Development occurs at the level of cells, tissues, organs, and/or organisms. The development of tissues from stem cells involves the action of many different proteins, including transcription factors. Using genetic, molecular, and genomic/proteomic strategies, the network of molecular components and interactions are being determined with the goal of understanding how root tissues develop from stem cells to fully differentiated tissues. Knowledge of the molecular mechanisms and networks underlying root development can facilitate applications aimed at crop improvement and the generation of biofuels.