Genetic engineering for complex or combined traits requires the simultaneous expression of multiple genes, and has been considered as the bottleneck for the next generation of genetic engineering in plants. Minichromosome technology provides one solution to the stable expression and maintenance of multiple transgenes in one genome. For example, minichromosomes can be used as a platform for efficient stacking of multiple genes for insect, bacterial and fungal resistances together with herbicide tolerance and crop quality traits. All the transgenes would reside on an independent minichromosome, not linked to any endogenous genes; thus linkage drag can be avoided. Engineered minichromosomes can be easily constructed by a telomere-mediated chromosomal truncation strategy. This approach does not rely on the cloning of centromere sequences, which are species-specific, and bypasses the any complications of epigenetic components for centromere specification. Thus, this technique can be easily extended to all plant species. The engineered minichromosome technology can also be used in combination with site-specific recombination systems to facilitate the stacking of multiple transgenes.