Abstract
Plants are simultaneously exposed to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Identification and characterization of the synergistic and antagonistic components of stress response mechanisms contributing to the cross talk between stresses is of high priority to explore and enhance multiple stress responses. To this end, we performed meta-analysis of drought (abiotic), bacterial (biotic) stress response in rice and Arabidopsis by analyzing a total of 386 microarray samples belonging to 20 microarray studies and identified approximately 3100 and 900 DEGs in rice and Arabidopsis, respectively. About 38.5% (1214) and 28.7% (272) DEGs were common to drought and bacterial stresses in rice and Arabidopsis, respectively. A majority of these common DEGs showed conserved expression status in both stresses. Gene ontology enrichment analysis clearly demarcated the response and regulation of various plant hormones and related biological processes. Fatty acid metabolism and biosynthesis of alkaloids were upregulated and, nitrogen metabolism and photosynthesis was downregulated in both stress conditions. WRKY transcription family genes were highly enriched in all upregulated gene sets while ‘CO-like’ TF family showed inverse relationship of expression between drought and bacterial stresses. Weighted gene co-expression network analysis divided DEG sets into multiple modules that show high co-expression and identified stress specific hub genes with high connectivity. Detection of consensus modules based on DEGs common to drought and bacterial stress revealed 9 and 4 modules in rice and Arabidopsis, respectively, with conserved and reversed co-expression patterns.
Highlights
Crop productivity and survival is tightly linked to its environment which is being altered due to climate change, biodiversity loss and degradation of land and freshwater [1] threatening the food security of the world while the food demand is estimated to increase by 70% in 2050 [2,3,4]
Conserved expression status of genes common to drought and bacterial stresses We identified a total of 5084 and 1618 Differentially expressed genes (DEGs) referred as stress responsive genes (SRGs) in rice and Arabidopsis, respectively, combining the DEGs in drought and bacterial stresses together that were below percentage of false predictions (PFP) ≤0.01 (Figure 1)
Among the 1214 SRGs common to the stresses studied in rice, majority of the genes were expressed in same direction (72% or 874) with 565 up and 309 downregulated in both drought and bacterial stresses
Summary
Crop productivity and survival is tightly linked to its environment which is being altered due to climate change, biodiversity loss and degradation of land and freshwater [1] threatening the food security of the world while the food demand is estimated to increase by 70% in 2050 [2,3,4]. According to latest World Agricultural Supply and Demand Estimates (WASDE) report by United States Department of Agriculture (USDA), about 80% of agricultural land is experiencing drought and over 2,000 U.S counties had been designated as disaster areas [5]. Rice and Arabidopsis are both model plant organisms representing monocots and dicots respectively. Both the plants have extensive biological knowledgebase and resources including complete genome sequence and highest number of microarray studies in the plant kingdom. Analysis of stress responsive genes within and between rice and Arabidopsis for different kinds of stresses would reveal a number of pivotal attributes spanning across the major plant division, angiosperms
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