- Collectively, these results suggest that these varieties may have improved adaptability to cold stress.. - Full list of author information is available at the end of the article. - indica cv IR64 in response to cold stress. - Reports suggest that rice plants are more susceptible to cold stress during the seedling, tillering, panicle development and flowering stages. - Continued exposure to cold stress causes tissue necrosis and ultimately, cellular death [1–4]. - This rise in the mem- brane rigidity causes increased electrolytic leakage from the cell, which acts as the primary signal for triggering cold response via activation of the cold-responsive gene expression [6–9]. - gene expression to impart cold stress tolerance [17].. - Such studies provide a better understanding of the complexity of cold signaling that greatly enhances growth and grain productivity. - Moreover, the response to cold stress in rice varies with tissue type, as well as varying develop- mental stages. - In the present scenario, the knowledge of cold-responsive genes, and the cold-tolerant QTLs triggered at various stages, during cold stress can be exploited for breeding cold-tolerant rice varieties. - This study was aimed at identifying genes that undergo differ- ential expression in response to early cold stress in the IR64 rice variety and further extended to different indica cultivars to understand the early signaling events associ- ated with the cold stress response.. - Cold shock induces differential gene expression in IR64 indica rice. - This work aimed at studying the early cold stress re- sponse in rice (Oryza sativa L. - Normalized expression profiling was done on the aligned reads resulting in the identification of 32,161 transcripts expressed in at least one of the four samples profiled. - When compared between control and cold data sets of the transcripts were expressed in both, indicating a basal level of expression.. - We used Deseq2 package for differential expression analysis of the genes. - comprises of the differentially expressed genes, upregu- lated under cold shock, whereas, Clusters II and IV con- stitute the downregulated genes under cold shock. - To understand the biological function of the cold induced differentially expressed genes (DEGs), GO enrichment was performed using an FDR adjusted p-value of ≤0.05 as the cut-off. - Comparative analysis of the upregulated and downregu- lated GO terms indicates cell division (GO:0051301), pro- liferation (GO:0008283), developmental processes (GO:. - 0046274) were significantly enriched under cold shock.. - 1 Differential Gene Expression in IR64 plants due to 2 h cold shock (a) Venn Diagram showing the distribution of the total 32,161 transcripts obtained in the RNA-seq replicates. - Gene regulatory network induced during early cold stress Analysis of the DEGs showed the presence of a milieu of stress responsive genes upregulated, which included heat shock protein genes (Os02g0758000, Os03g0266900, Os06g0253100) Terpene synthases (OsTPS1, OsTPS31), Dehydrins, LEA and RAB group of proteins coding genes (OsDHN1, OsLEA28, OsRAB16, OsLEA14),. - 3 Differentially expressed stress-responsive genes under cold shock conditions. - The legend for the colour of the nodes and edges are included in the figure. - These findings suggest that the generation of ROS occurs during early cold shock and is essential for activating the redox signaling at the later stages of the stress response. - Downregulated genes included nine transcription factors needed for growth and develop- ment of the plant, which consisted primarily of bHLH TFs, and growth-related TFs such as OsGIF3 (Os03g0733600), OsGRAS1(Os01g0646300) and OsGRF7 (Os12g0484900) (Additional file 3). - HOX transcrip- tion factors constitute a secondary network which may con- tribute to cold stress response (Fig. - Differential expression of DREB1 regulon genes is integral to early cold stress response. - 4 Differentially expressed transcription factors under cold shock conditions. - This included 15 genes from upregulated DEGs and 10 genes from downregulated DEGs of the cold shock transcriptome. - This indicates that the transcription factors which recognize the DRE motif are triggered early during cold shock, to induce downstream regulators for mounting the entire cold stress response in rice plants. - b Validation of upregulated genes of the DREB regulon using qRT-PCR. - Twenty genes from the 107 upregulated DREB regulon genes were validated, among which expression of the genes coding for AP2/ERF transcription factor OsERF102 (Os09g0457900), Calcium-binding