@aart , I once had a discussion with one of the genetic gurus no longer active on here, Tim Adkerson, about parent-offspring breeding versus full-sibling breeding. Unfortunately I lost that conversation when the site changed to a new format.
In essence there is no difference in loss of genetic diversity between breeding full siblings versus parent to offspring. Of course half siblings would mean even less loss of genetic diversity. Since you are dealing with gene pairs and the genes on different sides of some of those gene pairs can be different the math gets messy, I'm an engineer and I struggle with the math, but I have gotten it to work with simplifying assumptions. That's why i questioned Tim to start with. Saying that "Parent to offspring is fine, siblings not so much" is no quite correct from a genetic diversity aspect, which is what a lot of the people on this forum are worried about.
The reason breeders usually use parent-offspring crosses instead of sibling crosses is that you can control which genes get enhanced better by using a parent with certain outstanding qualities over their offspring. If you cross full siblings the randomness of which genes get passed down is all over the board. With parent to offspring that overall randomness is the same but it is more confined to certain genes so you have more control over the specific genes you want, if that makes sense.
@Mowglimommychick the best way to avoid getting malformed chicks is to select which ones get to breed with some care. If you see any deformities or traits yo do not want, do not allow them to breed. When you breed related chickens, parent-offspring, full siblings, half siblings, or cousins you give recessive genes a better chance to pair up and show up. Sometimes these effects can be unwanted. Dominant effects are pretty easy to see and get rid of, but recessives can hide under dominant genes and be really hard to eliminate.
Another problem is that some genes are partially dominant, not fully dominant. With these genes if both genes at that gene pair are the same you get one effect. If only one of those are the partially dominant gene you get a different effect. If neither are that partially dominant gene you get no effect. Another issue is that some genes only act if something else is present.
I'll use colors to demonstrate this but this type of effect could be on any trait. If you have two copies of the blue feather gene then any feather that would typically have been black will be splash. If one of those genes is the blue feather gene but the other is not, black feathers are modified to be blue. If neither of those genes at that gene pair are the blue feather gene then feathers that would be black appear black. But this effect is only on black feathers. Red or white feathers are not affected. If you dig deep enough chicken genetics can get complicated. And there are exceptions to practically everything. A lot of that is because of those partially dominant or selectively dominant genes.
There are different ways to deal with loss of genetic diversity. That's what we are worried about. If you lose too much genetic diversity your flock can lose productivity, health, or fertility among other things. It is a real issue.
A model to manage this has been used by farmers and others for thousands of years until today, Greeks, Egyptians, Chinese, South American, all over the world. They often keep a flock to provide eggs and meat for their families. The typical model is to keep replacement breeders from your flock (whether offspring, siblings , or cousins) for several generations. The larger your flock the longer you can go. But at some point, say five generations just to pick a number, they bring in a new rooster to reset genetic diversity. Serious breeders, whether breeding for show, developing a new breed, or developing a new color/pattern of a recognized breed, use different techniques. The major hatcheries we often buy chicks from use a different technique.
Don't stay awake nights worrying about losing genetic diversity. It is always possible you could have some screwed up genetics, life just works that way. If that happens you will have to deal with it. But for the vast majority of us, especially if you get your chicks from a major hatchery, that problem will be pushed down several generations.
