The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Indica Group
PROVIDER: GSE116422 | GEO | 2018/06/29
REPOSITORIES: GEO
Similar Datasets
Project description:The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
| PRJNA478446 | ENA
Project description:The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size
2020-04-01 | E-GEOD-116422 | ExpressionAtlas
Project description:Comparison of gene expression profiles of wild-type and apetala2 inflorescences. This series contains the data for three replicate experiments performed with three sets of biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wild type-Cy5 mutant-Cy3 Set 2: wild type-Cy3 mutant-Cy5 Set 3: wild type-Cy5 mutant-Cy3 Keywords: repeat sample
2004-05-02 | GSE1266 | GEO
Project description:Comparison of gene expression profiles of wild-type and apetala2 inflorescences. This series contains the data for four replicate experiments performed with four sets of biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wild type-Cy3 mutant-Cy5 Set 2: wild type-Cy5 mutant-Cy3 Set 3: wild type-Cy3 mutant-Cy5 Set 4: wild type-Cy5 mutant-Cy3 Keywords: repeat sample
2004-05-02 | GSE1271 | GEO
Project description: Not available
| S-EPMC549491 | biostudies-literature
Project description:The AZ and NAZ of the materials that were loss of shattering (DZ129) and easy to shattering (W517) were used to perform RNA-Seq, and high-quality differential expression profiles were obtained.
2022-12-14 | GSE211952 | GEO
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | GEO
Project description:Interventions: Black seed capsule (containing fresh black seed powder) in the amount of 1000 mg three times a day (it is better to take black seed capsule 2 hours before or 2 hours after a meal)..
Primary outcome(s): Cancer antigen 19-9 (CA19-9). Timepoint: Baseline, 3 months following the treatment and the end of treatment. Method of measurement: Blood test.;Carcino Embryonic Antigen (CEA). Timepoint: Baseline, 3 months following the treatment and the end of treatment. Method of measurement: Blood test.
Study Design: Randomization: N/A, Blinding: Not blinded, Placebo: Not used, Assignment: Single, Purpose: Treatment.
| 2496470 | ecrin-mdr-crc
Project description:The emerging picture of transcriptional regulation is one of unexpected complexity. It is now clear that single transcription factors control hundreds, if not thousands, of direct targets by binding their genomic loci, but it is not understood how many of these are major players and how many are supporting cast. To address this, we leverage a well-characterized developmental network in Arabidopsis and map genome-wide binding of related proteins in multiple tissues. The transcription factor APETALA2 (AP2) has numerous functions, including roles in floral organ identity, seed development and stem cell maintenance. We focus on the role of AP2 in the floral transition and map direct targets on a genome-wide scale. We show that ap2 mutants flower early in long and short days, and that AP2 binds to many loci, most prominently floral pathway integrators, microRNAs and floral organ identity genes, many of which exhibit AP2-dependent transcription. Opposing, logical effects are evident in AP2 binding to two developmental microRNA genes that control AP2 expression, with AP2 positively regulating miR156 and negatively regulating miR172, forming a complex direct feedback loop, which also included all but one of the AP2-like miR172 target clade members. We also seek conserved targets by comparing the genome-wide direct target repertoire of AP2 with that of SCHLAFMÜTZE (SMZ), another member of the AP2-like miR172 target clade that shares partial redundancy, as evidenced by a hexuple mutant for the entire clade that flowered extremely early. Clear similarities and divergence are exposed in the AP2 and SMZ direct target repertoires. Finally, using an inducible expression system, we demonstrate that AP2 has dual molecular roles. It functions both as a transcriptional activator and repressor, directly inducing the expression of the floral repressor AGAMOUS-LIKE 15 (AGL15), and directly repressing the transcription of floral activators like SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). ChIP-Seq of two biological replicates for ATH-AP2 and respective control samples
2010-04-13 | E-GEOD-21301 | biostudies-arrayexpress
Project description:Sorghum plants (Btx623 background) were grown in a glasshouse between March and May 2014. At panicle emergence, two biological replicates of flag leaf tissue and two biological replicates of emerging panicle tissue were harvested and used for RNA extraction. Btx623 is a non-shattering Sorghum accession, thus in the future we would like to add additional samples from accessions with varying degrees of seed shattering. This dataset will be useful for future comparisons of 1) shattering individuals at these stages and 2) additional flowering developmental time points in a variety of accessions (http://www.rnaseqforthenextgeneration.org/profiles/carrie-thurber.html#research)
2015-08-19 | E-MTAB-4203 | biostudies-arrayexpress