It depends on your goals and your breeding stock. The stuff in italics comes from a real expert in chicken genetics. It came from a discussion we had on the subject so it may not read really clear. I had to read it and study it several times to get the gist of it.
The big advantage in father/daughter or mother/son crosses comes when you have either a rooster or a hen with really superior characteristics. If you breed a parent with superior characteristics to an offspring you are going to concentrate those traits. If you breed siblings instead, there is more randomness involved in which traits are enhanced.
Another advantage in parent/offspring crosses is that if you have undesirable recessive traits in the gene pool, they normally come out faster than with sibling crosses, but that depends on which parent is introducing the undesirable recessive gene. Knowing which parent has the undesirable recessive gene may help direct your choice of which chickens should breed.
If you are just after general diversity in your flock, which is one of my goals, and your breeding flock is not highly inbred, which mine is not, sibling crosses are probably better.
I told you this stuff gets serious.
If the parents of a cross are genetically identical, then crossing siblings or in back crossing to a parent- there is no difference in the two crosses with respect to the genetic diversity in the second generation. The first and second generations would be genetically identical to the original parents in either cross.
It is when the two parents show some genetic variation that the crosses make a difference. In a back cross, the second generation offspring will become more like the original parent but will have some of the genes from the other original parent.
In a sibling cross (1st generation), it all depends on how the genes segregate when forming the egg and sperm. The second generation from this cross will show genetic diversity because each offspring can have a different combination of genes.
I would agree that sibling crossing or back crossing make no difference when one is working with an older closed flock. If there are detrimental gene combinations in the flock, they would show after a few years of line breeding. The genes will show up faster if back crossing is performed vs it would take a bit longer with sibling crosses.
Breeding depression is associated with the culmination of a number of recessive gene sets (polygenetic). It may be that the one original parent carries some of the genes but they are not homozygous for any of the genes (A/a, B/b, C/c and D/d) so they do not express any breeding depression and the other parent could be the same but missing some of the recessive genes (A/A, B/b, C/c, D/D) and does not express any breeding depression. It is when the future generation offspring start to inherit recessive gene sets (homozygous) that the breeding depression begins to be expressed in the offspring (a/a, b/b, c/c d/d).
For example, let’s say there are genes A, B, C and D. These genes are dominant so a bird that is A/a, B/b, C/c and D/d will not show any signs of breeding depression but can give the recessive genes to his or her future offspring. It is the recessive gene pairs that will cause the breeding depression. A future generation bird inherits a/a, b/b, c/c and d/d from the parents- this bird will express breeding depression because it has inherited all the recessive gene sets that are deleterious.
Back crossing can increase the probability of the offspring inheriting a pair of recessive alleles if both parents carry one allele from a gene pair (A/a x A/a). If one parent does not carry an allele in a recessive gene pair (that parent is A/A) and the offspring are back crossed to the non-carrying parent then the recessive allele from the other parent (A/a) cannot pair with another recessive allele- the offspring will be carriers (A/a) and not have the two alleles from the gene pair and not have the ability to express breeding depression.
As you can see, it all depends on the genes carried by the birds in a closed flock which way one would breed. You never know. A person would have to pay close attention to their breeding to understand which breeding regimen is the best for the flock.
