A Simple Method to Evaluate the Transcriptom of Micro Root Cells in Rice

The plants’ roots, especially deep roots are the most important organ to absorb and translocate water from the deep soil under drought, but the genetic mechanism regulating the development of deep rooting is largely unknown. The angle and length of roots are two major elements decide deep rooting in plants, and the root angle mainly depends on the differential growth between the up side and the down side cells of apical meristem in root tip.

We developed a new method to detect the transcriptom of micro root cells (about 100 cells) locating different positions in root tips separating by frozen-sectioning. Using this technique, we successfully amplified and sequenced micro cells from two layers of apical meristem (ups and downs) in two rice varieties with obverse rooting distribution (ZS97B VS IRAT109). At the P<0.05, 1453 DEGs (differentially expressed genes) were found between ZS97B and IRAT109. Meanwhile, 87 and 84 DEGS of the up and down cells from the same root tips were detected in ZS97B and IRAT109, respectively. Compared with the normal transcriptom of adequate roots sample (21104-22758, fpkm>0.5), 19213 genes were detected with fpkm>0.5 averagely by this method. The result of PCA analysis and KEGG classification are reasonable and useful. This new method gives consistently high detection efficiency, accuracy and reproducibility for micro root cells transcriptom research.