Genome modifications are generated, among others, by shuffling elements in a process called genetic recombination. Recombination occurs under different circumstances. When a piece of DNA integrates anywhere into the genome, the process is called illegitimate recombination. It is for instance what happens when transposons move or when a plant is transformed via A. tumefaciens. Almost all transgenic plants are obtained this way.
Illegitimate recombination is the predominant mechanism of recombination in most organisms.
Toward increased diversity When using conventional breeding methods, the presence of a significant variability in the plant genome is a necessity. In the twentieth century, variability have been increased by submitting plants to ionising radiations. Most of the main crops cultivars we use today are the offspring of such mutated parents. Many plant species, potato and orange tree for instance, spontaneously propagate without sexual reproduction. Thus, propagation by taking cuttings, layering, grafting and, more recently, by in vitro cultures has been carried out.