The Genetics of Fibromelanosis in the Sikie and Ayam Cemani

[tadkerson]

 

[Dipsy Doodle Doo]

*Average person* here, hoping for explanation : )

 

[urjtobreed]

So in order for a bird to have the Fm phenotype- it must carry at least  the above *Fm allele and an *N allele which looks like this.

That is not how I understand it. They are calling the whole duplication event the FM locus. It is in their abstract:

Abstract

Dermal hyperpigmentation or Fibromelanosis (FM) is one of the few examples of skin pigmentation phenotypes in the chicken, where most other pigmentation variants influence feather color and patterning. The Silkie chicken is the most widespread and well-studied breed displaying this phenotype. The presence of the dominant FM allele results in extensive pigmentation of the dermal layer of skin and the majority of internal connective tissue. Here we identify the causal mutation of FM as an inverted duplication and junction of two genomic regions separated by more than 400 kb in wild-type individuals. One of these duplicated regions contains endothelin 3 (EDN3), a gene with a known role in promoting melanoblast proliferation. We show that EDN3 expression is increased in the developing Silkie embryo during the time in which melanoblasts are migrating, and elevated levels of expression are maintained in the adult skin tissue. We have examined four different chicken breeds from both Asia and Europe displaying dermal hyperpigmentation and conclude that the same structural variant underlies this phenotype in all chicken breeds. This complex genomic rearrangement causing a specific monogenic trait in the chicken illustrates how novel mutations with major phenotypic effects have been reused during breed formation in domestic animals.

Explanation done.

 

[tadkerson]

 

[urjtobreed]

This is the whole duplication event. The abstract does not explain the genetics of the Fm phenotype. And do not forget the definitions of an allele and a gene. The other individuals on this thread are waiting to read your explanation. And please include examples of the results of crosses. Tim

That is their best guess at what the duplication event looks like. They did not say for certain that is what it looks like. Whatever is inherited as a unit that results in fibromelanosis IS the Fm allele, no matter what it looks like. What other explanation is needed?

 

[tadkerson]

 

[urjtobreed]

You have not spent five years taking the time and effort to simplify and explain difficult concepts to individuals that want to learn more about genetics and conceptualize genetics in a way they can understand.

Guess what. You can go for it because I am leaving the community. When people send me emails wanting to know things I will send them to you and you can explain things to them. You might start by explaining the genetics involved in the inheritance of the phenotype Fm. I will not be around to do it- maybe you and Marvin can team up and come up with an explanation,

Tim

If this is how you approached your 5 years of helping, then maybe they are better off without you.

I encouraged your efforts here, and was trying to help you make your guide more clear and accurate. I guess it easier to run away, than to admit that you may have been wrong in one aspect of your explanation (Fm/Fm/Fm/Fm) which turned out to be more confusing and wrong than simple and clear. What you were attempting to do and put a lot of effort into is admirable, but no one is perfect, even after 5 years of explaining. I don't claim to be perfect, nor wish to take up your torch. If you think of yourself as such a good teacher, I would just give you a piece of advice: A good teacher is also a good listener.

 

[KazJaps]

As you can imagine, nomenclature for mouse genetics is very advanced, needing to deal with quite complex scenarios:

STANDARDIZED NOMENCLATURE
http://www.informatics.jax.org/silver/chapters/3-4.shtml

Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat​

​

http://www.informatics.jax.org/mgihome/nomen/gene.shtml#trdef

Quote:
There are several known coding elements within the first duplicated region including ATP5E (ATP synthase epsilon subunit), TUBB1 (tubulin, beta 1), SLMO2 (slowmo homolog 2) and EDN3 (endothelin 3).

NCBI Map viewer of EDN3 & the other genes within the duplicated region on Microchromosome 20:
http://www.ncbi.nlm.nih.gov/project...0]-r&QSTR=ATP5E&QUERY=uid(-2146617769)&zoom=1
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Using the above mouse genetics nomenclature rules, the old Fm nomenclature could be expressed as EDN3Fm for the Fibromelanosis mutation, and EDN3+ for the wild-type. Ie once the structural gene is identified, you combine old allele symbols with the structural gene.
Therefore, you wouldn't do EDN3FmFm for the Fibromelanosis allele, as "Fm" defines all the sequence for the Fibromelanosis mutation. You don't use the old allele nomenclature to express structural gene duplications & other modifications. Also it wouldn't be accurate to leave out other structural genes within the duplicated region.

 

[Henk69]

Short remark (also to subscribe to this topic):

The classic mutation is a point mutation, a change to one basepair in the coding sequence of a gene. But duplications, inversions, deletions are also mutations. Fm is the old symbol and appears to be a duplication.

To use the spangled notation conserving the coding regions the Fm heterozygote would be: fm+-fm+//fm+ instead of Fm-Fm//Fm
Fm//fm+ does have its charm ...

Or would it be:
fm+-+ɯɟ//fm+
?

 

[urjtobreed]

----------------------------
Using the above mouse genetics nomenclature rules, the old Fm nomenclature could be expressed as EDN3[SUP]Fm  [/SUP]for the Fibromelanosis mutation, and EDN3[SUP]+ [/SUP]for the wild-type. Ie once the structural gene is identified, you combine old allele symbols with the structural gene.
Therefore, you wouldn't do EDN3[SUP]FmFm  [/SUP]for the Fibromelanosis allele, as "Fm" defines all the sequence for the Fibromelanosis mutation. You don't use the old allele nomenclature to express structural gene duplications & other modifications. Also it wouldn't be accurate to leave out other structural genes within the duplicated region.

Thank you for your input!

Would Fm, *FM, and your EDN3[SUP]Fm [/SUP] be synonymous, or does EDN3[SUP]Fm [/SUP] provide additional meaning? What notation would be best to use and in what situations?