Distribution of hub gene clusters and the overlapped drought tolerance QTLs in rice chromosomes.

<p>Red and blue filled rectangles represent hub gene clusters and QTLs for rice drought tolerance, respectively.</p

Degree distribution of the drought-responsive gene co-expression network.

<p>A, the preliminary network without the maximum connection. B, the final drought-responsive gene network.</p

Heat map derived from the drought-responsive gene co-expression network.

<p>A, heat map of our network. Genes in the rows and columns have been ordered by a MCL algorithm. Each of the colored bars along the top horizontal and left vertical axes represents a gene module. Genes that do not belong to any module are colored gray. B, heat map of the WGCNA network based on power (β = 4). The genes are colored by module assignment in A.</p

Mapping the modules onto the drought-responsive gene co-expression network.

<p>The nodes are color-coded by modules and gray nodes represent genes unassigned to a module. The over-represented GO terms are shown for each module. Each pie chart represents the proportion of up- (yellow color) and downregulated (blue color) genes in the corresponding module.</p

Choosing Pearson correlation coefficient cutoff value.

<p>A, the actual number of edges and all possible edges among the non-singleton nodes as a function of correlation coefficient cutoff values. B, network density at different correlation coefficient cutoff values.</p

Tissue-specific expression of genes in the drought-responsive modules.

<p>The average expression level for each gene in different tissue types was calculated based on the normalized Affymetrix array data.</p

Module significance in response to drought stress in different rice varieties.

<p>Each column corresponds to module expression change in the drought stress response, row to a rice variety. Each cell contains the average of absolute log2-fold expression changes of module genes and the <i>p</i>-value for differences between the module average and the network average calculated by the t-test. The stars indicate that the average changes of modules are significantly greater than the network average (<i>p</i><0.001).</p

Functional enrichment of drought-responsive hub genes.

<p>Functional enrichment of drought-responsive hub genes.</p

Heat map of the putative <i>cis</i>-regulatory motifs enriched in the drought-responsive modules.

<p>The motifs in the rows and columns have been ordered by simple hierarchical clustering. A gradient of colors represent the Pearson correlation coefficients between motifs. The black line rectangles in the heat map indicate the similar motifs with a correlation coefficient >0.65. Functions of the merged motifs are indicated in the right-sided table.</p

UPGMA clustering of 95 rice accessions.

<p>A, clustering based on TILLING markers of promoters; B, clustering based on InDel loci. The arrows indicate the accessions being clustered into opposite sub-populations between two trees. The horizontal axis represents the coefficient of similarity.</p