There are known effects of Promoters used in expression of foreign DNA incorporated into the stranger host of choice but unknown effects of promoters used are not known. A promoter is used for the expression of foreign gene into the body of an organism.
Unforutately only two known sources of genetic biological transformation are based on bacteria and viruses which cause infections under natural conditions namely Agrobacterium and viruses.
In addtion to this physical methods of particle gun etc are less precise.
in all methods  selectable markers most commonly used are based on anitbiotic resistance genese but lately non antibiotic based selectable markers are used which are less harmful
however the reproter genes inclulding GUS and GFP are another risk factors.

In my openion there are three broad categories of genetically transformed plants or organisms.
1. genetic manipulation within the same species that is metabolic engineering like removing erucic acid gene from mustard to make it more palatable for western world.
2. genetic transformation between species of same genus like tobacco and solanum gene tansfer

3. In the third category we transfer gene from different Phyla from Bacteria to plants or bacteria to insects. This is more insecure in terms of expression potential of promoters used in unknown conditions and their spread due to pollination and seggregation process.
There is need to concentrate first on category 1 and 2 of gene transfer and take some more time and understanding for the third category. However America is world leader in exposing millions and millions ha of land to genetically modified crops and has done successfully. Others are skeptical for obious reasons. Let the scientists find some secure pastures to tread for the safe genetic transfers .