Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1229133 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR32506309_1.fastq.gz | Fastqsanger.gz | |||
| SRR32506309_2.fastq.gz | Fastqsanger.gz | |||
| SRR32506310_1.fastq.gz | Fastqsanger.gz | |||
| SRR32506310_2.fastq.gz | Fastqsanger.gz |
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Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. Here, we injected suspension spores into a susceptible indica rice cultivar 9311 booting panicle (infected water as mock) and divided the early disease symptom into 3 uninterrupted stages(S) at 6 day post inoculation (dpi): the infected pistil became expand (S1), the hyphae began to infect the bottom of anthers (S2) and the hyphae growth went on and surrounded the floral organ forming a floral-hyphae complex (S3). To gain insight into rice putatively differential responses to U. virens, all 3 infected and mock spikes with same spike length were collected and analyzed by Solexa/Illuminaâs digital gene expression (DGE) system, BGI. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection.
2013-11-14 | GSE32010 | GEO
Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. Here, we injected suspension spores into a susceptible indica rice cultivar 9311 booting panicle (infected water as mock) and divided the early disease symptom into 3 uninterrupted stages(S) at 6 day post inoculation (dpi): the infected pistil became expand (S1), the hyphae began to infect the bottom of anthers (S2) and the hyphae growth went on and surrounded the floral organ forming a floral-hyphae complex (S3). To gain insight into rice putatively differential responses to U. virens, all 3 infected and mock spikes with same spike length were collected and analyzed by Solexa/IlluminaM-CM-"M-BM-^@M-BM-^Ys digital gene expression (DGE) system, BGI. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection. Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed
2013-11-14 | E-GEOD-32010 | biostudies-arrayexpress
Project description:At the transition from vegetative to reproductive growth in rice, a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem (SAM) to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor. APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites by ChIP-seq analysis. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation at the reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.
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Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.
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Project description:We generated a genome-wide map of 5hmC in rice panicle using a sensitive chemical labeling method to capture DNA fragments with 5hmC modification, followed by NGS sequencing. We showed that the 5hmC peaks distribution is non-random, about 52% 5hmC was located in gene bodies, 25% in intergenic regions, 11% in promoters, and 12% in immediate downstream. It was significantly enriched in heterochromatic regions of chromosomes 4 and 10, and especially located around TE genes. Combined with RNA-seq transcriptome data, we found that the gene-specific alterations of 5hmC can result in gene activation or repression, suggesting a potential role for 5hmC in gene regulation. From the compared distribution analysis among super-hybrid rice cultivars LYP9, and its parental lines 93-11 and PA64s, we investigated the cultivar-specificity of both the global levels and locus-specific distribution of 5hmC. Our data provided an overview of the genomic distribution of 5hmC in rice panicle. This will set the stage for further functional characterization of this novel DNA modification and its biosynthesis in rice. Examination of 5hmC modifications in rice panicle This submission represents ChIP-Seq component of study.
2014-04-15 | E-GEOD-37242 | biostudies-arrayexpress
Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. In the previous study, 3 uninterrupted infecting stages were divided and each stage was monitored by Solexa/Illumina’s digital gene expression (DGE) system, and all data were submitted to NCBI (GSE32010). As the disease was greatly affected by environment and to eliminate environment factor, an experimental replication was done in 2011. Samples collection and analysis were described in GSE32010. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection.
2013-11-14 | GSE39048 | GEO
Project description:To gain mechanistic insights on OsMADS2 functions in rice spikelet development, we have employed global expression profilling to identify the genes regulated by OsMADS2. Transgenic rice panicle RNAs were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional OsMADS2 whereas upregulated genes will need OsMADS2 for their repression. Keywords: Comparative expression profile analysis
2007-07-31 | GSE7192 | GEO
Project description:Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. In the previous study, 3 uninterrupted infecting stages were divided and each stage was monitored by Solexa/Illumina’s digital gene expression (DGE) system, and all data were submitted to NCBI (GSE32010). As the disease was greatly affected by environment and to eliminate environment factor, an experimental replication was done in 2011. Samples collection and analysis were described in GSE32010. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection. Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed.
2013-11-14 | E-GEOD-39048 | biostudies-arrayexpress
Project description:Rice inflorescence meristem (IM) development is critical for panicle size and grain production. The transition from SAM to IM is an important development stage in rice. Here we report the application of ChIP-seq technology for profiling of H3K4me3 and H3K27me3 modification in SAM, IM, SDG711 RNAi IM and jmj703 IM which affect panicle size, respectively, and besides, RNA-seq technology for detecting gene expression diversity betwwen SAM, IM and SDG711 RNAi IM. We found that genome-wide H3K27me3 modification vary between SAM and IM, and thouands of genes lost H3K27me3 in SDG711 and jmj703. Also, we found H3K27me3/H3K4me3 ratio was an important factor for the differential expression of many genes during the transition. Differential expressed genes were found between SAM and IM, 711RNAi and WT, repectively. Many important genes involved in IM activity were repressed by SDG711-mediated H3K27me3 and some of which’s expressions were mis-regulated in SDG711 RNAi.
2015-05-14 | GSE68299 | 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.
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