The regulatory network of OsNAC6 targets drought-related genes orchestrating rice drought tolerance (RNA-Seq)
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE81069 | GEO | 2017/06/29
SECONDARY ACCESSION(S): PRJNA320410
REPOSITORIES: GEO
Similar Datasets
Project description:OsNAC6 is a stress responsive NAC transcription factor in rice known as a regulator for the transcriptional networks of the drought tolerance mechanisms. However, little is known about the associated molecular mechanisms for drought tolerance. Here, we identified OsNAC6-mediated root structural adaptation such as increased root number and root diameter that was sufficient to confer drought tolerance. Multiyear (5 years) drought field tests clearly demonstrated that OsNAC6 overexpression in roots produced higher grain yield under drought conditions. Genome-wide analyses revealed that OsNAC6 directly up-regulated 13 genes. Taken together, OsNAC6 is a valuable candidate for genetic engineering of drought-tolerant high-yielding crops.
2017-04-29 | GSE80986 | GEO
Project description:Plants have evolved to possess adaptation mechanism to cope with drought stress by reprograming transcriptional networks through drought responsive transcription factors, which in turn mediate morphological and physiological changes. NAM, ATAF1-2, and CUC2 (NAC) transcription factors are known to be associated with various developmental processes and stress tolerance. In this study, we functionally characterized the rice drought responsive NAC transcription factor OsNAC14. OsNAC14 was predominantly induced at meiosis stage, and induced by drought, high salinity, ABA and low temperature in leaves than roots. Overexpression of OsNAC14 resulted in drought tolerance at the vegetative growth stage and enhanced filling rate at vegetative growth. OsNAC14 overexpression elevated expression of genes related to DNA damage repair, defense response, strigolactone biosynthesis, which correlated with resistance to drought tolerance. Furthermore, OsNAC14 directly bound to the promoter of drought inducible OsRAD51A1, a key component in homologous recombination in DNA repair system. These results indicate that OsNAC14 mediate drought tolerance by recruiting factors involved in DNA damage repair and defense response to enable plant to protect from cellular damage caused by drought stress, thereby provide mechanism for drought tolerance.
2018-03-21 | GSE106150 | GEO
Project description:Drought is a major environmental constraint affecting physiological, biochemical and molecular changes of crops, causing loss in crop productivities. Understanding the molecular mechanisms of drought tolerance is important for crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, Rice outermost cell-specific gene 10 (Roc10), improves drought tolerance and grain yield by increasing lignin accumulation in ground tissues of rice plants. Overexpression of Roc10 significantly enhanced drought tolerance of transgenic rice plants at the vegetative stages of growth with highly effective photosystem and reduction of water loss rate as compared with non-transgenic control and RNAi plants. More importantly, Roc10 overexpression plants had higher drought tolerance at the reproductive stage of growth with higher grain yield over controls under field-drought conditions. We identified downstream and putative target genes of Roc10 by using RNA-seq and ChIP-seq data of rice shoots. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots with a concomitant increase in accumulation of lignin. The overexpression and RNAi lines showed opposite patterns of lignin accumulation. The Roc10 is mainly expressed in the outer cell layers including epidermis and vasculature of shoots that coincides with areas of increased lignification. Furthermore, the Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggested that the Roc10 confers drought stress tolerance by enhancing lignin biosynthesis in ground tissues of rice plants.
2018-01-06 | GSE93287 | GEO
Project description:Drought is a major environmental constraint affecting physiological, biochemical and molecular changes of crops, causing loss in crop productivities. Understanding the molecular mechanisms of drought tolerance is important for crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, Rice outermost cell-specific gene 10 (Roc10), improves drought tolerance and grain yield by increasing lignin accumulation in ground tissues of rice plants. Overexpression of Roc10 significantly enhanced drought tolerance of transgenic rice plants at the vegetative stages of growth with highly effective photosystem and reduction of water loss rate as compared with non-transgenic control and RNAi plants. More importantly, Roc10 overexpression plants had higher drought tolerance at the reproductive stage of growth with higher grain yield over controls under field-drought conditions. We identified downstream and putative target genes of Roc10 by using RNA-seq and ChIP-seq data of rice shoots. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots with a concomitant increase in accumulation of lignin. The overexpression and RNAi lines showed opposite patterns of lignin accumulation. The Roc10 is mainly expressed in the outer cell layers including epidermis and vasculature of shoots that coincides with areas of increased lignification. Furthermore, the Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggested that the Roc10 confers drought stress tolerance by enhancing lignin biosynthesis in ground tissues of rice plants.
2018-01-06 | GSE93288 | GEO
Project description:Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. The direct target genes were related to transmembrane/transporter activity, vesicle, plant hormone, carbohydrate metabolism, and transcription factors. The direct targets of each OsNAC are in a range of 4.0 to 8.7% of the genes up-regulated in RNA-Seq data sets. Thus, each OsNAC up-regulates of corresponding direct target genes that alters root system architectures of RCc3:OsNACs for drought tolerance. Our results provide valuable resources for functional dissection of the molecular mechanisms for plant drought tolerance.
2018-02-14 | GSE102920 | GEO
Project description:The AP2/ERF family is one of the plant-specific transcription factors (TFs) whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought-inducible OsERF48, a group Ib member of the rice ERF family that contains four conserved motifs, CMI-1, 2, 3 and 4. Transactivation assay in yeast revealed that the CMI-1 at the C-terminal end was essential for its transcriptional activity. When the OsERF48 was overexpressed in an either root-specific (ROXOsERF48) or whole-body (OXOsERF48) expression manner, both transgenic plants showed a longer and denser root phenotype than the nontransgenic (NT) controls. When plants were grown on a 40% PEG-infused medium, an in vitro drought condition, ROXOsERF48 plants showed a more vigorous root growth over OXOsERF48 and NT plants. In addition, the ROXOsERF48 plants exhibited higher grain yield under field-drought conditions than OXOsERF48 and NT plants. We constructed a putative regulatory network of OsERF48 by cross-referencing of RNA-seq data of ROXOsERF48 roots with a co-expression network database, revealing an involvement of 20 drought-related genes. These include genes for stress signaling, carbohydrate metabolism, cell-wall proteins, and drought-response. More importantly, OsCML16, a key gene for calcium signaling during abiotic stress, was identified to be the direct target of OsERF48 by the ChIP-qPCR and the protoplast transient assay. Thus, our results demonstrated that OsERF48 regulates OsCML16, a calmodulin-like protein gene that enhance root growth and drought tolerance.
2017-11-01 | GSE93081 | GEO
Project description:Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. The combination of constitutive and acquired traits governs drought tolerance, which is crucial for maintaining crop productivity under drought. Drought affects protein synthesis, to uncover the translational landscape with response to drought stress in rice, polysome bound mRNA sequencing at anthesis stage in resistant APO and sensitive IR64 genotypes were performed. Our results demonstrate that drought tolerant genotype maintains higher transcripts bound to poly-ribosomes which facilitate higher protien synthesis which impacted on photosynthesis, spikelet fertility, seed filing and yield under drought stress. We identified many novel LncRNAs and relevant genes associated with translation which can play important role in manitaing grain protein content with drought tolerance.
2024-03-20 | GSE232522 | GEO
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding. To investigate the epigenetic effect on histone mark distribution of the EUE/PEG selection we performed ChIP-seq analyses. Native ChIP using an anti-H3K4me3 and no antibody (background control) was done on PEG1 and control plants.
2015-06-28 | E-GEOD-65571 | biostudies-arrayexpress
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding.
2015-06-28 | GSE65572 | GEO
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding.
2015-06-28 | GSE65571 | GEO