For any future people writing about this.
Phytoene synthase (psy) was taken from daffodils but is now taken from maize for Golden Rice 2. This produces 23 times more carotenoids. Phytoene desaturase (crt1) is taken from the bacterium Erwina Uredovora. I believe CyanideScience is right that lycopene cyclase (lyc) is already present. It mentions that they thought they needed to put it in originally but found this was not necessary on the Golden Rice website! Very complicated website but one you can guarantee to be right as many site say conflicting things!
I think that the rDNA is then placed into agrobacteria. The agrobacteria is then placed in a petri dish with rice embryo. The agrobacteria will transfer rDNA to Rice DNA. Thats what I have understood from research anyway.