The present invention relates to a method for excising a nucleic acid sequence from the genome of a plant or a plant cell. This method is based on the steps of transforming a plant cell with a construct encoding a DNA double strand break inducing enzyme (DSBI), generating a transgenic plant line, performing a transient assay to analyze the functionality of the transgenic enzyme, crossing the plant line with a line containing a nucleic acid sequence to be excised and performing an immature embryo conversion or a tissue culture regeneration through callus formation. The method can also be reversed, which means that a plant cell is transformed with a construct encoding a nucleic acid sequence to be excised, and the crossing is performed with a plant line containing a DSBI. As an alternative to the crossing step, a re-transformation of a transgenic plant line with a second construct can also be performed. The invention is also directed to a plant obtained by this method, or progeny, propagation material, part, tissue, cell or cell culture, derived from such a plant. Finally, the invention relates to the use of a plant or progeny, propagation material, part, tissue, cell or cell culture, derived from this method, as aliment, fodder or seeds or for the production of pharmaceuticals or chemicals.