Abstract
The detrimental effect of high salinity on crop production is a serious problem. However, the number of genes with known functions relating to salinity tolerance is very limited in rice. To effectively address this limitation, selection of useful candidate genes and identification of major regulatory factors through global approaches are necessary. To this end, we used three data series of affymetrix array data produced with salt-treated samples from NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) and identified 653 rice genes commonly differentially expressed under three salt-stress conditions. While evaluating the quality of selected candidate genes for salt-stress responses, Gene ontology enrichment analysis revealed that responses to salt and water stresses of biological process category are highly overrepresented in salt-stress conditions. In addition, the major salt stress-responsive metabolism process and regulatory gene modules are classified through MapMan analysis, and detailed elements for further studies are suggested. Based on this, we proposed a salt stress-responsive signaling pathway in rice. The functional analysis of the main signal transduction and transcription regulation factors identified in this pathway will shed light on a novel regulatory metabolism process that can be manipulated to develop crops with enhanced salinity tolerance.
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Acknowledgments
This work was supported by a grant from “the Next-Generation BioGreen 21 Program (PJ01100401)” Rural Development Administration, Republic of Korea and Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (NRF-2013R1A1A2006040 to KHJ).
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Fig. S1. Graphic expression of 653 salt-stress-inducible genes.
Fig. S2. Heatmap analysis of salt-stress-responsive rice genes and Arabidopsis genes showing conserved ortholog genes between rice and Arabidopsis.
Fig. S3. MapMan analysis associated with 871 Arabidopsis salt-stress-inducible genes. Individual elements in the regulation overview (A), metabolism overview (B), transcription (C) and ubiquitin-dependent degradation overview (D) are represented by red rectangular boxes. The detailed information is listed in Table S8.
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Kim, SW., Jeong, HJ. & Jung, KH. Integrating omics analysis of salt stress-responsive genes in rice. Genes Genom 37, 645–655 (2015). https://doi.org/10.1007/s13258-015-0293-2
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DOI: https://doi.org/10.1007/s13258-015-0293-2