Expression profiles of 24 candidate miRNAs under hypoxia stress.

<p>Blue bars show the results of small RNA library in Hz32 under 4 h treatment. Red bars show the results of SLRT-PCR in Hz32 under 4 h treatment at 3 biological replicates. Vertical red line divides the expression profiles of 24 candidate miRNAs with 4 miRNAs (control expression profiles). Error bars show the standard deviation. Chi-square was applied on the small RNA library data and student t-test was performed on SLRT-PCR results. ** denotes the p value <0.01 and * denotes the p value <0.05.</p

Expression of zma-miR528a/b and one of its targets.

<p>A: SLRT-PCR results of miRNA528a/b at 3 biological replicates. B: qRT-PCR results of one of miRNA528a/b targets GRMZM2G039381 at 3 biological replicates. X-axis shows the inbred lines under different time point treatment compared to control. Y-axis shows the expression level. Error bars show the standard deviation. Student t test was performed on qRT-PCR results. ** denotes the p value <0.01 and * denotes the p value <0.05.</p

miRNA expression profile by SLRT-PCR and cluster analysis.

<p>A: Model of miRNA expression pattern. B: Heatmap of miRNA expression profile. The cluster was done on the basis of log₂ (expression level in treatment/expression level in control). Yellow shows down-regulation. Blue shows up-regulation.</p

miRNA-mediated gene regulatory sub-network of short-term waterlogging stress in B73.

<p>A. TF-miRNA and miRNA-target interactions are shown. B. Probable negative feedback loop between GAMYB and miR319b is shown. Upstream motifs and downstream targets are indicated as circular nodes whereas miRNA are denoted as diamond nodes. Teal color TF nodes represent the upstream motifs, light green nodes represent miRNA targets, whereas royal blue color nodes denote TFs which are involved in both upstream and downstream interactions. Yellow color miRNA shows down regulated miRNAs whereas violet color shows up regulated miRNAs. TF-miRNA interactions are shown as black arrows whereas downstream miRNA-target interactions are shown as red color lines.</p

Cluster miRNA targets expression profile.

<p>A: Model of miRNA target expression pattern. B: Heatmap of miRNA target expression profile. The cluster was done on the basis of log₂ (expression level in treatment/expression level in control). Yellow shows down-regulation. Blue shows up-regulation.</p

Flowchart of the experimental design.

<p>Red octagonal shows all the wet lab experiments. Aqua diamond shows the data analysis method. Blue square shows the computational prediction experiment. T: tolerant line. M: mid-tolerant line. S: sensitive line.</p

5′-RLM-RACE verification of predicted miRNA targets.

<p>Each top strand depicts a miRNA complementary site (targets), and each bottom strand depicts the miRNA. miR159 and miR319 shares the target sequence. Watson-Crick pairing (vertical dashes) and G:U wobble pairing (circles) are indicated. Arrows indicate the 5′termini of mRNA fragments isolated from roots of the maize seedlings, as identified by cloned 5′-RACE products, with the frequency of clones shown. Only cloned sequences that matched the correct target gene and had 5′ ends within a 100 nt window centered on the miRNA complementary site are counted.</p

Flowchart of the novel miRNA prediction pipeline.

<p>The flowchart shows the filtering criteria to reduce and refine the numbers of small RNAs to the most interesting subset based on the abundance, removal of repeats (uniqueness), removal of known miRNAs, other ncRNAs, and folding structure. 10 unique sequences were identified as potentially novel miRNA candidates. Light blue squares show the filtered out sequences. Blue squares show the sequences that passed the filter.</p

Short-term waterlogging phenotype-screening results of all three inbred lines.

<p>T: Waterlogging treatment. C: Control. RL: Root Length. LL: Leaf Length. RW: Root dry Weight. LW: Leaf dry Weight. TW: Total dry Weight. Error bars show the standard deviation. Student t-test was performed on the tolerant line (Hz32) and mid-tolerant line (B73), comparing with sensitive line (Mo17). ** denotes the p-value below 0.01 and * denotes the p-value below 0.05.</p

Phenotype and cytology raw data for CPB paper

Phenotype and cytology raw data for the paper "Morphological, cellular and molecular evidences of chromosome random elimination in vivo upon haploid induction in maize"