BYC Genetic/Breed Calculator Huge Task Ahead!

[Cyprus]

Thats a good idea.

I'm not thinking that people will use the calculator solely for the genetics of legs, comb, skin, etc.
Instead, I want us to gather this information and figure it out so that when we compute breed crosses the program can determine what color eggs, skin, legs, etc each cross will have. Make sense?

 

[sylviethecochin]

WOOO!!!! I got through the rest of that genetics miniseries today, I finally know that locus means location... and has nothing to do with grasshoppers. the thicker blooms will be darker because they're thicker, or possibly are thicker because they are forced to be darker by the extended black? I'm going to look into earlobe color tomorrow I think, to see how that relates to egg shell. I know comb types can affect it too. they're all tied together.

what do silkie eggs look like? on the inside?

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...

 

[Amer]

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/wId/Ideb/eb
Or Yellow legs w/wId/Idey/ey
so yellow legs are ewh if base color is wheaten, like buffs and wheatens, and it is eb if the e gene is partridge.
And the ey is recessive wheaten.
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! I'm so confused about this now. How will we link everything together correctly? Is there a documentation of how each gene affects melanin?
Edited. I think Sylvie knocked sense into me. One can only read genetic code for so long till she gets herself knocked in the head.

 

[Rose Quartz]

I'm not thinking that people will use the calculator solely for the genetics of legs, comb, skin, etc.
Instead, I want us to gather this information and figure it out so that when we compute breed crosses the program can determine what color eggs, skin, legs, etc each cross will have. Make sense?

yep. I know the main intention is to have something that will, show you what 2 breeds will do, and then possibly their offspring... (I'm sleep deprived ATM)

 

[Amer]

Hello—haven't been receiving updates from this thread.

I'm absolutely no good with computers, but I'm reasonably skilled at genetics research and scientific paper-decipherage (majored in Bio) so I'm offering my sort-of skilled help, if there's anything left that needs researched. Colors? e-locus genes (pattern genes)? Pictures of some breeds/crossbreeds, if you want them...

Also, shank color is different from skin color, if anyone's still confused. Shank color is mostly independent from skin color, and is the reason that birds have different colored legs and undersides of feet.

(Do have a full-time job, though, so help may be limited.)

Really? The skin color? I always thought it was whether the shanks were yellow or white under the melanin.

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...

23 genes! And I thought leg color was hard! I've cracked. A bit.

 

[Cyprus]

yep. I know the main intention is to have something that will, show you what 2 breeds will do, and then possibly their offspring... (I'm sleep deprived ATM)

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

 

[sylviethecochin]

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!

• • 

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...

EDT: 'Splains why Kippenjungle never accurately did Buff...

 

[Amer]

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!

I just realized this doesn't answer anything. I answered questions but it only brought up more.

 

[LilJoe]

I just figured it out! It's related to plumage and the distribution of black in the plumage! It's on the E locus with extended blackE/E, partridge, duckwing+, birchen ER, and wheaten. Yes E/E and ER/ER! I looked past the obvious first gene for Kippenjungle thinking it was a leg color, but it's actually a plumage color linked to stuff, especially the distribution of melanin overall, probably explaining the link between extended black, (E/E) and birchen(ER/ER) both dark colors with dark legs and the linkage between these different colors with dark eggs. I don't understand the part with the link between thickness of bloom, but with more melanin it would be darker! I got it!

I got it!

Look at kippenjungle. At the first locus. Plumage is linked with leg coloring!

You mean the hen with willow?


me too. Tinted. Like Silkie egg.

No...Family tree- leg colors

Yellow × slate - Slate × yellow - slate
~~~~
another
yellow × slate- willow × yellow- yellow
~~~~
last one
yellow × slate- white × yellow - yellow

 

[sylviethecochin]

Really? The skin color? I always thought it was whether the shanks were yellow or white under the melanin.

23 genes! And I thought leg color was hard! I've cracked. A bit.

It says that 23 have been found. There could be far fewer significant ones...

I happen to have chickens that have red and white earlobes. I don't think you're going to be able to do that one accurately. (Maybe make "leakage" notes?)