Methods and compositions are provided which allow for the production of an inverted repeat in a plant or plant part, which, when transcribed as an RNA can be used in some examples to decrease expression of a target polynucleotide of interest. The methods and composition provide precursor inverted repeat cassettes that are not capable of producing a hairpin RNA polynucleotide, and plants and plant parts comprising such precursor inverted repeat cassettes. The precursor inverted repeat cassettes are altered in planta by using a recombination system to produce a inverted repeat. Plants, plant parts, and seeds comprising the various components are also provided.