Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes

• Main Authors: Woo-Jong Hong, Xu Jiang, Hye Ryun Ahn, Juyoung Choi, Seong-Ryong Kim, Ki-Hong Jung
• Format: Article
• Language: English
• Published: MDPI AG 2020-09-01
• Series: International Journal of Molecular Sciences
• Subjects: rice; cold stress response; circadian clock; diurnal rhythm; transcriptome analysis; <i>sgr</i> mutant
• Online Access: https://www.mdpi.com/1422-0067/21/18/6872
• ISSN: 1661-6596; 1422-0067

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.