Abstract
Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as—‘photosynthesis’, ‘respiratory burst’, ‘response to hormone’, ‘signal transduction’, ‘metabolic process’, ‘response to water deprivation’, which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules.
Highlights
Abiotic stress severely affects both physical and biochemical properties of plant cells, which eventually alter survival and productivity
Microarray data were downloaded from NCBI Gene Expression Omnibus and EBI ArrayExpress Archive in March 2017.Each dataset contains more than 22,500 probesets representing approximately 24,000 genes
The raw data related to drought and cold stress were normalized by GCRMA approach and the relative quality of different samples within dataset was examined by ArrayQualityMatrics, R package
Summary
Abiotic stress severely affects both physical and biochemical properties of plant cells, which eventually alter survival and productivity. In most of the plant species, >50% growth reduction was observed due to abiotic stress [1]. Plants have to encounter more than one stress simultaneously and try to acclimate to changing the climate. They have evolved several physiological, molecular and metabolic mechanisms that eventually leads to stress tolerance by achieving a homeostatic state [2,3,4]. The stress adaptation mechanisms are largely unknown, elucidating these tolerance mechanisms is essential to accelerate plant adaptability to natural field conditions in order to enhance their growth and yield
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