You said "The genes for all the secialized forsm are present in the original." What did you mean by that, if not that the original had more genes than the specialized forms do? Where was the "variability that was initially present" stored, if not in the genes?
OK, short version of this.
Male parent - traits for legs X= longer O = shorter
Female Parent - Same traits.
They BOTH have the vaiability to produce either shorter or longer legged offspring. Their offspring have the possibility of:
1 XX
2 XO
1 OO
If you are breeding for a shorter legged animal, you select those that are OO and breed them to produce the traits you wanted. In doing so, you have specialized them, removing the variability. There is NO more X trait, a net loss.