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Genome-wide Mapping of the Ozone-responsive Transcriptomes of Rice Panicle and Seed Tissues Reveals Novel Insight into their Regulatory Events

ABSTRACT: The ‘O3-responsive transcriptome’ behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. Obtained results showed that O3 differentially regulated 620 and 130 genes in the panicles and grains separately, by at least two-fold changes. However, only five genes were found to be common in both the tissues, suggesting towards the tissue specific O3-sensitivity in rice plants. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulated in rice panicle; whereas, 24 and 106 genes in rice grain, respectively. Further mapping onto various regulatory events revealed that, the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O3-responsive novel genes were identified, including the brassinosteroid insensitive-1 receptor kinase, wall-associated kinase like receptor, calcium-dependent protein kinases, phosphatidylinositol kinases, G-protein components, ethylene insensitive-3, cellulose synthases, pectatelyase, etc. Inventory of 745 O3-responsive genes and their mapping will surely expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O3 world.

ORGANISM(S): Oryza sativa

PROVIDER: GSE37478 | GEO | 2012/04/25

SECONDARY ACCESSION(S): PRJNA161855

REPOSITORIES: GEO

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Genome-wide Mapping of the Ozone-responsive Transcriptomes of Rice Panicle and Seed Tissues Reveals Novel Insight into their Regulatory Events

Project description:The ‘O3-responsive transcriptome’ behavior in the panicles and grains of rice plant was studied individually through high-throughput oligo-DNA microarray technique. Obtained results showed that O3 differentially regulated 620 and 130 genes in the panicles and grains separately, by at least two-fold changes. However, only five genes were found to be common in both the tissues, suggesting towards the tissue specific O3-sensitivity in rice plants. Among the O3-responsive genes, 176 and 444 genes were up- and down-regulated in rice panicle; whereas, 24 and 106 genes in rice grain, respectively. Further mapping onto various regulatory events revealed that, the majority of differentially expressed genes were mainly involved in signaling, hormonal, cell wall, transcription, proteolysis, and defense events. Many previously unknown O3-responsive novel genes were identified, including the brassinosteroid insensitive-1 receptor kinase, wall-associated kinase like receptor, calcium-dependent protein kinases, phosphatidylinositol kinases, G-protein components, ethylene insensitive-3, cellulose synthases, pectatelyase, etc. Inventory of 745 O3-responsive genes and their mapping will surely expand our knowledge on novel regulatory processes in both panicles and grains of rice; and, serve as a resource towards the designing of rice crops for future high-O3 world. Comparison between healthy rice plant panicles and ozone treated plant panicles (for 8 h) and seed (grain) of healthy rice plants and of rice plants grown under ozone for their lifeftime was performed. Three biological replicates (panicle or seed; pooled) were used, and dye-swaped.

2012-04-24 | E-GEOD-37478 | biostudies-arrayexpress

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.

2013-08-20 | GSE49963 | GEO

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2012-05-01 | GSE37650 | GEO

Global identification of genes specific for rice meiosis

Project description:The leptotene-zygotene transition is a major step in meiotic progression during which pairing between homologous chromosomes is initiated and double strand breaks occur. OsAM1, a homolog of maize AM1 and Arabidopsis SWI1, encodes a protein with a coiled-coil domain in its central region that is required for the leptotene-zygotene transition during rice meiosis. To gain more insight into the role of OsAM1 in rice meiosis and to identify additional meiosis-specific genes, we characterized the transcriptomes of young panicles of Osam1 mutant and wild-type rice plants using RNA-Seq, bioinformatic and statistical analyses. As a result, a total of 25,750 and 28,455 genes were expressed in young panicles of wild-type and Osam1 mutant plants, respectively, and 4,400 differentially expressed genes (DEGs; log2 Ratio ≥ 1, FDR ≤ 0.05) were identified. Of these DEGs, four known rice meiosis-specific genes were detected, and 22 new putative meiosis-related genes were found by mapping these DEGs to reference biological pathways in the KEGG database. We identified eight additional well-conserved OsAM1-responsive rice meiotic genes by comparing our RNA-Seq data with known meiotic genes in Arabidopsis and fission yeast. We sequenced the transcriptome of young panicles of Osam1 mutant and wild-type rice.

2015-07-01 | E-GEOD-66469 | biostudies-arrayexpress

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2012-04-30 | E-GEOD-37650 | biostudies-arrayexpress

Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

2013-08-20 | E-GEOD-49963 | biostudies-arrayexpress

Global identification of genes specific for rice meiosis

2015-07-01 | GSE66469 | GEO

DCL4-Dependent Clusters of PhasiRNAs in Rice.

Project description:The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. Further analyses identified two conserved 22-nucleotide motifs among the cleavage sites of the 21- and 24- phasiRNA loci, and the cleavage sites of over 90% of 21- and 24-nucleotide phasing clusters were confirmed by PARE/degradome analysis from 93-11 panicles. MiR2118 and miR2275, expressed specifically in panicles, were predicted to trigger cleavages at 21- and 24-nucleotide phasiRNA clusters, respectively. The triggers of phasiRNAs are more dependent on Os DCL4 than Os DCL1. Furthermore, the processing of 21-nucleotide phasiRNAs was largely Os DCL4-dependent, whereas the processing of 24-nucleotide phasiRNAs was slightly affected by Os DCL4, but not by Os DCL3a and Os DCL1. Our results revealed distinct roles of Os DCL4 in a novel 21- and 24-nucleotide phasiRNA biogenesis pathway in rice. Six small RNA libraries were constructed from seedlings and panicles of 93-11 (a wild-type Indica rice variety) and osdcl4-1, as well as those from Nipponbare panicles and seedlings (a wild-type Japonica rice variety).

2012-03-29 | E-GEOD-22763 | biostudies-arrayexpress

Expression data from panicle in heat tolerant and heat susceptible rice under high temperature stress

Project description:To better understand the mechanisms that regulate the heat stress response in rice, we conducted a comparative analysis of transcriptome profile in panicles from two rice lines, heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082) using rice Affymetrix GeneChip. In HTL252 panicles, 1538 differentially expressed genes (DEGs) genes with at least four-fold expression changes compared with the control under heat treatment were considered heat-responsive (HR). Of these DEGs, 522 genes were up-regulated while 1016 genes were repressed. Among DEGs in HSL082, 496 genes were induced and 1707 genes were repressed. Out of the 370 common DEGs found between HTL252 and HSL082, 129 genes were induced and 241 genes were repressed.

2019-06-20 | GSE83542 | GEO

Microarray analysis of rice plants fumigated with ozone

Project description:In this study, integrated transcriptomics, proteomics and metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of two-weeks old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h. Based on the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice. Also investigated were the molecular responses in the leaves of two-weeks old rice (cv. Nipponbare) seedlings under continuous light and pure air (as a positive control for ozone exposure experiments) for a period of 24 h. Transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that continuous light and growth for 24 h also triggers a chain reaction of altered gene expressions involved in multiple cellular processes in rice, but different from those against ozone, in general. Keywords: Ozone fumigation response

2008-04-24 | GSE11157 | GEO

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