Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA144723 | ENA |
REPOSITORIES: ENA
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Project description:Higher temperature conditions during the final stages of rice seed development (seed filling and maturation) are known to cause damage to both rice yield and rice kernel quality. Japan, especially western and central parts, has seen record high temperatures in the last decade, and the rice kernel quality has decreased; specifically a reduction the first-grade of rice has been seen. In this study, we specifically looked at the harvested rice in a town of the central Kanto-plains (Japan) during the year 2010, which saw day-time temperatures go above the critical limits ranging from 34 to 38C at the final stages of seed development and maturity to investigate high-temperature effects in the actual field condition. Three sets of dry mature rice seeds (commercial) were obtained Japan Agriculture (JA Zen-Noh) branch in Ami-town of Ibaraki prefecture in September 2010, as grade 1 (labeled as Y1), grade 2 (labeled as Y2), and grade 3 (out-of-grade, labeled as Y3). The research objective was to examine in particular alterations in gene expressions genome-wide in grade 2 (Y2) and grade 3 (Y3) seeds over the grade 1 (Y1) following the high-temperature spike using a high-throughput omic-approach DNA microarray (Agilent 4 x 44K rice oligo DNA chip) in conjunction with MapMan bioinformatics analysis. Rice seed quality analysis revealed, as expected, low quality in Y3 > Y2 over Y1, in taste, amylose, protein and fatty acid degree, but not in water content. Transcriptome profiling data revealed 124 and 373 up-regulated and 106 and 129 down-regulated genes in Y2 and Y3, respectively. Bioinformatics analysis of differentially expressed genes revealed changes in function of genes related to metabolism, including starch metabolism (e.g., alpha amylase), defense/stress response, fatty acid biosynthesis and hormones. This research provides for the first time the seed transcriptome profile for the classified low grades (2 and out-of-grade) of rice under an actual stressed environmental condition of high temperature.
2016-03-21 | GSE79405 | GEO
Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment. Whole plants of two rice cultivars Zhonghua11 (low temperature sensitive) and Hanfeng (low temperature tolerance) were treated at 14°C for 2 days during seed development stage. The plants without treatment serve as controls. Rice seeds were harvested for RNA extraction.
2012-02-19 | E-GEOD-31077 | biostudies-arrayexpress
Project description:RNA-seq analysis during low temperature germination in rice
| PRJDB17450 | ENA
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:Expression data from additional fertilization rice seeds
| PRJNA215001 | ENA
Project description:We analyzed the transcriptome profiles for rice grain from heat-tolerant and -sensitive lines in response to high night temperatures at the early milky stage using the Illumina Sequencing method. On the 8th day after the labeled florets flowered, plants with the same label were transferred to chambers and maintained at a temperature of 38.0â±â0.5°C (treatment) or 25.0â±â0.5°C (control) for the dark period (10 h), and 26.0â±â0.5°C (both treatment and control) for the light period (14 h). Three biological replicates of the temperature treatments were grown under the same conditions. After 48 h of treatment, samples containing 45 grains with labels from the same region (middle to bottom part) of labelled ears were harvested, packed in aluminum foil, and flash-frozen in liquid nitrogen until further use. A total of 12 rice grain samples were harvested, i.e., controls (TC1, TC2 and TC3) and treatments (TT1, TT2 and TT3) of the three biological replicates of the heat-tolerant line, and controls (SC1, SC2 and SC3) and treatments (ST1, ST2 and ST3) of the three biological replicates of the heat-sensitive line.
2014-12-01 | E-MTAB-4348 | biostudies-arrayexpress
Project description:We characterized a rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which CYP96B4 gene (Cytochrome P450 96B subfamily) was identified as the target gene by map-based cloning and complementation test. A point mutation in CYP96B4 leads to a substitution of Thr to Lys in the SRS2 region. The sd37 leaves, panicles and seeds are all smaller compared with those of wild-type, and histological analysis showed that the decreased cell number was the main reason for the dwarf phenotype. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up- and down- regulated genes during this process.
2013-07-09 | GSE48593 | GEO
Project description:Cellularization is a key event during the development of the endosperm. Our understanding of the developmental regulation of cellularization has been limited for plants other than Arabidopsis. We found that the activation of OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization. Many genes involved in endosperm development or starch biosynthesis were prematurely activated in the caryopsis at two days after fertilization. The results implied that OsbZIP76 is involved in the regulation of cellularization in rice. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity. However, it was able to interact with OsNF-YB9 and OsNF-YB1, two nuclear factor Y (NF-Y) family transcription factors, both in yeast and in planta. OsbZIP76 and OsNF-YB9 showed similar endosperm-preferential expression patterns and the transiently expressed proteins were colocalized in the epidermal cells of tobacco. As with osnf-yb1 mutants, the osbzip76 mutants showed reduced seed size and reduced apparent amylose content of the seeds. We also confirmed that OsbZIP76 is an imprinted gene in rice, the expression of which depended on the genetic background. Our results suggested that OsbZIP76 is an endosperm-expressed imprinted gene to regulate development of the endosperm in rice.
2019-12-28 | GSE139445 | GEO
Project description:Expression data for stress treatment in rice seedlings
| PRJNA98147 | ENA
Project description:To understand the dynamics and global gene reprogramming in the early response to mechanical wounding in rice, the transcriptional response to mechanical injury was analyzed. A time-course experiment revealed the highly dynamic nature of the wound response in rice. Mechanical wounding triggered extensive gene expression reprogramming in the locally wounded leaf, affecting various physiological processes, including defense mechanisms and potentially tissue repair and regeneration. The rice response to mechanical wounding displayed both differences and similarities compared to the response to jasmonate treatment. These results highlight the importance of early JA signaling in response to mechanical stress in rice. This analysis provides an overview of the global transcriptional response to mechanical stress in rice, offering valuable insights for future studies on rice's response to injury, insect attack, and abiotic stresses.
2024-10-21 | GSE279814 | GEO