A method for modifying at least one target locus in a plant cell, comprising: a) providing a plant cell comprising at least one target locus comprising at least one homologous region A and at least one homologous region B and comprising at least one nucleotide sequence Z of 1 to 50.000 base pairs length located between at least one homologous region A and at least one homologous region B and comprising at least one donor locus comprising at least one homologous region C and at least one homologous region D and comprising at least one nucleotide sequence X of 1 to 50.000 base pairs length located between at least one homologous region C and at least one homologous region D, wherein homologous region(s) A and homologous region(s) C have at least 70% sequence identity over at least 100 base pairs to be able to recombine via homologous recombination and homologous region(s) B and homologous region(s) D have at least 70% identity over at least 100 base pairs to be able to recombine via homologous recombination and wherein the at least one target locus and the at least one donor locus are integrated in the chromosomal DNA of the plant cell and wherein the at least one target locus comprises one or more rare cleaving nuclease cutting site(s) of at least 10 base pairs in length located between at least one homologous region A and at least one homologous region B and wherein the at least one donor locus comprises one or more rare cleaving nuclease cutting site(s) of at least 10 base pairs in length flanking a nucleotide sequence of the donor locus comprising at least one homologous region C and at least one homologous region D, b) providing the plant cell of step a) with at least one rare cleaving nuclease being able to cut at least one rare cleaving nuclease cutting site of at least 10 base pairs in length located in the at least one donor locus or located in the at least one target locus and at least one donor locus, c) allowing the rare cleaving nuclease to cleave at least one of the rare cleaving cutting sites of step a), d) allowing homologous region A and homologous region C of step a) to recombine and allowing homologous region B and homologous region D of step a) to recombine, wherein the at least one rare cleaving nuclease of step b) is provided by e) stable or transient transformation with at least one expression cassette being able to express at least one rare cleaving nuclease in the in the plant cell of step a) or a progeny cell thereof, or f) infection with a viral vector comprising at least one expression cassette being able to express at least one rare cleaving nuclease in the plant cell of step a) or a progeny cell thereof, or g) inducing expression of at least one rare cleaving nuclease in the plant cell of step a) of claim 1 or a progeny cell thereof, or h) introduction of m-RNA coding for at least one rare cleaving nuclease in the plant cell of step a) of claim 1 or a progeny cell thereof, or i) introduction of at least one rare cleaving nuclease via particle bombardment or bacterial Seclll or SecIV secretion systems, or peptide mediated cell-membrane transfer in the plant cell of step a) or a progeny cell thereof. a) providing a plant cell comprising at least one target locus comprising at least one homologous region A and at least one homologous region B and comprising at least one nucleotide sequence Z of 1 to 50.000 base pairs length located between at least one homologous region A and at least one homologous region B and comprising at least one donor locus comprising at least one homologous region C and at least one homologous region D and comprising at least one nucleotide sequence X of 1 to 50.000 base pairs length located between at least one homologous region C and at least one homologous region D, wherein homologous region(s) A and homologous region(s) C have at least 70% sequence identity over at least 100 base pairs to be able to recombine via homologous recombination and homologous region(s) B and homologous region(s) D have at least 70% identity over at least 100 base pairs to be able to recombine via homologous recombination and b) providing the plant cell of step a) with at least one rare cleaving nuclease being able to cut at least one rare cleaving nuclease cutting site of at least 10 base pairs in length located in the at least one donor locus or located in the at least one target locus and at least one donor locus, c) allowing the rare cleaving nuclease to cleave at least one of the rare cleaving cutting sites of step a), d) allowing homologous region A and homologous region C of step a) to recombine and allowing homologous region B and homologous region D of step a) to recombine, e) stable or transient transformation with at least one expression cassette being able to express at least one rare cleaving nuclease in the in the plant cell of step a) or a progeny cell thereof, or f) infection with a viral vector comprising at least one expression cassette being able to express at least one rare cleaving nuclease in the plant cell of step a) or a progeny cell thereof, or g) inducing expression of at least one rare cleaving nuclease in the plant cell of step a) of claim 1 or a progeny cell thereof, or h) introduction of m-RNA coding for at least one rare cleaving nuclease in the plant cell of step a) of claim 1 or a progeny cell thereof, or i) introduction of at least one rare cleaving nuclease via particle bombardment or bacterial Seclll or SecIV secretion systems, or peptide mediated cell-membrane transfer in the plant cell of step a) or a progeny cell thereof.