4. Integration of transgenes into plant genomes: Aspects of possible unintended effects in transgenics

Single copy or repeated or multiple insertions of exogenous DNA may occur during genetic engineering transformation [21]. In addition, multiple insertions can take place into linked or unlinked sites [22, 23]. Moreover, following transformation, the transgene may be unstable within the host genome, and the insertion site may also be unstable owing to the transgene instability [24, 25].

Directed and inverted repeats are some of the complex integration patterns which have been found to result from Agrobacterium-mediated transformation [26]. Inversion [23] and translocations [27] have been found to be some of the types of chromosomal rearrangements linked to T-DNA insertion occurring at the insertion site in the plant genome. Vector-based filler DNA (non-T-DNA sequence from the transformation vector backbone) has also been observed following the integration of exogenous DNA into the plant genome. Plant-based filler DNA has been found between T-DNA repeats [25, 28], whereas vector-based filler DNA sequences were found outside the left and right borders of the T-DNA [29]. The plant-based filler DNA is regarded as an important facilitator of the integration of T-DNA into plant chromosomes [25].

Agrobacterium-based integration occasionally causes the recurrent integration of T-DNA vector backbone sequences into the transgenic plant genome [30]. It is possible to have vector backbone flanking the right border (RB) integrated into the host plant genome following transgene insertion [31]. This event has been hypothesized to be the result of T-DNA processing that occurred where, instead of the insertion initiated at from the RB, this initiation site is skipped and T-DNA insertion occurs from the LB.

Transformation methods directed at the chloroplast has the advantage of minimizing the insertion of unnecessary DNA that may accompany nuclear genome transformation. Furthermore, gene insertion into the chloroplast genome is not associated with inadvertent inactivation of a host gene due to transgene integration and, due to a less compact chromatin structure, does not exhibit positional effects [18].
