The short answer is no - there is no impact of the GMO crops on soil. More specifically, this can be viewed from three perspectives:
1. The genetically modified crops themselves break down in exactly the same manner as non-GMO crops. The genetic composition is organic in nature, and is quickly broken down by the soil microbial community. The genes themselves are no different than the genes for flowering characteristics, seed production, or chorophyll synthesis, they are simply DNA and all of the constituents associated with the composition of the plant.
2. In the case of tolerance to pesticides, the pesticide residues in soil follow the same pathway of degradation and dissipation as with any other application. In many instances the pesticides associated with GMOs have a much safer environmental profile, and shorter persistence characteristics, than other pesticides, so a favorable environmental profile is associated with GMOs.
3. Crops that contain the genetics for producing the Bt endotoxin, which is used for controlling many insects, do release the Bt endotoxin into the soil. However, Bt endotoxin has been widely studied and shown to be quite safe, and short-lived in the soil environment. In fact, since it is naturally produced by a microorganism, Bt endotoxin is considered an organic pesticide, and approved for use in organic farming. The Bt endotoxin is broken down very quickly in the soil, regardless of whether it is applied via conventional application methods or through the GMO crop.