Pollination process is disrupted by use of a pollination-disruption polynucleotide that renders the pollen unable to fertilize a sexually compatible ovule. The non-lethal nature of the pollen disruption polynucleotide is advantageous, particularly when operably linked to a transgenic polynucleotide of interest and prevents transmission of the polynucleotide through pollen. non-lethal markers are employed in an embodiment in which transgenic and non-transgenic seed can be sorted. A recombinase excision system is employed in an embodiment to activate the pollen disruption polynucleotide.