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Coexpression network analysis associated with call of rice seedlings for encountering heat stress

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Abstract

Coexpression network analysis is useful tool for identification of functional association of coexpressed genes. We developed a coexpression network of rice from heat stress transcriptome data. Global transcriptome of rice leaf tissues was performed by microarray at three time points—post 10 and 60 min heat stress at 42 °C and 30 min recovery at 26 °C following 60 min 42 °C heat stress to investigate specifically the early events in the heat stress and recovery response. The transcriptome profile was significantly modulated within 10 min of heat stress. Strikingly, the number of up-regulated genes was higher than the number of down-regulated genes in 10 min of heat stress. The enrichment of GO terms protein kinase activity/protein serine threonine kinase activity, response to heat and reactive oxygen species in up-regulated genes after 10 min signifies the role of signal transduction events and reactive oxygen species during early heat stress. The enrichment of transcription factor (TF) binding sites for heat shock factors, bZIPs and DREBs coupled with up-regulation of TFs of different families suggests that the heat stress response in rice involves integration of various regulatory networks. The interpretation of microarray data in the context of coexpression network analysis identified several functionally correlated genes consisting of previously documented heat upregulated genes as well as new genes that can be implicated in heat stress. Based on the findings on parallel analysis of growth of seedlings, associated changes in transcripts of selected Hsps, genome-wide microarray profiling and the coexpression network analysis, this study is a step forward in understanding heat response of rice, the world’s most important food crop.

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Acknowledgments

This work was supported by funding from Centre for Plant Molecular Biology and Centre for Advanced Research and Innovation on Plant Stress and Developmental Biology, Department of Biotechnology, Government of India. AG is thankful to Department of Science and Technology, Government of India for the J.C. Bose fellowship award. We thank Prof. Sang Bong Choi, Myongji University, South Korea for helpful discussions. We thank John Wyrick, Washington State University, USA for help with Osiris database.

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Correspondence to Anil Grover.

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11103_2013_123_MOESM4_ESM.pptx

Supplementary Fig. 1. Functional categories of genes. Pie diagrams represent the various functional categories by COG (http://www.ncbi.nlm.nih.gov/COG/old/) analysis of up-regulated and down-regulated genes in three stress treatments. (PPTX 803 kb)

11103_2013_123_MOESM5_ESM.pptx

Supplementary Fig. 2. Hierarchical clustering of genes during heat stress and recovery. Microarray analysis of leaf tissue was performed as mentioned in the text. Twofold up- or down-regulated genes in at least one of the treatments in microarray were analyzed for hierarchical clustering. A-D are the clusters described in the text. (PPTX 56 kb)

11103_2013_123_MOESM6_ESM.pptx

Supplementary Fig. 3. Semi-quantitative RT-PCR analysis of selected genes. RT-PCR was performed in duplicate and the results of one set are presented. Details of primers and the number of cycles are listed in Supplementary Table 1 (PPTX 6670 kb)

Supplementary Fig. 4. Interactome analysis of Os03g12820 and Os03g60080 genes in STRING database. (PPTX 737 kb)

Supplementary Fig. 5. Expression analysis of coexpression network genes in genevestigator. (PNG 63 kb)

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Sarkar, N.K., Kim, YK. & Grover, A. Coexpression network analysis associated with call of rice seedlings for encountering heat stress. Plant Mol Biol 84, 125–143 (2014). https://doi.org/10.1007/s11103-013-0123-3

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