Figure 1.
Venn diagrams constructed based on significantly different transcript abundance in gravistimulated rice shoot base.
Venn diagrams show the distribution of transcripts that were significantly changed in abundance by at least 2-fold (P value <0.05) between the lower flank and upper flank of the rice shoot base at 0.5 h and 6 h after gravitropic stimulation.
Figure 2.
Changes of transcripts in the auxin related pathway at 6 h after gravistimulation.
Visualization of modulated gene expression in the auxin pathway: lower flank at 6 h vs. upper flank at 6 h. Significant fold changes in transcript abundance were log transformed and represented as up-regulated (red square) or down-regulated (blue square).
Figure 3.
Changes of transcripts for GA metabolism at 6 h after gravistimulation.
A. MapMan output was used to illustrate the significant transcriptional changes across the tissue in GA metabolism at 6 h after reorientation. The reported values are log transformed ratios of transcripts in the lower flank to that in the upper flank. Each transcript is indicated as up-regulated (red square; increase in the ratio of the lower to upper transcript values) or down-regulated (blue square; decrease in the ratio of the lower to upper transcript values). Squares arranged in rows and columns represent individual transcripts at a single time point in the process. An individual square in a given area has the same color as the guide bar in the same column. A filled circle indicates that no transcript was detected. B. qRT-PCR analysis of OsGA20ox4 (Os05g34854), OsGA2ox7 (Os01g11150) and OsGA2ox9 (Os02g41954) expression after horizontal reorientation. Relative changes in transcript abundance after gravity stimulation compared to the vertical control at each time point were analyzed by qRT-PCR, and results were compared with the microarray data. Relative changes in transcript abundance of qRT-PCR were all determined using the non-reoriented control at the relevant time point as reference. 0.5 h down, 0.5 h up, 6 h down and 6 h up represent for lower flank at 0.5 h, upper flank at 0.5 h, lower flank at 6 h and upper flank at 6 h, respectively. The relative gene transcript abundance was calculated as the ratio between the control and gravistimulated samples at each time point. Values are means ± SD; n = 3; □ real-time PCR results; ▪ microarray data.
Figure 4.
Changes of transcripts for JA metabolism at 6 h after gravistimulation.
A. MapMan output was used to illustrate significant transcriptional changes across the tissue on JA metabolism at 6 h after reorientation. The reported values are log transformed ratios of transcripts in the lower flank to the upper flank. Each transcript is indicated as being up-regulated (red square; increase in the ratio of the lower to upper transcript values) or down-regulated (blue square; decrease in ratio of the lower to upper transcript values). Squares arranged in rows and columns represent individual transcripts at a single time point in the process. An individual square in a given area has the same color as the guide bar in the same column. A filled circle indicates that no transcript was detected in the process. B. qRT-PCR analysis of lipoxygenase 1 (Os03g49260), cytochrome P450 (Os02g12690) and 12-oxophytodienoate reductase 2 (Os06g11200) expression after horizontal reorientation. Relative changes in transcript abundance after gravity stimulation compared to the vertical control at each time point were analyzed by qRT-PCR, and results were compared with the microarray data. The relative gene transcript abundance was calculated as the ratio between the control sample and gravistimulated sample at each time point. Values are means ± SD; n = 3; □ real-time PCR results; ▪ microarray data.
Figure 5.
Changes of transcripts for cell wall precursors and cell wall protein related pathways between lower and upper half flanks at 6 h after gravistimulation.
MapMan output was used to illustrate the significant transcriptional changes across the tissue of cell wall precursors and cell wall proteins at 6 h after reorientation. The reported values are log transformed ratios of transcripts in the lower flank to the upper flank. Each transcript is indicated as being up-regulated (red square; increase in the ratio of the lower to upper transcript values) or down-regulated (blue square; decrease in ratio of the lower to upper transcript values). Squares arranged in rows and columns represent individual transcripts at a single time point in the process. The individual square in a given area has the same color as the guide bar in the same column. A filled circle indicates that no transcript was detected in the process. Significantly changed transcripts in each process were marked with a series of numbers.
Figure 6.
Changes of transcripts for glycolysis and the TCA cycle at 0.5 h and 6 h after gravistimulation.
MapMan output was used to illustrate the significant changes across the tissue on glycolysis and the TCA cycle at 0.5 h and 6 h after reorientation. Reported values are log transformed ratios of transcripts in the lower flank to the upper flank. Each transcript is indicated as being up-regulated (red square; increase in the ratio of the lower to upper transcript values) or down-regulated (blue square; decrease in ratio of the lower to upper transcript values). Squares arranged in rows and columns represent individual transcripts at a single time point in the process. An individual square in a given area has the same color as the guide bar in the same column. A filled circle indicates that no transcript was detected in the process.
Figure 7.
Changes of transcripts for sucrose-starch metabolism at 6 h after gravistimulation.
MapMan output was used to illustrate significant transcriptional changes across the tissue in cell wall precursors and cell wall proteins at 6 h after reorientation. The reported values were log transformed ratios of transcripts in the lower flank to the upper flank. Each transcript is indicated as being up-regulated (red square; increase in the ratio of the lower to upper transcript values) or down-regulated (blue square; decrease in the ratio of the lower to upper transcript values). Squares arranged in rows and columns represent individual transcripts at a single time point in the process. An individual square in a given area has the same color as the guide bar in the same column. A filled circle indicates that no transcript was detected in the process.
Figure 8.
qRT-PCR validation of microarray analysis results.
Relative changes in transcript abundance after gravity stimulation compared to the vertical control were analyzed by the microarray assay, and relative changes in transcript abundance observed by qRT-PCR all utilized the non-reoriented control at the relevant time point as a reference. A. qRT-PCR analysis of OsCML27 (Os03g21380), OsCPD2 (Os11g04710), a transcript encoding a putative receptor protein kinase (Os04g45730), Aux2 (Os09g37500) and LGC1 (Os02g30780) expression. B. qRT-PCR analysis of OsIAA20 (Os06g07040), and coding genes for cytochrome P450 (Os02g12690), UDP-D-xylose (Os12g25690), auxin efflux carrier component (Os01g51780), α-glucosidase precursor (Os06g46284), β-fructofuranosidase 1 (Os02g01590). 0.5 h down, 0.5 h up, 6 h down and 6 h up represent for lower flank at 0.5 h, upper flank at 0.5 h, lower flank at 6 h and upper flank at 6 h, respectively. The relative mRNA abundance was calculated as the ratio between the control sample and gravistimulated sample at each time point. Values are means ± SD; n = 3; □ real-time PCR results; ▪ microarray data.