I'll post it again (with some preliminary stuff he had said to me as well this time) since it still seems to be coming up a lot .... from VillageChicken:
"Genes can be seen as cars occupying a parking lot. Each gene has its assigned parking space. Most parking spaces have just two options - the dominant car is parked there or the recessive car is parked there.
For example - skin color. White skin is the dominant variation, yellow is the recessive. For chickens, there are two parking spaces for each "trait", with the exception of some of the sex-linked genes, where hens only get one parking space. So for the skin color trait, there are two spaces, and you can have two yellow cars, one white car and one yellow, or two white cars. Because white is dominant, when there is one white gene and one yellow gene, the bird has white skin.
Okay, enough of the car and parking lot analogy. The parking space in the genetic world is called a locus, or loci when you're talking about more than one. The cars that can park in any one given parking space are called alleles. Yellow skin and white skin are alleles of the same locus.
The feathered shanks have two loci. Technically they are called pti-1 and pti-2. Marans shank feathering is found at the pti-1 allele. pti-2 is for cochin type feathering and is an additional gene that gets added to pti-1 for the heavy cochin feathers. It gets confusing because at the pti-1 locus there are THREE alleles. So it would be like if at the skin color locus, there were a third variation for pink skin.
At pti-1 there is the recessive (no feathers) gene, a Langshan type gene and a Brahma type gene. Langshan - outer toe feathered, Brahma - adds middle toe feathered. So any one of these 3 genes can be present at this allele. Actually since almost all genes are in pairs, you can have any TWO of these 3 genes at the pti-1 allele.
So you can have the recessive clean shank gene paired up with a Lanshan type - that would be heterozygous for Langshan type feathering. Or clean shank gene with the Brahma type - heterozygous for Brahma type feathering. You can even have the Langshan paired up with the Brahma type.
The phenotype (what it looks like) is not always predictable or consistent. ( Love this statement!!!!! So true and encompasses everything, not just the shank feathering aspect.) The heterozygous Langshan could have very light feathering. The heterozygous Brahma type actually LOOKS like the homozygous Langshan type. This confuses many folks in the Marans world. In other words, if your bird carries one clean shank gene, and one feathered shank with middle toe feathers gene, it might have perfect Marans lightly feathered shanks. But paired with a genetically correct marans that has two Langshan type feathering genes, you will produce sparsely feathered shanks, and middle toe feathers from two "correctly" feathered parents.
Add to this mix the fact that there are known recessive inhibitors that suppress feathered shanks even when the feathering genes are present. So you may have parent birds with correct pti-1 Langshan genes, but if they each have one recessive inhibitor gene (you need two recessives for them to work) you will find offspring that are clean shanked.
This fall I single mated my wheatens and BC's and will never use a rooster with anything on his middle toes. I crossed a middle toe feathered roo with a very lightly feathered hen, and got almost all middle toe feathered offspring. Some that had fuzz on the toes at hatch aren't showing feathers now, but I know the messed up genes are in there.
I also paired two correctly feathered wheatens, and got middle toe feathers on about 1/3rd of the chicks. ( I have made this pairng too and had the same results )
Feathered shanks can be a big challenge to get right, to get it to breed true, without tons of culling.
One more thing that makes these Marans one tough bird to get right."