MysteryChicken]

I do have a Silver Duckwing OEGB hen with Dark Bay/Red Bay eyes. Makes the eyes look fiery.

 

[nicalandia]

Over the years I've been obsessed with brown eyes, especially those of my d'Anvers. I stare into the dark depths and ponder. All this pondering led me to wonder: How come no matter what breed you have, brown eyes come with quail coloring?
In my female-line d'Anvers I get brown/dark red eyes in hens and bay eyes in the cocksView attachment 3578240View attachment 3578241
But in male breeder lines dark-eyed males are achieved because they have more melanin.
View attachment 3578279(I really struggled to find a good example of this because d'Anver cock beards tend to obscure the eyes. Also the website this photo came from is completely gone)
And dark eyed quail females are the defaults in all breeds:
View attachment 3578258(Old English credited to Larson's Miniatures http://larsonsminiatures.com/old-english-game-bantams.html)
And maybe it came obvious to those are familiar with genetics and I am annoying you with my "breakthrough" that was already well known. But when I looked up causes for brown eyes it said extended black and id+. And the sexlinked brown eye gene.
https://www.backyardchickens.com/threads/eye-color-genetics-help-me-help-me.293503/
But quail-colored birds obviously aren't E and it would be weird if somehow the sexlinked brown gene happened to be involved whenever the quail pattern emerged in different breeds.
I think it is caused by the interaction of id+ and Ml. Dark eyes are found in Spangled and pencilled Hamburgs and Silver Sebrights but not in Wyandottes which lack the slate legs. Since both ER based Hamburgs and e^b based Hamburgs have dark eyes, we can extrapolate that it is the id+ gene and not the base color that affects the eye color in Sebrights vs. Wyandottes.
Interestingly, I can't think of an example of a quail chicken with light-colored legs, but if my theory is correct, it would have bay eyes. I feel like that would be the ultimate test.
@KristenG @nicalandia
@MysteryChicken
Writing this post was difficult because quail are an entirely different species of bird and I needed the language to indicate chickens, lol.

Melanotic and other melanin enhancers tend to Darken chicken eggs, Diluters like Barring, Dominant White and Sex Linked Id makes them Lighter.

Birchen is the second most melanized e allele and when not Diluted by known diluter it will have dark eyes

 

[KristenG]

Ok, it looks like I might have something interesting to add here, so I may as well pipe up. Thanks for the tag @Amer

You all should know that I did start with hatchery stock in my initial flock of d’Anvers in 1998. None of the Quail D’Anvers I started with had dark brown eyes. So I prioritized things other than eye color. When I purchased a pair of show quality Blue Quail, they also had reddish bay eyes instead of brown. I didn’t worry about it and figured eye color would be relatively easy to bring in and fix later. Unfortunately, I was wrong about the process of bringing it in being easy. It is anything but!! Now it seems I am struggling to maintain brown eyes even in my brown-eye sublineage. Eye color, it seems, is more complicated than I imagined.

You should also know that in my black d’Anvers, my initial pair had a female with green eyes. The male had brownish red. Even though most of my black d’Anvers have at least light brown eyes in the females, and reddish brown eyes in the males, I still cannot seem to keep green eyes and red eyes from popping up out of my blacks!

How confusing, right?!

I know from breeding to BBR d’Anvers this year that my all my Quail colored birds definitely carry Melanotic. But clearly, brown eye color is not controlled by the same genes as Melanotic. However, they may be located on the same chromosome and so often inherited together. Unfortunately, Since I my d’Anver eye color is not breeding true, I’m not sure I can tell much about the linkage between brown eyes and melanotic genes even through a purposeful hybridization. I won’t be able to tell on my current hybrids since the quails I used had red eyes. They have red eyes because my goal was to improve type on a BBR and the standard eye color for BBR is red. So, I can only speak to the Melanotic gene not being the same as brown eyes.

I also know that brown eyes are not linked to any of the so called recessive black genes that occur in both quail and black ( both varieties have a number of the same recessive black genes, which is why interbreeding the two varieties causes a lot less disturbance to either variety than it would if you bred to other non-black patterns). I know this because my Brassy Back d’Anvers (products from my interbreeding of black and quail, since not all my blacks carry Columbian) have red eyes. And I selected for so many recessive black melanizers in them that I turned the males nearly 100% solid black -or blue since the blue gene was in there- without the extended black locus. Their eyes? Red. And their legs a paler slate than a true extended black.

But you know what I found IS linked to more brown in the eye? Extended black itself. Indeed, while I still hatch green, gold, marbled, red and brown and dark brown eyes out of my blacks, when I breed them to my quail and get those F2 babies from the outcross, I have hatched a couple hundred of these, the brown eyes are almost always inherited by the blacks, but there are a small percentage of quail that develop them. This suggests that extended black doesn’t cause the darker eyes but that it does have a chromosomal linkage between extended black and a gene that causes more melanin deposition in the eyes.

I really ought to go take some photos for you all!

