BYC Genetic/Breed Calculator Huge Task Ahead!

[Rose Quartz]

My Silkie eggs are white on the inside. Slightly tinted if they're thin.

"The study has revealed the white/red earlobe trait is polygenic and sex-linked in Rhode Island Red chickens. In the genome significant ~2.38 Mb region, twenty-three genes were found and some of them could play critical roles in the formation of white/red earlobe color, especially gene SLCO4C1. Taken together, the candidate genes findings herein can help elucidate the genomic architecture of response to white/red earlobe and provide a new insight on mechanisms underlying earlobe color in Rhode Island Red chickens and other breeds."

Interesting, but I wonder how they got funding for this...

Also, looks like people agree that it's linked, but no-one's quite sure how. With 23 possible genes and little research into it...

uh, something I read... somewhere... said some of it had to do with where the genes are located. The first thing I noticed was the similarity in the gene name you just shared

the SLCO1B3 gene influences biliverdin, & the O mutation modified expression of SLCO1B3 in the shell gland/uterus of blue egg laying chickens.

I have no idea if that means that they would be close together, but it would make sense? I guess. if they were.

 

[Amer]

• • 

E-locus (aka MC1R)
« on: March 08, 2015, 01:54:45 PM »

http://www.edelras.nl/chickengenetics/mutations1.html#gen_mut_elocus


The E locus Chicken/Down Color Pattern
Quote
The E locus alleles produce the base primary colour/patterns to which varieties are build upon.


Each Ameraucana variety is based on an e-locus gene. Since birds get a gene from each parent it is important that the pair of genes at the e-locus (location of the "e" genes) are the same. There are at least 9 e-locus genes, but the main ones that are associated with Ameraucanas, in order of dominance are...
E = Extended black, sometimes just referred to as Extended
ER = birchen aka crowwing
eWh = dominant wheaten
e+ = wildtype, normal or sometimes duckwing
eb = brown, was also called partridge (ep)
ey = recessive wheaten, "y" stands for Yellowish-white chick down

Here are some of the varieties that can be built from these foundational genes...
E = black, white, lavender, blue, splash
ER = brown red, blue, splash, birchen, lavender, white, black
eWh = buff, wheaten, blue wheaten
e+ = silver
eb = partridge, buff
ey = wheaten, blue wheaten, buff

I've underlined the varieties that I think are best based on these e-locus genes. Note I don't think blacks and blues should be based on the same e genes, so they shouldn't be bred together as most of us have done in the past. To get the best blacks they should be based on E, but the best laced blues may be based on ER.

Mike Gilbert replied...

Oh! This makes so much more sense! One question answered with ease and no questions coming out of it. I better study genetics myself!

 

[Rose Quartz]

White legs=W+/W+Id/Idewh/ewh
Slate= W+/W+id+/id+e+/e+ carrying white
Slate= w/wid+/id+e+/e+ carrying yellow
Yellow legs=w/wId/Idewh/ewh
Or Yellow legs=w/wIdeb/eb
The only problem is, there could also be the ey gene there, and I don't know what it does. If I don't know what it it does, then we probably can't use it, because it's probably linked to something. One gene to go though. And I understand it now! (Yay) so yellow legs are ewh if base color is wheaten, like buffs and wheatens, and it is eb if the e gene is partridge. But what is ey?
Id (melanin inhibitor) allows clear yellow legs on E and ER birds.
So yellow can also be w/wId/IdER/ER! Or maybe even w/wId/IdE/E!
Willow legs=w/wid+/id+e+/e+
Guess what else? Barring inhibits pigment in the legs of black and birchen birds as well. Sometimes barring can dilute black pigment to white. So we don't need the Id gene! Id/Id gets thrown out the window!
And blue dilutes dark slate to a blue color! So everything we know about leg color gets thrown out the window! It's impossible!

heh heh heh... yeah.

the langshan over barred rock hen crosses that were male and had feathers on their legs did have the barring in their feathers, but I didn't notice it on their legs... I might have to go look for pictures of them to be sure of that though.

 

[Rose Quartz]

Me too. I'm falling asleep at my keyboard, at 9:20pm, awaiting answers on my pullet.

do you have a poultry vet? oh, or I suppose you've made a thread here...

 

[sylviethecochin]

uh, something I read... somewhere... said some of it had to do with where the genes are located. The first thing I noticed was the similarity in the gene name you just shared

the SLCO1B3 gene influences biliverdin, & the O mutation modified expression of SLCO1B3 in the shell gland/uterus of blue egg laying chickens.

I have no idea if that means that they would be close together, but it would make sense? I guess. if they were.

Sometimes. Usually, no. Usually, it's a description of what the gene does, but shortened to one short thing. Or it's biologists trying to be funny: MADD = Map-kinase activating death domain (they worked really hard to make Mothers Against Drunk Driving, no?)

https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation

If you look up a gene on the ncbi site, you can find its location, but it's been a while since I did that, and I'm not sure if I remember how. Genes that are close together are more likely to be inherited together, though.

EDT: SLCO1B3 is on chromosome 1.
SLCO4C1 is on chromosome Z

They're nowhere close to each other.

 

[Cyprus]

do you have a poultry vet? oh, or I suppose you've made a thread here...

I made a thread

 

[centrarchid]

It needs to have a way to consider not all alleles and interactions are known.

 

[sylviethecochin]

It needs to have a way to consider not all alleles and interactions are known.

I wanna call it the "leakage" note.

 

[LilJoe]

I wanna call it the "leakage" note.

That word reminds me... are we gonna add a leakage option?

 

[Rose Quartz]

Sometimes. Usually, no. Usually, it's a description of what the gene does, but shortened to one short thing. Or it's biologists trying to be funny: MADD = Map-kinase activating death domain (they worked really hard to make Mothers Against Drunk Driving, no?)

https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation

If you look up a gene on the ncbi site, you can find its location, but it's been a while since I did that, and I'm not sure if I remember how. Genes that are close together are more likely to be inherited together, though.

Do you have any clue as to why pink would be the only color of an egg shell, visible on the inside of a shell, (from a normally blue egg layer line) or why if there are only supposed to be White or Blue shell color, with brown as a outer "paint", we could see in a bunch of medium brown eggs we cracked open today, the brown on the inside on the egg, where it should have been white?

I realize probably not. That's what I've been trying to figure out all day though. I'm thinking it might have to do with color suppressing genes(for the pink) but I have only come across one mention of that and aside from the abbreviation "pr" and that it affects this one affects the brown pigment I haven't seen anything else about it.