Difficulties in producing transplastomic plants
The major difficulty in engineering plastid genome for production of transplastomic plants is due to the presence in a cell, a large number of plastids (10-100), each having up to 100 copies of the plastid genome, thus making 1,000 to 10,000 copies of the plastid genome within a cell. Transformation of plastid genome actually involves introduction of transgene into the cell by biolistic process, followed by insertion of foreign gene into plastid genome due to two recombination events facilitated by plastid DNA sequences flanking the foreign gene. Since only one or few plastid genomes can be transformed in this manner, several generations are needed to dilute out the copies of the wild type plastid genome (which outnumber the transformed genomes) to achieve homoplastomic state in the calli, before plant regeneration takes place in culture.

For instance in the year 2001, in tomato, following altered conditions were used to facilitate plastid transformation; (i) low light conditions during selection phase, thus extending the selection phase and (ii) use of smaller leaf pieces to increase the number of transformed genomes relative to untransformed genomes. Such efforts in future will be made in other crops also to overcome problems that are specific to individual corps.