Drought is the primary abiotic stress limiting crop yields. However, water is typically available in unexplored soil regions during intermittent drought. Therefore, a deeper and denser root system is desirable as it can increase the amount of water available for transpiration, maintenance of turgor, and metabolism. Currently there is little is known about the molecular mechanisms controlling root development in crop species. However, genomic resources are available for several plant species, including both crops and model organisms. Furthermore, numerous independent large-scale transcriptomics studies have been conducted in different species using various root tissues and cell types. These data have been used in this investigation to construct a systems biology model of the root. The network was reverse engineered from promoter information and mRNA expression profiles of root predominant genes. Conservation and divergence in regulatory elements were identified for networks within different regions of the root. Transcription factors have been identified that are likely to regulate genes involved in root development and response to drought. The potential biotechnological applications of novel promoters identified in this analysis are being investigated. This study identifies multiple regulatory elements for further investigation.