Oryza sativa Japonica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA139159 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression. Control condition experiment, root or shoot of WT vs. MIT knockdown plant. Two replicates each comparison, including a dye swap.
2011-04-07 | E-GEOD-28428 | biostudies-arrayexpress
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO
Project description:Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions.
2017-11-09 | GSE77046 | GEO
Project description:Improvement of chilling tolerance is a key strategy to face potential menace from abnormal temperature in rice production, which depends on the signaling network triggered by receptors. However, little is known about the QTL genes encoding membrane complexes for sensing cold. Here, Chilling-tolerance in Gengdao/japonica rice 1 (COG1) was isolated from a chromosome segment substitution line containing a QTL (qCS11-jap) for chilling sensitivity. The major gene COG1 was found to confer chilling tolerance in japonica rice. In natural rice populations, only the haplogroup1 encoded a functional COG1. Evolutionary analysis showed that COG1 originated from Chinese O. Rufipogon and was fixed in japonica rice during domestication. COG1, a membrane-localized LRR-RLP, targeted and activated the kinase OsSERL2 in a cold-induced manner, promoting chilling tolerance. Furthermore, the cold signal transmitted by COG1-OsSERL2 activates OsMAPK3 in the cytoplasm. Our findings reveal a cold-sensing complex, which mediates signaling network for the chilling defense in rice.
2023-06-18 | PXD042294 | Pride
Project description:To validate transcription of the japonica non-exonic TARs and to understand their transcriptional relation with annotated genes, we constructed a new array (designated the re-array) to surrogate 44,385 non-TE gene models and 25,313 TARs in japonica each with five independent 36mer probes. Using the re-array, we obtained triplicate expression estimates from 11 rice tissue. Keywords: gene expression
2007-02-06 | GSE6921 | GEO
Project description:Previously, we successfully introduce the bacterial blight resistance trait from Oryza meyeriana into O. sativa using asymmetric somatic hybridization with O. meyeriana as the donor species. After years of breeding, a progeny named Y73 was generated with recurrent parent O. sativa L. ssp. japonica cv. Dalixiang, and it shows high resistance to broad-spectrum of bacterial blight pathogens Xanthomonas oryzae pv. Oryzae (Xoo). However, the resistance mechanism of Y73 is remain undiscovered. To provide insights into the high resistance phenotype of these plants, we examined the transcriptome response in leaves of Y73 to the bacterial blight infection in this study. Xoo inoculated and mock inoculated rice plants were grown in growth room and the global analysis of gene expression events in rice leaves at 24 hours post inoculation (hpi) were analyzed using Affymetrix Rice GeneChip microarrays. We used microarrays to detail the global programme of gene expression underlying Xoo infection in rice Y73.
2012-02-27 | GSE36093 | GEO
Project description:Genome sequencing project of japonica rice varieties
| PRJDB4518 | ENA
Project description:The lem mutant was discovered in a doubled haploid (DH) line derived from the F1 of Gui-630 (Indica)xTaiwanjing (Japonica) by anther culture. The lem mutant did not affect other traits but caused all other floral organs (including palea, lodicule, stamen and carpel) to homeotically transform into lemma or lemma-like structures and caused floral meristem to be indeterminate, thus resulting in the mutant floret consisting of whorls of lemma and lemma-like organs. To identify the global gene expression changes mediated by LEM, we used 57K Affymetrix rice whole genome array to investigate the differences of genome-wide transcriptome between the young panicles of mutant lem versus WT samples during flower development stage. Keywords: rice (Oryza sativa L.),wild-type and lemmata mutant We generate gene expression profiles of rice cultivar Gui-630 (indica)x Taiwanjing (japonica) and mutant lemmata by using 57K Affymetrix rice whole genome array.
2010-03-23 | E-GEOD-20522 | biostudies-arrayexpress
Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other
2005-04-09 | GSE2500 | GEO
Project description:Oryza sativa Japonica (rice) is the staple food for all over world population. At the time of germination, the exposure to light may play an important role in the early development of the rice seedling. In order to survey the genes, their functions and role in biological processes, an RNA-Seq based study of 6 libraries prepared from poly-A rich mRNA fraction was carried out to explore transcriptional programs operating in dark and light conditions. For each treatment type, three individual plants were used as biological replicates.
2022-12-01 | E-MTAB-5689 | biostudies-arrayexpress