Nitrogen and water limit global crop production. Root hairs comprise the major surface area of plant roots for nitrogen and water absorption. Despite this, no studies have reported how added nutrients or water alter global gene expression in root hairs in any plant species. I demonstrate that within 3 h of added nitrate, >876 genes in maize root hairs switch up or down. These genes overlapped with relevant maize QTLs. I also demonstrate that within 3 h of adding water to drought-stressed roots, 1831 genes show altered expression in root hairs. These results demonstrate that root hairs are rapid sensors of the soil environment. Following root uptake of nitrate, it is assimilated into amino acids for transport to the shoot; a process that involves families of genes. Understanding where and when these genes switch on/off may facilitate improved use of nitrogen. Here, the expression of 65 nitrogen uptake and assimilation probes was analyzed in 50 maize tissues, from germination to seed development. The results demonstrate that subsets of nitrogen-related genes are selectively expressed in specific organs at specific stages of development. This result identifies a higher network level of control over nitrogen-related gene expression in maize. An important clue to identify the master regulators responsible for such coordinated changes in gene expression can come from identifying their promoter targets. No software program has been adapted to serve this purpose in maize. I have created an online software tool for the maize community, called Promzea that is able to retrieve DNA motifs over-represented in the promoters of co-expressed genes, will be described. Using Promzea, over-represented motifs were identified associated with co-expressed genes in root hairs, diverse maize organs and different developmental phases. These results should aid in the design of synthetic promoters for targeted maize gene expression. As such genetic transformation will involve improving in vitro regeneration in maize, in my last study, I describe the transcriptome effects of two QTLs that improve in vitro plant regeneration, using a model system.