The Genetics of Fibromelanosis in the Sikie and Ayam Cemani

[tadkerson]

 

[urjtobreed]

I am not frustrated.

I was willing to discuss the issue if you presented quotes from research manuscripts and so far you have not presented the quotes or backed your position with information from research manuscripts. It is fine to have an opinion but do not keep insisting what I am doing is wrong. I have given evidence over and over that there are at least four genes involved in the trait.

Secondly, I have simplified the information and I have been accurate. Black bone birds that have the darkest skin color and the greatest internal pigmentation carry  4 EDN3 genes. Birds with less internal pigmentation and dark skin color contain three EDN3 genes (F1 hybrids see quote below). Birds that do not express hyperpigmentation have one or two EDN3. The researchers believe that the EDN3 gene is the most viable candidate gene for the fibromelanosis phenotype.




From the above quotes it is plain that the researchers believe the EDN3 gene is the gene responsible for fibromelanosis and that the increased expression levels of EDN3 (mRNA) are causing the fibromelanosis (hypermelanization). Only two genes can not express enough mRNA to cause fibromelanosis it requires 3 or 4 genes

None of the research that you or I have quoted, states that a chicken can have just one EDN3 gene! I have not seen any mention of deletions of entire EDN3 genes that would be required for a chicken to have one EDN3 on one chromosome and none on the other. All chickens come with an EDN3 on each chromosome 20 at minimum.

I am not providing additional research quotes, because we are reading the same research, we are just interpreting it differently. You provide quotes and research, but some of your statements don't mesh with the research.

None of the research uses Fm and EDN3 interchangeably as you do. Yes a bird can have 4 EDN3. But that doesn't mean you should state the genotype as Fm/Fm/Fm/Fm and state that a bird can have 1 to 4 Fm genes. The first two native EDN3 are not dominant for expression of FM, but that is what your notation is saying. That notation also doesn't address the fundamental difference between the original EDN3 genes that are always there and are wild type, and the extra CNV EDN3 genes that can be present or completely absent.

Have you found information on the proper notation of CNV's? The only thing I found, stated that they follow Mendelian inheritance and therefore standard allelic notation may be used (fm+,Fm). I'll try and find that reference again, but it didn't say much more than that.

 

[urjtobreed]

Wild type indicates the original gene found in the Red Jungle fowl and the mutated gene is the other gene at the wild type locus. The wild type gene and mutated gene are different both in genetic sequencing and in phenotypic expression. The Fm gene in the duplicated section can be exchanged with the fm+ ( your terminology) in the original section and not effect the phenotype. This indicates that both the Fm and fm+ (your terminology) are one in the same gene. If one gene is an  fm+ it must be different than the Fm gene. That is not the case,

The genetics behind the Fm phenotype does not fit the conventional model for wild type and mutated wild type alleles. The extend black allele ( the mutation) and the wild type allele are located at the same locus and are not duplicates of the same gene. There can be no comparison between the two models.


Tim

Yes, I think we are getting somewhere. I agree with everything that you said except for exchanging fm+ with Fm. I should have said that fm+ is the absence of the extra EDN3 CNV. I had said fm+ was having only the original 2 EDN3 genes, which is saying the same thing, but emphasizing the wrong point.

With this CNV, the extra gene makes a different phenotype and therefore the extra copy IS the mutation. The extra copy itself is the dominant Fm gene. Fm+ is not actually referring to the original EDN3 genes, but actually the absence of the extra EDN3.

Fm+ refers to the absence of the Fm gene and therefore the absence of the extra EDN3 at the locus of the extra copy.

That is how CNV's are fundamentally different. They are either present or absent rather than different versions of genes.

Hopefully this is much clearer. I wish I had explained it this way sooner.

 

[urjtobreed]

Okay thanks.   Suspected that would be the answer but genes can play in very strange ways and just like to be completely sure.

Many sources make mention of Fm crosses as having light mouths and not as dark skin. Assuming dark mouth is an indicator of Fm/Fm, how come it seems to be a common experience(including mine) to be extremely hard to hit on dark mouthed chicks? If it is simple autosomal, there should be 25% or 1 out of 4 average.. yet it often feels like dark mouths comes up for one per 30 or 40 chicks.. a fair bit skewed.

also a common comment is fibro birds from projects or even 'purebred' silkies are not as solid, dark skinned like cemanis. Is this imagined due to exaggeration of Cemani traits or if the difference is real, then what exactly do the cemani have that are lacking in other fibro birds?  I've never seen a pure cemani in person, so I don't know what to make of comments in regards to cemanis being "obviously darker than silkies".   In many pictures they seem so DARK and I would not say mine are that jet black dark, even the dark mouthed ones.