As to the actual genetics? It seems to be a polygenic trait. The gene for an extra light brown layer of melanin in the eye that is linked to dominant black seems dominant. The rest of the genes seem to be recessive. This makes for a complex set of genes to get to work together since polygenic traits don’t behave as we would like nor How we expect. Not only is it polygenic, but the sex and age of the bird changes its expression. All baby chickens I have seen are born with grayish or greenish or yellowish or dark eyes, or some combination . Mine are usually yellowish green. They start developing the brown tint around 3 months of age and it is the darkest you will see it 5-9 months of age. From there, the melanin fades. This is especially true in the cocks, whose dark brown eye color peaks around 4-5 months before those eyes start turning red. Because of this I always grade my cockerels for eye color at this time and tag the ones with the best eye color. I have had a rare male that has had dark brown eyes that lasted a few years but these boys are so rare in my line ( I bet if you had a line where this was a set trait it wouldnt be an issue though). Females will hold on to the darkness for a their first year- or a few years if that color was dark enough. Right now that is not common for me. Instead, mine start off with a lighter brown eye shade then this will also fade to Amber or a burnt orange later in life. If you get a male that can hold onto his dark eye - that is an asset in my opinion!

My goal is dark brown eyes but I find that there is a medium brown in my quails that is enhanced by the dominant brown from my blacks. I can easily get these medium brown genes into my blacks so I can get really dark eyes from them more often. Now, If only I could get their light brown gene to transfer to the quail d’Anvers without the extended black gene! Someday…

Or maybe I will break down and outcross my birds to make that final step. I want to make sure my brown eyes are breeding true first.

Hopefully this has been interesting and/or helpful!

 

[KristenG]

Ok, I went and got some pictures. First three are all baby pictures. Slate eyes. Variety doesn’t matter. Self blue and black day old d’Anvers babies. Then a BBR d’Anvers week old chick. Eye color stays like this for about the first month. Then by three months it turns yellow to orange for most of them

Then at 4 months old the true color begins to show. This 4 month old quail d’Anvers has what I call the red eyes. They are more of a golden orangey-bay, I guess. She will always have this color. It is too light.

At about this time, the birds with the brown eyes should be starting to show. Here are some of her male hatch mates. First is a quail d’Anvers cockerel showing medium brown eyes. This is the color I strongly favor in my boys because it is the darkest I have hatched in them yet. As I only recently introduced it into one sublineage, it is still quite rare.

To see the degree of contrast, take note of this next quail d’Anvers male- same hatch group, different subline. You might be interested to know he is from the male color line, so he is a deeper red and is heavy on the black markings. But his eyes don’t really care. They are a bright yellow orange (again, what I probably inaccurately call the red eye - these eyes do seem to gain red pigment with age but not a lot):

And I am getting the same things in my black d’Anvers. Here is a 3-month-old accidental male rumpless d’Anvers showing the brown pigment beginning to deposit in his eyes- plus a full body pic:

And then we have another 3-month old d’Anvers cockerel showing the orange eye. How unfortunate… Note he is still sound in his color in every other way:

And then I may as well show you the other eye color variations. The good news is only one bird (a 3-month black pullet) this year seems to be showing any indication of the “green” eye. The green eye is really a pale yellow that has usually has some brown pigment leaking through. The combination lends the yellow a greenish cast. Sometimes the whole eye will be this color. Most often, it is just part of the eye. I have been working hard to cull against it.

And I was going to show you the marbled eye. I only had one pullet end up with it this year - a white d’Anvers. It is striking. No the pupil is not irregular. Normal pupillary reflex and all that. That is just dark pigment. That is the nature of the marbled eye. I do not know what causes it but I try to get rid of it. I find it seems to be somewhat related to the green eye as the two tend to occur together in families. This particular white is descended from my blacks.

 

[KristenG]

Oh, forgot to show the effect of age.
Here is a blue Quail d’Anvers cock that had nice medium brown eyes like the first quail cockerel above when he was 4-6 months old. He is now 2-1/2 years and this is what those eyes turn into on an older cock:

And here is a 1-1/2 year old hen that had medium brown eyes as a pullet. As a fairly young adult hen, her pigment has faded out to reddish bay! Disappointing. (And yes, they do groom the beards off each other)

And finally, this is the eye color I would love love love to see in all my black and quail d’Anvers - brown like in this 2-1/2 year old hen who had almost black eyes as a pullet. Her eyes have faded too, but they are still reddish brown. As good as it gets here. You may notice that female eyes are much more likely to be brown and often appear darker. The higher frequency of brown in females suggests this may indeed be sex-linked brown eye. Very dark eyes are possible in the males, but far less probable, complicated by the fact the male eyes tend to go red no matter the color they had as a cockerel ( so you don’t observe it in adult males as easily). I know this is not true in all strains, but this is where I’m at.

I’m just going to add that in the big picture, eye color is a little thing. I’ve gone into a lot of detail about this one nitpicky little trait and it would be easy for someone to hyperfocus on it, since it is easy for a beginner to latch onto. All these years I haven’t been working on eye color I have been working on so many other attributes that I do love in my birds. No, I’m not going to give up my lines for darker eyes. I plan to work through this like I have everything else in my flock. And, eventually, I hope to have the same compact, lovable and friendly, disease resistant, curious, egg-laying and typey chicken packages with darker eyes. It is no different than any other trait that needs bred out. I just thought it would be a single recessive gene but it seems there is more at play than just that. Fun stuff!