Identification of putative drought-responsive genes in rice using gene co-expression analysis

Abstract

Drought is one of the major abiotic stresses causing yield losses and restricted growing area for several major crops. Rice being a major staple food crop and sensitive to water-deficit conditions bears heavy yield losses due to drought stress. To breed drought tolerant rice cultivars, it is of interest to understand the mechanisms of drought tolerance. In this regard, large amount of publicly available transcriptome datasets could be utilized. In this study, we used different transcriptome datasets obtained under drought stress in comparison to normal conditions (control) to identify novel drought responsive genes and their underlying molecular mechanisms. We found 517 core drought responsive differentially expressed genes (DEGs) and different modules using gene co-expression analysis to specifically predict their biological roles in drought tolerance. Gene ontology and KEGG analyses showed key biological processes and metabolic pathways involved in drought tolerance. Further, network analysis pinpointed important hub DEGs and major transcription factors regulating the expression of drought responsive genes in each module. These identified novel DEGs and transcription factors could be functionally characterized using systems biology approaches, which can significantly enhance our knowledge about the molecular mechanisms of drought tolerance in rice.

Keywords: WGCNA; co-expressed genes; drought; network analysis; transcriptome.

Figure 1

Identification of drought responsive core DEGs in rice. (A) Expression profiles of whole genome datasets based on FPKM values. (B) Venn Diagram showing conserved drought responsive DEGs. (C) Expression profiles of core drought responsive DEGs based on FPKM values.

Figure 2

GO (A) and KEGG analysis (B) of core drought responsive DEGs.

Figure 3

Matrix showing Module-Trait Relationships (MTRs) of different modules under control and drought stress.

Figure 4

Gene ontology (A) and KEGG analysis (B) of DEGs belonging to blue module under drought stress in rice.

Figure 5

Gene ontology (A) and KEGG analysis (B) of DEGs belonging to turquoise module under drought stress in rice.

Figure 6

Gene ontology (A) and KEGG analysis (B) of DEGs belonging to grey module under drought stress in rice.

Figure 7

Co-expression network analysis of blue (A), turquoise (B) and grey (C) modules. The size of node circle is positively correlated with the number of genes it interacts.