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.
Highlights
Rice is a model plant species and a major staple food crop among cereal feeding around half of the world population [1]
Encyclopedia of genes and genomes (KEGG) analysis to identify enriched pathways contributed by 517 core drought responsive differentially expressed genes (DEGs)
Plant hormone signal transduction was the most significantly enriched pathway followed by carbohydrate metabolism with 24% and 21% of the core DEGs involved in these pathways, respectively, indicating that particular hormones played key roles in drought tolerance (Figure 2B, supplemental material 4)
Summary
Rice is a model plant species and a major staple food crop among cereal feeding around half of the world population [1]. Rice has very high-water requirements for good production, drought is a major cause for its yield reduction and limits the growing area worldwide [2]. Several projects were launched for the annotation of rice genome which enabled researchers to utilize the genomeannotation information for the functional characterization of rice genes. The reduced cost of transcriptome analysis and availability of efficient omics tools have shifted the attention of molecular biologists to utilize the genome annotation information via computational approaches. Since most of the biological pathways involve coordinated regulation of dozens-to-hundreds of genes (known as co-expressed genes), identification of these co-expressed genes provides useful information for the characterization of key genes via systems level approaches. The development of various omics databases such as the gene ontology (GO) consortium, 2017
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