The studies described herein explore the biological implications behind genes determined to be significant during the response of maize seedling roots to nitrate and the development of nodes in rice utilizing microarray technology to explore the genetic interactions of these two biological processes and analysis of functional annotation assigned to these sets of genes. In the first study, a total of 465 genes were identified to be differentially regulated in maize seedling roots following exposure to 5mM calcium nitrate at two time points (early: 0.5 hour and late: 24 hours). Considering the functional annotation of these genes and comparisons to previous studies performed in different biological systems, the pentose phosphate pathway, glycolysis, and Calvin cycle appear to play important roles in nitrate response. This study identified novel genes in these pathways as being differentially expressed following nitrate exposure, and implicated a unique role played by malate dehydrogenase between C3 and C4 plants. The second study describes the molecular genetics of node development in rice over four anatomical and four temporal points (nodes 1-4; days 46, 53, 60, and 67 post-planting). A total of 1,945 genes were found to be significantly differentially regulated in at least one of the 38 possible comparisons. Further, these genes were found to cluster into 10 groups of co-regulated expression. Exploration of these 10 clusters as well as consistency of differential expression between comparisons indicate that transcription is relatively stable over time for a given node, but varies to a much wider extent among nodes on a given day. The difference in expression between spatially divided nodes is especially pronounced when comparing the basal node to higher nodes. In addition, the current study has identified five putative transcription factors that may play important roles in regulating differential expression between node 1 and higher nodes.