Microarray Analyses and Comparisons of Upper or Lower Flanks of Rice Shoot Base Preceding Gravitropic Bending

<div><p>Gravitropism is a complex process involving a series of physiological pathways. Despite ongoing research, gravitropism sensing and response mechanisms are not well understood. To identify the key transcripts and corresponding pathways in gravitropism, a whole-genome microarray approach was used to analyze transcript abundance in the shoot base of rice (<i>Oryza sativa</i> sp. japonica) at 0.5 h and 6 h after gravistimulation by horizontal reorientation. Between upper and lower flanks of the shoot base, 167 transcripts at 0.5 h and 1202 transcripts at 6 h were discovered to be significantly different in abundance by 2-fold. Among these transcripts, 48 were found to be changed both at 0.5 h and 6 h, while 119 transcripts were only changed at 0.5 h and 1154 transcripts were changed at 6 h in association with gravitropism. MapMan and PageMan analyses were used to identify transcripts significantly changed in abundance. The asymmetric regulation of transcripts related to phytohormones, signaling, RNA transcription, metabolism and cell wall-related categories between upper and lower flanks were demonstrated. Potential roles of the identified transcripts in gravitropism are discussed. Our results suggest that the induction of asymmetrical transcription, likely as a consequence of gravitropic reorientation, precedes gravitropic bending in the rice shoot base.</p></div

Venn diagrams constructed based on significantly different transcript abundance in gravistimulated rice shoot base.

<p>Venn diagrams show the distribution of transcripts that were significantly changed in abundance by at least 2-fold (<i>P</i> 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.</p

Changes of transcripts for GA metabolism at 6 h after gravistimulation.

<p>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 <i>OsGA20ox4</i> (Os05g34854), <i>OsGA2ox7</i> (Os01g11150) and <i>OsGA2ox9</i> (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.</p

Changes of transcripts for glycolysis and the TCA cycle at 0.5 h and 6 h after gravistimulation.

<p>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.</p

Changes of transcripts for JA metabolism at 6 h after gravistimulation.

<p>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 <i>lipoxygenase 1</i> (Os03g49260), <i>cytochrome P450</i> (Os02g12690) and <i>12-oxophytodienoate reductase 2</i> (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.</p