protein OsCCD1 (Os06g0683400), and the exocyst subunit EXO70 family protein, OsEXO70FX14 (Os01g0905300) exhibited high levels of significant upregulation (Fig. - We extended our study to ten different indica rice culti- vars that were never characterized for cold stress re- sponse. - factor IIS, Pyridoxal phosphate dependent transferase, OsERF102, OsCCD1, Pectin-glucuronyltransferase, and OsEXO70FX14 genes post cold shock treatment in the majority of the varieties (Fig. - In the case of the downregulated genes, OsGRF7, OsPRP1, OsbHLH155 showed consistent down-regulation in all varieties in re- sponse to cold shock treatment (Fig. - Our data indi- cated that expression of majority of the cold-responsive genes was significantly upregulated in the CB1, and Heera cultivars under control conditions, compared to the other varieties. - This higher level of expression of cold-responsive genes under control condition in CB1 and Heera varieties prompted us to examine the physio- logical response of the indica rice varieties used in this study.. - The germination experiments performed in this study revealed that the indica rice variety CB1 remains nearly unaffected by cold stress (72 h) prior to germination, whereas, the variety IR36 shows the highest sensitivity to the same. - g Images showing germination of different indica varieties post cold stress. - percent germination, which suggests their high level of sensitivity to cold stress conditions. - All the other indica varieties used in this study exhibit low to moderate sen- sitivity to cold stress as shown by their percent germin- ation (Fig. - The electrolyte leakage of the indica rice varieties IR64, IR36, Hamsahamas, CB1, and Heera under control and cold stress conditions (4 °C treatment for 2 h, 4 h, 24 h, 48 h, and 72 h) was studied by determining the relative electrical conductivity (REC%) of leaf tissue sam- ples of 14 days old seedlings. - shows a significant increase under cold stress in IR64, IR36, and Hamsahamas varieties. - There was no significant change in REC% in CB1 and Heera during initial cold stress time points.. - The ROS generation of the five indica varieties, under control and cold stress conditions (4 °C treatment for 2 h, 4 h, 8 h, and 24 h) was quantitated using H 2 DCFDA.. - However, the ROS generation decreases after 24 h of cold treatment in IR64, IR36 and Hamsahamas, suggesting the induction of the ROS scavengers during later stages of cold stress.. - The tolerant varieties CB1, and Heera show no signifi- cant changes in the ROS levels during cold stress.. - Studies have implicated cold stress as a major threat for indica rice plants in upland areas. - This study was designed to identify the early changes in the expression associated with cold stress response in IR64 indica rice variety. - Interestingly, when compared with previous reports of cold stress responsive genes in indica varieties, IR64 early cold response is associated with a higher number of upregulated genes unlike late chilling stress response in 93–11 variety (4 °C for 72 h), (2298 upregulated and 3992 downregulated DEGs, [42]).. - The role of DREB1 genes, a subtype of AP2/EREBP TF family, in cold stress response via the ABA-independent pathway has been well established in rice plants [4, 46–. - Interestingly, our results show similar upregulation of the DREB1 genes: OsDREB1B, OsDREB1A, OsDREB1C, OsDREB1E, OsDREB1G, and OsDREB1H genes in indica rice IR64 within 2 h of cold shock. - further indicating the importance of the AP2/EREBP TFs in early cold stress response [49]. - Sensing of the low temperature occurs via changes in the membrane fluidity or by sensor proteins such as. - The role of these proteins is to transduce the cold signal in the cytosol and activate stress responsive transcription factors and various hydrophilic polypeptides such as LEA and Dehydrin, to stabilize against cold-stress injuries in plant cells. - Increased electrolytic leakage in IR64 rice variety was evident from a significant increase in the relative electrical conductivity (REC%) for plants subjected to cold 2 h stress treatment at 4 °C (Fig. - Several LEA, dehydrins and low temperature-induced [62] genes were upregulated in our data set (Additional file 3), suggesting the onset of de- hydration response during initial cold stress conditions.. - Our result shows upregulation of Os71Z6, CYP78A9, OsKO4, OsABAox2, CYP701A8, and OsNR1 genes of the cytochrome family in response to cold shock. - Upregulation of these oxalate oxidases during cold stress response in our study agrees with the finding that ROS generation