Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice

Running title: Analysis of SSRs in Arabidopsis thaliana

Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thalian

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 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

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

Functional enrichment of drought-responsive hub genes.

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

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

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