We use a broad range of technologies:
1. We start with protein engineering to improve the function of the enzymes which make the glowing reaction. We are using a process called directed evolution to achieve this: http://en.wikipedia.org/wiki/Directed_evolution
2. Then we recode the genes coding for our enzymes so that they can be read by plants - here we test a large number of combinations. This uses a whole suite of technologies: Genome Compiler software to design the sequence, DNA synthesis of the parts, DNA assembly using transcriptics and then transient experiments to test the DNA sequence in plants as described here: http://en.wikipedia.org/wiki/Agroinfiltration
3. Finally when we have a DNA sequence which is working well we insert that into the plant germline (so that it's inheritable) using a gene gun:http://en.wikipedia.org/wiki/Gene_gun
How much control does the gene gun process give you over where the new sequence ends up? Is it in the same place in all of your production seeds or do they structurally differ? I guess a related question is if all the seeds come from one ancestor cell where the insertion was done or if you do the insertion multiple times?
(I work with human genetics and am fascinated by the prevalence of structural variation.)
The gene gun inserts randomly. We do a large number of insertions and will then test to see which are the best plants and take those forward to production. All the seeds shipped will however come from a single parent.