Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes
Rice (<i>Oryza sativa</i> L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the...
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doaj-902d0812e3054737afc5b25812f1d4f82020-11-25T03:33:03ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-09-01216872687210.3390/ijms21186872Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological ProcessesWoo-Jong Hong0Xu Jiang1Hye Ryun Ahn2Juyoung Choi3Seong-Ryong Kim4Ki-Hong Jung5Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, KoreaGraduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, KoreaGraduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, KoreaDepartment of Life Science, Sogang University, Seoul 04107, KoreaDepartment of Life Science, Sogang University, Seoul 04107, KoreaGraduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, KoreaRice (<i>Oryza sativa</i> L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein–protein interaction network encompassing four hub genes and analyzed the roles of the <i>Stay-Green (SGR)</i> gene in regulating crosstalk with <i>sgr</i> mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.https://www.mdpi.com/1422-0067/21/18/6872ricecold stress responsecircadian clockdiurnal rhythmtranscriptome analysis<i>sgr</i> mutant |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Woo-Jong Hong Xu Jiang Hye Ryun Ahn Juyoung Choi Seong-Ryong Kim Ki-Hong Jung |
spellingShingle |
Woo-Jong Hong Xu Jiang Hye Ryun Ahn Juyoung Choi Seong-Ryong Kim Ki-Hong Jung Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes International Journal of Molecular Sciences rice cold stress response circadian clock diurnal rhythm transcriptome analysis <i>sgr</i> mutant |
author_facet |
Woo-Jong Hong Xu Jiang Hye Ryun Ahn Juyoung Choi Seong-Ryong Kim Ki-Hong Jung |
author_sort |
Woo-Jong Hong |
title |
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes |
title_short |
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes |
title_full |
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes |
title_fullStr |
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes |
title_full_unstemmed |
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes |
title_sort |
systematic analysis of cold stress response and diurnal rhythm using transcriptome data in rice reveals the molecular networks related to various biological processes |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1661-6596 1422-0067 |
publishDate |
2020-09-01 |
description |
Rice (<i>Oryza sativa</i> L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein–protein interaction network encompassing four hub genes and analyzed the roles of the <i>Stay-Green (SGR)</i> gene in regulating crosstalk with <i>sgr</i> mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change. |
topic |
rice cold stress response circadian clock diurnal rhythm transcriptome analysis <i>sgr</i> mutant |
url |
https://www.mdpi.com/1422-0067/21/18/6872 |
work_keys_str_mv |
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