Genome-wide study of ONAC127 and ONAC129 regulatory network in rice caryopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE140165 | GEO | 2020/03/26
REPOSITORIES: GEO
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Project description:ONAC127 and ONAC129 are NAC transcription factors that involved in abiotic stress response and play key regulatory roles in apoplasmic transportation during rice caryopsis filling. To reveal the transcription regulatory network of ONAC127 and ONAC129 in rice caryopsis, we identified significantly differentially expressed genes by RNA-Seq analysis using the caryopses of the CRISPR-mutants(CR) and overexpression lines(OX) of ONAC127 and ONAC129 under natural heat stress(H) and normal cultivation condition(N).
2020-03-26 | GSE140166 | GEO
Project description:To reveal the underlying molecular mechanism of Gif1 action in the control of grain filling and yield improvement, we performed transcriptional profiling of wild type Zhonghua11 and mutant gif1 plants in early filling stage on a global scale using the Affymetrix GeneChip Rice Genome Array Experiment Overall Design: Rice caryopsis were harvested in 7 days after flowering and three biological repeats were performed on Zhonghua11 (wild-type) and gif1 (mutant), respectively.
2008-11-06 | E-GEOD-9498 | biostudies-arrayexpress
Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice
2015-01-01 | E-GEOD-62200 | biostudies-arrayexpress
Project description:The OsCPK4 gene is a member of the complex gene family of the Calcium-dependent protein kinases (CPKs) in rice. Expression of OsCPK4 is induced by high salinity, drought and the phytohormone abscisic acid. The OsCPK4 protein localizes to the plasma membrane. Transgenic rice overexpressing OsCPK4 enhances tolerance to salt and drought stress, the transgenic plants having stronger water-holding capability than control plants. Microarray analysis of OsCPK4 rice plants revealed up-regulation of genes involved in metabolism, particularly lipid metabolism, as well as genes involved in oxidative stress and redox control. Meanwhile, OsCPK4 overexpression has no impact on the expression of the well-characterized abiotic stress-associated transcription factors (i.e. DREB and NAC), or the typical salt and drought-inducible genes (i.e. LEA genes, including Dehydrin genes). Under salt stress conditions, the OsCPK4 transgenic lines showed lesser membrane lipid peroxidation as compared to control plants, indicating that OsCPK4 rice plants have a better capacity to prevent oxidative damage in cellular membrane lipids. Collectively, our data suggest that OsCPK4-mediated processes protect the plant cell from uncontrolled redox reactions affecting membrane functions, which, in turn, results in salt and drought tolerance. OsCPK4 shows great promise for genetic improvement of tolerance to abiotic stress in rice.
2014-07-03 | GSE52353 | GEO
Project description:Rice reproductive development is highly sensitive to high temperature stress. In rice flowering occurs over a period of at least 5 days. Heat stress alters the global gene expression dynamics in panicle especially during pollen development, anthesis and grain filling. Some of the rice genotypes like Nagina 22 show better spikelet fertility and grain filling compared to high yielding and popular rice cultivars like IR 64. We carried out microarray analysis of 8 days heat stressed panicles of Nagina22, heat and drought tolerant aus rice cultivar and IR64, a heat susceptible indica genotype along with unstressed samples of Nagina22 and IR64 so as to understand the transcriptome dynamics in these two genotypes under heat stress and to identify the genes important for governing heat stress tolerance in rice.
2021-01-31 | GSE136746 | GEO
Project description:To comprehend the gene expression profile in rice panicle under high temperature, Agilent 4×44k rice oligo microarray experiments were carried out using rice panicle of post-meiosis at 0 min, 10min, 20 min, 60 min, and 2 hr after the treatment of 40 degree centigrade, and the differentially expressed genes at the time course were involved in binding, catalysis, stress response, and cellular process. The significantly expressed genes were mainly up-regulated. Among HR genes, the predominant transcription factor gene families were Hsf, NAC, AP2/ERF, WRKY, MYB, and C2H2. The MapMan analysis demonstrated that, under heat treatment, the HR genes were enriched in the pathways related to biotic stress, abiotic stress including heat and cold, and cell cycle and development, ubiquitin-proteasome , lipid and secondary metabolisms, which revealed the great importance of cross-talk and protein homeostasis in response to heat in rice panicle of post-meiosis.
2013-11-27 | GSE51426 | GEO
Project description:Rice NF-YC11 is a transcription factor that plays a key regulatory role in storage substance accumulation during rice grain filling. To reveal the transcription regulatory network of NF-YC11 in rice, we performed genome-wide identification of NF-YC11 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the NF-YC11-overexpression plants.
2019-08-21 | GSE119575 | GEO
Project description:Chromium (Cr) is a non-essential metal for normal plants and is toxic to plants at high concentration. In spite of many previous studies having been conducted on the effects of Cr stress, the precise molecular mechanisms and signaling pathways of action of Cr remain poorly understood. In this study, the transcriptome at the early of Cr (VI) stress were assayed in rice roots. To gain more insight into these cellular responses, we analyzed whole-genome transcriptome of rice expose to Cr (VI) for 1 and 3 h. Analysis revealed 1,261 and 267 up and down-regulated genes by Cr (VI). Cr (VI) stress triggered changes in transcript levels of genes related to secondary metabolism process, biosynthetic process, specially jasmonic acid biosynthetic process, response to abiotic stress, specially response to toxin, transcription regulator activity, specially transcription factors activity. The most predominant transcription factor families were WRKY, AP2/ERF, NAC, C2H2, MYB. In addition, many protein kinase, including eight MAPKKK, two CDPK, and one MAPK, showed significant increase in transcriptional level under Cr (VI) stress. Molecular mechanisms for the excess Cr(VI) in rice roots Comparison of mock control and rice seedlings treated with 200 M-NM-<M Cr(VI); Biological replicates: 3 control replicates, 3 Cr(VI)-treated replicates.
2013-10-31 | E-GEOD-33376 | biostudies-arrayexpress
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:Heat stress is one of the major abiotic stress factor that affects wheat yield. Especially, heat stress during grain filling affects grain yield besides reduced grain quality. So, in our present study, three genotypes with varied levels of tolerance to heat stress were chosen. They were subjected to heat stress at two stages for three days viz., early (11-14days-post-anthesis) and late (27-30dpa) grain filling independently under controlled conditions. At 14 and 30dpa, the spikes were harvested from control and stress conditions from all the three genotypes, grains were isolated and pulverized. Hence pulverized tissues are used for RNA extraction and further for transcriptome sequencing using HiSeq 4000. Data were analyzed to identify the genes involved in imparting heat stress tolerance.
2019-12-16 | E-MTAB-6140 | biostudies-arrayexpress