Chloroplasts, the organelles in which photosynthesis takes place, have their own DNA that is inherited separately from the nuclear DNA. Like mitochondria, which also have their own DNA, chloroplasts of an organism are inherited entirely from the organism's "mother". In the case of plants, the "mother" means the female gamete which supplied half the information carried in the organism's nuclear DNA.
Genetic engineering of the nuclear DNA was the first category of genetic engineering developed for plants. In this process, the sequence of base pairs (the building blocks that carry information in DNA) is altered to created new genetic sequences. These new sequences are inserted into the nucleus of cells that then are stimulated to divide, creating a new plant.
Rather than manipulating the sequence of base pairs in nuclear DNA, in chloroplast genetic engineering new sequences are inserted into chloroplasts, which then are inserted into plant cells whose original chloroplasts have been removed.
Since chloroplasts and the DNA within them are inherited separately from a plant's nuclear DNA, chloroplast genetic engineering offers advantages: Genes are contained within chloroplasts and thus their effects can be more easily controlled. Genes are expressed to a higher degree as opposed to the case of nuclear genetic engineering in which expression often is low.