Oryza sativa
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PROVIDER: PRJNA1032162 | ENA |
REPOSITORIES: ENA
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Project description:The rice gene SUB1A-1 confers flooding tolerance restricting shoot growth during submergence. Rice with SUB1A also show more rapid recovery after submergence ends, but mechanisms by which SUB1A improves recovery from submergence had not been examined. In this study, the transcriptome was sequenced at five time points over a 24 hour submergence recovery period in near-isogenic rice genotypes with and without SUB1A.
2017-09-01 | GSE102494 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response
2010-03-09 | GSE17704 | GEO
Project description:Chilling stress is a major abiotic stress that affects rice growth and development. Rice seedlings are quite sensitive to chilling stress and this harms global rice production. Comprehensive studies of the molecular mechanisms for response to low temperature are of fundamental importance to chilling tolerance improvement. The number of identified cold regulated genes (CORs) in rice is still very small. Circadian clock is an endogenous timer that enables plants to cope with forever changing surroundings including light–dark cycles imposed by the rotation of the planet. Previous studies have demonstrated that the circadian clock regulates stress tolerances in plants show circadian clock regulation of plant stress tolerances. However, little is known about coordination of the circadian clock in rice chilling tolerance. In this study, we investigated rice responses to chilling stress under conditions with natural light-dark cycles. We demonstrated that chilling stress occurring at nighttime significantly decreased chlorophyll content and photosynthesis efficiency in comparison with that occurring at daytime. Transcriptome analysis characterized novel CORs in indica rice, and suggested that circadian clock obviously interferes with cold effects on key genes in chlorophyll (Chl) biosynthesis pathway and photosynthesis-antenna proteins. Expression profiling revealed that chilling stress during different Zeitberger times (ZTs) at nighttime repressed the expression of those genes involved Chl biosynthesis and photosynthesis, whereas stress during ZTs at daytime increases their expression dramatically. Moreover, marker genes OsDREBs for chilling tolerance were regulated differentially by the chilling stress occurring at different ZTs. The phase and amplitude of oscillation curves of core clock component genes such as OsLHY and OsPRR1 are regulated by chilling stress, suggesting the role of chilling stress as an input signal to the rice circadian clock. Our work revealed impacts of circadian clock on chilling responses in rice, and proved that the effects on the fitness costs are varying with the time in a day when the chilling stress occurs.
2022-03-01 | GSE146174 | GEO
Project description:Analysis of the impact of plant growth regulators on submergence tolerance of rice at gene expression level. The hypothesis tested in the present study was that the submergence-tolerance was improved by foliar application of paclobutrazol under sumergence stress conditions.
2017-10-12 | GSE104035 | GEO
Project description:Rice NSF45K microarray experiment to dissect submergence tolerance response in submergence tolerant rice plant, M202(Sub1): We previously characterized the rice (Oryza sativa L.) Sub1 locus encoding three Ethylene Responsive Factor (ERF) transcriptional regulators. Genotypes carrying the Sub1A-1 allele are tolerant of prolonged submergence. To elucidate the mechanism of Sub1A-1 mediated tolerance, we performed transcriptome analyses comparing the temporal submergence response of Sub1A-1 containing tolerant M202(Sub1) with the intolerant isoline M202 lacking this gene at three duration of submergence (0d, 1d, and 6d) with two biological replicates and one or two dye-swaps. We identified 898 genes displaying Sub1A-1-dependent regulation. Keywords: Abiotic stress tolerance response Three-condition experiment, M202(Sub1) vs wild type control (M202) at three durations of submergence (0d, 1d and 6d). Biological replicates: 2, independently grown and harvested. Technical replicates replicates: 1-2 control.
2010-03-08 | E-GEOD-17704 | biostudies-arrayexpress
Project description:An ERF transcription factor, Submergence-1A (Sub1A), dramatically enhances the tolerance to prolonged submergence in rice. For instance, rice accessions which lack Sub1A (e.g. M202) die within 7-10 d of complete submergence. By contrast, genotypes which posses Sub1A (e.g. M202(Sub1)) can endure submergence stress for 14 d. In this study, the two near isogenic lines with and without Sub1A were subjected to microarray analysis using Affymetrix Gene Chip technology. This analysis provided beneficial information to elucidate general response to submergence stress and to estimate Sub1A-dependent defense response to the stress at mRNA accumulation level.
2010-02-04 | GSE18930 | GEO
Project description:Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. The analysis results for the sequencing data showed that 6,867 transcripts were differentially expressed in the leaves (2,216 up-regulated and 4,651 down-regulated) and 4,988 transcripts in the roots (3,105 up-regulated and 1,883 down-regulated). Among these differentially expressed genes, the detection of many transcription factor genes demonstrated that multiple regulatory pathways were involved in salt stress tolerance. In addition, the differentially expressed genes were compared with the previous RNA-Seq analysis of salt-stress responses in cultivated rice Nipponbare, indicating the possible specific molecular mechanisms of salt-stress responses for Dongxiang wild rice. A large number of the salt-inducible genes identified in this study were co-localized onto fine-mapped salt-tolerance-related quantitative trait loci, providing candidates for gene cloning and elucidation of molecular mechanisms responsible for salt-stress tolerance in rice.
2016-01-13 | GSE73181 | GEO
Project description:This study evaluated transcriptomic responses to submergence in elongating and non-elongating leaves of rice near-isogenic lines with and without SUB1A using RNA-Seq. SUB1A is an ERF transcription factor gene and the key regulator of submergence tolerance in rice, restricting underwater elongation and avoiding starvation under the stress. Submergence induces mRNA accumulation of SUB1A similarly in elongating and non-elongating leaves. This study uncovered SUB1A-dependent and independent regulation of adaptive responses to submergence in the two functionally distinct leaves at the global level.
2022-08-01 | GSE181336 | GEO
Project description:Most rice (Oryza sativa L.) cultivars die within several days of complete submergence, but some indica cultivars, such as FR13A, can survive up to 2 weeks of complete submergence. In FR13A, a major quantitative trait locus (QTL), named Sub1, provides mature plants with submergence tolerance. However, the Sub1 locus can not confer flooding tolerance during germination to FR13A. Another indica cultivar, Goda Heenati, shows both tolerance to flooding during germination and submergence in mature plants. It was once reported that submergence tolerance in FR13A and Goda Heenati cultivars was controlled by their respective genetic locus. These evidences indicate that tolerance to submergence in these two cultivars may involve differential mechanisms. To gain insight into their putatively differential responses to submergence stress, the Agilent rice genome 4×44 K oligonucleotide microarray was used to explore the transcriptome of FR13A and Goda Heenati under control and submergence-stressed conditions. Two-way ANOVA analysis with Benjamini-Hochberg false discovery rate demonstrated that at an overall P＜0.01 level, 2810, 8207, and 4 probes were significantly regulated for genotype, treatment, and genotype×treatment interaction, respectively. To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and unpaired t-test P value < 0.01 was uesd for both FR13A and Goda Heenati. A total of 504 probes were up-regulated and 592 probes were down-regulated in FR13A under submergence stress. In Goda Heenati, 998 probes were induced and 1186 probes were suppressed by submergence treatment.
2010-12-01 | GSE23574 | GEO