Oryza sativa Japonica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA135843 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To assess the role of POLA in relation to ovule development, embryogenesis and endosperm development, we analyzed gene expression profiles by using microarray. Compared to the wild-type plants, several groups of transcription factors in the pola mutant plants and POLA RNAi lines showed up- or down-regulation at meiotic stage and ripening stages of floral development. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as biosynthesis, transport, signal transduction, and degeneration of hormone, sugar, starch, fatty and lipid, protein and amino acid. These results supported that MADS protein POLA could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes involved in developmental and hormonal pathways. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at meiotic and ripening stage. For meiotic stage RNA sample, panicle of pola mutant were prepared at early to late meiotic stage, and panicle of POLA RNAi line(T2) were prepared at ten to fifteen days after pollination stage for ripening stage RNA sample.
2010-12-01 | E-GEOD-25693 | biostudies-arrayexpress
Project description:To assess the role of POLA in relation to ovule development, embryogenesis and endosperm development, we analyzed gene expression profiles by using microarray. Compared to the wild-type plants, several groups of transcription factors in the pola mutant plants and POLA RNAi lines showed up- or down-regulation at meiotic stage and ripening stages of floral development. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as biosynthesis, transport, signal transduction, and degeneration of hormone, sugar, starch, fatty and lipid, protein and amino acid. These results supported that MADS protein POLA could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes involved in developmental and hormonal pathways.
2010-12-01 | GSE25693 | GEO
Project description:Embryo and endosperm gene expression profile at ripening stage
| PRJNA170877 | ENA
Project description:mRNA/sRNA expression analyses in rice meiotic anthers
| PRJDB5291 | ENA
Project description:The study of climacteric fruit ripening in tomato has been facilitated by the spontaneous ripening mutants Colorless non-ripening (Cnr), non-ripening (nor), and ripening inhibitor (rin). These mutants effect the genes encoding ripening transcription factors (TFs) SPL-CNR, NAC-NOR, and MADS-RIN causing pleiotropic defects to the ripening program. Here, we demonstrate that some ripening processes occur in the mutant fruit but at later stages of development compared to the wild type. The rin and nor mutant fruit exhibit similar quality traits to wildtype at later stages of ripening and senescence and delayed expression of ripening-associated genes. In addition, we propose that the Cnr mutant has a broader range of effects to fruit development than just fruit ripening. Cnr fruit show distinct differences from wild type in ripening phenotypic traits and gene expression profiles prior to the initiation of ripening. We provide new evidence that some mutants can produce more ethylene than basal levels and demonstrate ABA accumulation is also affected by the mutations. Studies have examined the relationship between the CNR, RIN, and NOR TFs based on protein-protein interactions and transcriptional regulation during fruit ripening. We describe the genetic interactions affecting specific fruit traits by using homozygous double mutants. Cnr predominantly influences the phenotype of the Cnr/nor and Cnr/rin double mutants but additional defects beyond either single mutation is evident in the transcriptome of the Cnr/nor double mutant. Our reevaluation of the Cnr, nor, and rin mutants provides new insights the utilization of the mutants in breeding and studying fruit development.
2020-12-24 | GSE163745 | GEO
Project description:Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner. A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets. We monitored global gene expression in normal (PK331 cultivar) and rin mutant (PK353 cultivar) tomatoes at the pre-ripening (mature green, G) and ripening (pink coloring, P) stages using microarray with three biological replicates for each sample.
2012-04-01 | E-GEOD-28564 | biostudies-arrayexpress
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant
2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress
Project description:Differentially expressed genes from different developmantal stages in rice
| PRJNA99403 | ENA
Project description:Unripening mutant was identified from natural population of cv. Arka Vikas and the mutant was characterized with un ripened with light yellowish colour pericarp. Differential gene expression studies were carried out between unripening mutant and wild type using the whole genome microarray expression profiling as a discovery platform. Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of unripening mutant and wild type was used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals genes involved in the pathway altered in the unripening mutant. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in unripening mutant.
2018-12-01 | GSE92645 | GEO
Project description:Transcriptome analysis in rice smos1 mutant
| PRJNA236314 | ENA