The present invention provides nucleotide sequences and corresponding amino acid sequences for plant cytokinin oxidase proteins. Also provided are vectors, host cells, and transgenic plants comprising such sequences as well as methods for stimulating root growth and/or enhancing the formation of lateral or adventitious roots and/or altering root geotropism using such sequences. Also provided by the present invention are methods for altering various plant phenotypes including increasing seed size and/or weight, embryo size and/or weight, and cotyledon size and/or weight using cytokinin oxidase proteins and/or nucleic acid molecules encoding cytokinin oxidase.