Abstract
Rice (Oryza sativa 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 Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.
Highlights
Rice (Oryza sativa L.) is a model crop plant and a staple crop across the globe, Asia
For systematic analyses aimed at revealing the unknown molecular mechanisms of cold stress response and circadian rhythm, we identified candidate genes responsive to cold stress and diurnal rhythm expression patterns
We identified rice genes unique to cold stress response using a meta-expression dataset consisting of four abiotic stress responses such as drought, salt, cold, and submergence
Summary
Rice (Oryza sativa L.) is a model crop plant and a staple crop across the globe, Asia. Circadian clock greatly affect plants, regarding synchronizing biological processes and increasing the efficiency of photosynthesis owing to the non-motile feature of these organisms [12,13,14] It is involved in various physiological regulatory roles, including flowering time, by controlling the expression and photostability of CONSTANS proteins, which induce FLOWERING LOCUS proteins for flowering [15]. We constructed a protein–protein interaction (PPI) network and validated it using the stay-green (sgr) mutant for the regulation of the crosstalk between the cold-response and circadian clock Based on these results, we proposed that a hypothetical molecular network mediates interplay among various biological processes, including the circadian clock, cold stress response, hormone signaling, and senescence. Our systems biology approach regarding the cold stress response and circadian clock identified some details of the molecular network which could be used to improve the productivity and regional adaptation of rice
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