Global Transcriptome Profiles in the Nodes of Rice During Spatial and Temporal Development

The following study was conducted to better understand the genetics of the spatial and temporal development of rice, especially as this relates to the development of lignocellulosic tissues. To do so, an oligonucleotide array was designed and created by the Plant Sciences Institute at Iowa State University. A total of 43,776 spots were printed on two separate platforms, the first contained 23,040 spots while the second contained 20,736. RNA was collected from nodes of rice seedlings at several different time points, as nodes are highly lignified tissues. Comparisons were performed to identify those genes exhibiting differential regulation across time at an anatomical position as well as across anatomical distance. For example, node 1 was compared across days 46, 53, 60, and 67 and at day 67 node 1 was compared to nodes 2, 3, and 4. Similar comparisons were performed for nodes 2, 3, and 4 where applicable. Keywords: Time course and anatomical development in rice For each comparison, 6 replicates and multiple power settings were considered. Dye-swaps were performed between replicates. A diagram of the comparisons made in this experiment may be found in ISU_RiceArray_LoopDesign.pdf (linked below as a Supplementary file).