Abstract: A method of generating genotypic variation in a genome of a plant is disclosed. The method comprising introducing into a gamete or a gamete producing tissue of the plant at least one viral expression vector encoding at least one chimeric nuclease which comprises a DNA binding domain, a nuclease and a localization signal to a DNA-containing organelle, wherein the DNA binding domain mediates specific targeting of the nuclease to the genome of the plant, wherein the introducing is performed such that the gamete or gamete producing tissue expresses the chimeric nuclease but not all plant tissues express the chimeric nuclease, thereby generating genotypic variation in the genome of the plant.