Analysis of global gene expression in Brachypodium distachyon reveals extensive network plasticity in response to abiotic stress

Abstract

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Figure 1. Differential expression of Brachypodium distachyon genes in response to stress.

A. Numbers of genes up-regulated (light grey bars) and down-regulated (dark grey) are shown as a function of time in hours after stress onset. B. Heatmap of expression differences between control and indicated stress arrays. Similar expression profiles are clustered in the dendrogram. Positive (green) and negative (red) differences between stress and control arrays are shown for all genes called as differentially expressed by SAM analysis. Columns are time points. Expression values are saturated at +/− 4 RMA, for display purposes. C. Venn diagram showing overlap of up-regulated genes in response to the four assayed abiotic stresses: cold (blue), heat (yellow), drought (purple) and salt (green). Area of overlaps is not proportional to the overlap. The numbers of genes in each region of the diagram are indicated. D. Venn diagram depicting intersections of sets of down-regulated genes in response to the four assayed abiotic stresses.

Figure 2. Weighted gene co-expression network of Brachypodium stress responsive genes.

Major network modules are labeled by proximal numbers, which are identical to those listed in Tables 1 , 2 , and 3 . Tight node grouping indicates mutually strong edges and therefore high adjacency. All adjacency values plotted are greater than 0.45.

Figure 3. Expression profiles of modules as a function of time in each stress condition.

Shaded area around lines indicates standard error. Values plotted are the average point-by-point RMA expression value differences between control and stress arrays for the member genes of the module. N indicates the cardinality of the module in question. Color overlays indicate stress, from left to right: cold (blue), drought (brown), heat (red), and salt (grey).

Figure 4. Scatterplot of transcription factor/target gene correlations.

The x- and y-coordinates of any single pair of genes is determined by their correlation in the indicated subset. Colors are determined by the number of pairs that fell at a particular point according to the scale shown. Dashed lines indicate the minimum difference required before a TF-TG pair's correlations were considered significantly different between conditions. A. The correlations of TF-TG pairs in a random subset of data are compared against the correlations of those pairs in the drought assays. B. The correlations of TF-TG pairs in the salt stress and drought stress datasets are plotted. Large amounts of scatter are observed, in contrast to limited scatter in random samples, indicating that when compared across conditions, TF-TG correlations can be highly plastic.