What Markers Are Not
Another tool of biotechnology is the use of DNA markers to help create a new crop variety. A very common misconception is thinking that DNA markers physically put a transgene exactly where the scientist wants it in a crop's chromosome (Genetic Engineering Step #4). 
At the moment, it is a completely random chance where a gene gun or Agrobacterium will insert a transgene into a plant's chromosome. There is some work being done with something called Zinc Fingers, which is showing potential for allowing a specific insertion, but for now, it is not being used routinely with plants.
What DNA Markers Are
DNA markers are a set of tools playing a role in one of 3 ways:
- Providing a tool in plant breeding (known as Marker Assisted Selection)
- Identifying successful GMO events
- Distinguishing varieties