Methods and compositions for modulating plant development are provided. Polynucleotide sequences and amino acid sequences encoding cytokinin oxidase polypeptides are provided. The sequences can be used in a variety of methods including modulating root development, modulating floral development, modulating leaf and/or shoot development, modulating seed size and/or weight, modulating tolerance under abiotic stress, and modulating resistance to pathogens. Polynucleotides comprising CKX promoters are also provided. The promoters can be used to regulate expression of a sequence of interest. Transformed plants, plant cells, tissues, and seed are also provided.