There are probably multiple unknown genetic factors that affect the level of expression of fibromelanosis. They appear to be recessive and hard to recover when outcrossed. That is why most silkies in the U.S. are not as dark as they once were. Even if silkies were not bred with other breeds, it would still take careful attention to maintain these FM enhancing genes since they are so variable and don't breed true.

There are also known FM enhancing genes such as extended black(E). The blackest of my own birds appear to have both E and melanotic (Ml) genes.

I think that figuring out the genetic recipe behind the darkest FM, is what makes working with FM so challenging and interesting.

Hopefully as people share their experiences, it will become clearer.

 

[Kev]

The wild type gene and mutated gene are different both in genetic sequencing and in phenotypic expression. The Fm gene in the duplicated section can be exchanged with the fm+ ( your terminology) in the original section and not effect the phenotype. This indicates that both the Fm and fm+ (your terminology) are one in the same gene. If one gene is an fm+ it must be different than the Fm gene. That is not the case,


Tim

If a wild type red junglefowl was engineered to have every chromosome to suddenly have duplication of EDN3, would this bird suddenly express fibromelanosis?

 

[Kev]

There are probably multiple unknown genetic factors that affect the level of expression of fibromelanosis. They appear to be recessive and hard to recover when outcrossed. That is why most silkies in the U.S. are not as dark as they once were. Even if silkies were not bred with other breeds, it would still take careful attention to maintain these FM enhancing genes since they are so variable and don't breed true.

That was one of my thoughts- if the phenotypic difference is real, then possibly unknown modifiers are involved. An intimidating thought also-if the modifiers are unique/almost unique to cemanis then without crossing out to cemanis with modifier(s), it's possible no amount of breeding darkest to darkest in a project flock would achieve any even close to the jet black cemanis.

It'd have to be incredibly dark skinned silkie for me to consider as outcross. Haven't seen any.
Quote:
Seems that way to me also. A few eb birds had dark skin, but cockerels lightening up as they matured was a constant issue. eWh is horrible for dark fibro expression, imagine that's no surprise to anybody though.

 

[tadkerson]

 

[Kev]

Thanks Tim, nice video also.

So I understand you are saying the Fm phenotype is due to this: EDN3EDN3/EDN3EDN3 or EDN3EDN3/EDN3, correct?

If so, my initial understanding was incorrect. spelling it out as Fm/Fm/Fm/Fm threw me off and led me to think it worked in a different way, somehow. I get now what you were trying to say, though.

For example I would 'read' R/R P/P c/c as a walnut comb white. Fm/Fm/Fm/Fm id+/id+ made my head spin trying to 'read' it.

 

[nicalandia]

That was one of my thoughts- if the phenotypic difference is real, then possibly unknown modifiers are involved. An intimidating thought also-if the modifiers are unique/almost unique to cemanis then without crossing out to cemanis with modifier(s), it's possible no amount of breeding darkest to darkest in a project flock would achieve any even close to the jet black cemanis.

It'd have to be incredibly dark skinned silkie for me to consider as outcross. Haven't seen any.

Seems that way to me also. A few eb birds had dark skin, but cockerels lightening up as they matured was a constant issue. eWh is horrible for dark fibro expression, imagine that's no surprise to anybody though.

This is correct, Cemani must carry Extended Black E/E , MelanoticMl/Ml, sex linked recessive Dermal id+/id+, Fibromelanotic Fm/Fm, and other recessive enhancers, I suspect many of those genes are found on the Sumatras, with this formula I was going to recreate a Cemani look alike with Native fibromelanotic Stock and Leghorns, but I never got past the F1s..

Native Stock, they lay blue eggs

 

[Kev]

Cool birds, that skin seems to be the typical Fm outside cemanis.

I would so love to have a Cemani to test out the unknown modifiers idea. Two initial crosses- one with my Fm naked necks, one with fm+ naked necks.

The first to see if there's any clear immediate results in the F1, if not then intercross the F1.

The second to see if Cemani outcrossed to fm+ produces different Fm phenotype than non-Cemani Fm bred to fm+ then intercross and backcross- keeping this line totally separate from any other Fm birds. Do you agree if this line produces several birds clearly very dark that would be suggestive of Cemanis having modifiers?

Naked neck just because I love them but also it is a brutally honest signal of fibro quality. If the skin isn't that dark, it is way plain for all to see.