is induced as a primary abiotic stress response [70]. - Various other cold stress response genes established by previous studies, such as OsTPP2 [73], OsTPS1 [74], OsPHS1 [75], were significantly up- regulated during cold 2 h shock in this study.. - The Dehydration Responsive Element (DRE) cis-acting elements are involved in both osmotic and cold stress induced gene expression. - While osmotic stress response involves changes in DREB2 regulon gene expression, DREB1 genes are majorly responsible for mounting the cold stress response in plants [76]. - In this study, sig- nificant upregulation of the DREB1 gene cassette prompted us to focus on the DREB regulon genes. - This suggests that under cold shock inhibition of chromo- somal segregation occurs that may lead to inhibition of the cell cycle. - further emphasizing the nega- tive effect of cold stress on the cell cycle. - Germination experiments were employed to identify indica rice varieties with contrasting physiological re- sponse to cold stress. - This indicated that electro- lytic leakage and ROS generation are triggered early dur- ing cold stress response in the sensitive rice varieties, as opposed to the tolerant lines, CB1 and Heera. - The low level of REC% and ROS production, together with the expression profile of the cold-responsive genes in CB1 and Heera rice varieties further validate their high level of tolerance to the low-temperature condition (Fig. - Furthermore, transcription of some of the cold stress responsive genes and cold induced DREB regulons were found to be higher in CB1 and Heera varieties under control conditions suggesting that these varieties may be primed to mount the stress response during cold shock. - cold stress response especially in cereal plants like rice.. - This study was aimed at identifying some of the key re- sponsive genes activated early under cold stress (2 h) in IR64 indica rice variety. - A large number of Ca 2+ binding proteins and kinases indicate that calcium signalling as an essential cellular mediator of the cold signal perception and response. - Triggering of the ROS generation is also evident as numerous ROS producing oxidases were upregulated in the cold shock transcrip- tome. - An aliquot of the samples was run on an (Agilent) RNA Bioanalyzer chip to check for integrity.. - Better and complete annotation of the Japonica rice was the rationale behind using it as the ref- erence genome [86]. - The ex- tracted region sequences of the differentially regulated genes were and examined for the DRE core-motif (A/. - In case of the expression studies in different indica varieties (Fig. - Percent germination under cold stress condition. - Surface sterilized seeds of the nine indica rice varieties (IR64, IR36, Hamsahamas, Rasi, Ratna, Heera, CB1, GB1, and GB3) were incubated at 4 °C for varying time points:. - The percent germination of the varieties was calculated as under:. - The relative electrical conductivity (REC) of five indica rice varieties (IR36, IR64, Hamsahamas, CB1, and Heera) was measured under cold stress condition, to determine the variation in the physiological response of these var- ieties. - under control and cold stress treatment (at 4 °C for 2 h, 4 h, 8 h, and 24 h) conditions. - The ROS generation of the samples was expressed as fluorescence units/mg of protein [104].. - Differentially regulated gene list with DRE-core motif in 1 kb upstream of the transcription start site.. - CS: Cold shock treated seedlings. - All the authors reviewed the results and approved the final version of the manuscript.. - Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci. - Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network. - Phosphorylation of the transcriptional repressor MYB15 by mitogen-activated protein kinase 6 is required for freezing tolerance in Arabidopsis. - Rice and cold stress:. - Cloning of the DREB-like transcription factor from Chaling wild rice and the construction of plant expression vector. - Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress. - Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. - Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. - Signal transduction during cold stress in plants.. - Overexpression of the trehalose-6- phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice.. - Overexpression of the Arabidopsis CBF3transcriptional activator mimics multiple biochemical changes associated with cold acclimation. - Regulons involved in osmotic stress- responsive and cold stress-responsive gene expression in plants. - Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt