Insights into Barley Root Transcriptome under Mild Drought Stress with an Emphasis on Gene Expression Regulatory Mechanisms

Abstract

Root systems play a pivotal role in coupling with drought stress, which is accompanied with a substantial transcriptome rebuilding in the root tissues. Here, we present the results of global gene expression profiling of roots of two barley genotypes with contrasting abilities to cope with drought that were subjected to a mild level of the stress. We concentrate our analysis on gene expression regulation processes, which allowed the identification of 88 genes from 39 families involved in transcriptional regulation in roots upon mild drought. They include 13 genes encoding transcription factors (TFs) from AP2 family represented by ERFs, DREB, or B3 domain-containing TFs, eight WRKYs, six NACs, five of the HD-domain, MYB or MYB-related, bHLH and bZIP TFs. Also, the representatives of C3H, CPP, GRAS, LOB-domain, TCP, Tiffy, Tubby, and NF-Ys TFs, among others were found to be regulated by the mild drought in barley roots. We found that drought tolerance is accompanied with a lower number of gene expression changes than the amount observed in a susceptible genotype. The better drought acclimation may be related to the activation of transcription factors involved in the maintenance of primary root growth and in the epigenetic control of chromatin and DNA methylation. In addition, our analysis pointed to fives TFs from ERF, LOB, NAC, WRKY and bHLH families that may be important in the mild but not the severe drought response of barley roots.

Keywords: barley; drought; roots; stress; transcription factors.

Figure 1

Venn diagrams representing several groups of differentially expressed genes (DEGs). (A) The comparison of a number of DEGs between roots and leaves of CamB and Maresi genotypes. (B) The comparison of a number of up- and down-regulated DEGs in leaves. (C) The comparison of a number of up- and down-regulated DEGs in roots. (D) The comparison of a number of up- and down-regulated DEGs encoding transcription factors and gene expression regulatory proteins identified in the roots of CamB and Maresi.

Figure 2

An overview of the gene number and root-specific differentially expressed genes (DEGs) encoding transcription factors differentially expressed after mild drought treatment in roots of CamB and Maresi genotypes. Cam—CamB genotype, Mar—Maresi genotype.

Figure 3

Putative targets and predicted regulatory network of these TFs, which possess significantly over-represented targets within root DEGs identified after mild drought stress. Violet—DEGs common to CamB and Mar genotypes; orange—DEGs specific to Maresi; blue—DEGs specific to CamB. Asterisk—DEGs encoding TFs.

Figure 4

An overview of the number of TFs genes differentially expressed in roots after mild and severe drought treatment.

Figure 5

The expression pattern of DEGs encoding transcription factors, which were differentially expressed in roots of barley seedlings subjected to mild and severe drought regimes. Green: down-regulation of a gene; red: up-regulation of a gene.