Gibberellin-induced gene expression in maize mesocotyl under deep-sowing condition
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ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Guoying Wang
PROVIDER: E-GEOD-15048 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M. In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of IAA treatment and TIBA (an auxin transportation inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.
2009-03-26 | E-GEOD-15371 | biostudies-arrayexpress
Project description:In order to elucidate the molecular mechanism of gibberellin (GA)-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying GA promotion of maize mesocotyl elongation. These studies showed that the GA receptor GID1, the transcriptional factor MYB, and the genes encoding DELLA protein DWRF8, kinases, Raf, LRR, RLCK, and involved in flavonoid biosynthesis, aminosugars metabolism, cell wall synthesis and modification, might play critical roles in maize mesocotyl elongation.
2009-03-07 | GSE15048 | GEO
Project description:In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M.
2009-03-26 | GSE15371 | GEO
Project description:The phytohormone GA controls multiple important developmental processes in plants such as germination, elongation growth and flowering time. In this experiment, we look for early GA response genes in 7 day-old light-grown Arabidopsis seedlings. To this end we compare four data sets: (1) a GA biosynthesis mutant ga-1 (SALK_109115) mock treated for 1 hr; (2) a GA biosynthesis mutant ga-1 (SALK_109115) treated for 1 hr with 100 µM GA3; (3) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant mock treated for 1 hr; (4) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant treated for 1 hr with 100 µM GA3. In a comparison of the two ga-1 samples, GA regulated genes can be identified, and the assumption is that bona fide GA regulated genes are not responding in the gid1a-1 gid1b-1 gid1c-2 GA receptor mutant. Experiment Overall Design: We compare four samples of 7 day-old light-grown growth-medium grown seedlings (3 independent biological replicates each): (1) a GA biosynthesis mutant ga-1 (SALK_109115) mock treated for 1 hr; (2) a GA biosynthesis mutant ga-1 (SALK_109115) treated for 1 hr with 100 µM GA3; (3) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant mock treated for 1 hr; (4) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant treated for 1 hr with 100 µM GA3. In a comparison of the two ga-1 samples, GA regulated genes can be identified, and the assumption is that bona fide GA regulated genes are not responding in the gid1a-1 gid1b-1 gid1c-2 GA receptor mutant.
2008-06-15 | E-GEOD-7353 | biostudies-arrayexpress
Project description:The phytohormone GA controls multiple important developmental processes in plants such as germination, elongation growth and flowering time. In this experiment, we look for early GA response genes in 7 day-old light-grown Arabidopsis seedlings. To this end we compare four data sets: (1) a GA biosynthesis mutant ga-1 (SALK_109115) mock treated for 1 hr; (2) a GA biosynthesis mutant ga-1 (SALK_109115) treated for 1 hr with 100 µM GA3; (3) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant mock treated for 1 hr; (4) a gid1a-1 gid1b-1 gid1c-2 GA receptor triple mutant treated for 1 hr with 100 µM GA3. In a comparison of the two ga-1 samples, GA regulated genes can be identified, and the assumption is that bona fide GA regulated genes are not responding in the gid1a-1 gid1b-1 gid1c-2 GA receptor mutant. Keywords: phytohormone response
2007-03-24 | GSE7353 | GEO
Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize. In two independent experiments, we generate maize gene expression profiles during drought stress and re-watering through comparing genome-wide expression patterns of drought stress treatment and re-watering treatment by using 17,555 Affymetrix maize whole genome array.
2010-06-16 | E-GEOD-16567 | biostudies-arrayexpress
Project description:Background: Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine. Results: In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed. Conclusions: Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.
2020-07-20 | GSE153169 | GEO
Project description:The goal of this study was to search for DELLA-independent GA-regulated genes in tomato. RNA deep sequencing (RNA-seq) was performed to GA-treated M82 and pro∆GRAS mutant. Using a two fold increased or decreased cutoff we identified 81 GA-up regulated and 15 GA-down regulated genes, from which five genes were DELLA-independent. M82 and pro∆GRAS seedlings were treated with Paclobutrazol (10mg/l) once a day for three days followed by a single GA3 application (100 µM). Three hours after the GA treatment, young leaves were collected and RNA was extracted for Illumina HiSeq 2500 sequencing. A total of eight samples were analyzed, each treatment had two biological replicates.
2015-07-09 | E-GEOD-68018 | biostudies-arrayexpress
Project description:Brassinosteroid (BR) and gibberellin (GA) promote many similar developmental responses in plants; but their relationship remains unclear. Here we show that BR and GA act interdependently through a direct interaction between the BR-activated BZR1 and GAinactivated DELLA transcription regulators. GA promotion of cell elongation required BR signaling, whereas BR or active BZR1 can suppresssed the GA-deficient dwarf phenotype. DELLAs directly interacted with BZR1 and inhibited BZR1-DNA binding both in vitro and in vivo. Genome-wide analysis defined a BZR1-dependent GA-regulated transcriptome, which is enriched with light-regulated genes and genes involved in cell wall synthesis and photosynthesis/chloroplast. GA promotion of hypocotyl elongation requires both BZR1 and the phytochrome interacting factors (PIFs), as well as their common downstream targets PREs. The results demonstrate that GA releases DELLA-mediated inhibition of BZR1, and that the DELLA-BZR1-PIF4 interaction defines a core transcription module that mediates coordinated growth regulation by GA, BR and light signals. Wild type Arabidopsis and bzr1-1D were grown in media containing 1 uM PAC and 0 or 2 uM PPZ for 4.5 days in dark, then treated with 10 uM GA3 or mock solution for 12 hr. Total RNA was extracted with Spectrum Plant Total RNA Kit (Sigma) and the mRNA sequencing libraries were constructed with barcodes using TruSeqTM RNA Sample Preparation Kit (Illumina). Six barcoded libraries were pooled together and sequenced by Illumina HiSeq2000.
2012-06-25 | E-GEOD-35408 | biostudies-arrayexpress
Project description:The plant hormone gibberellin (GA) represents an important regulator of growth and development. Early transcriptional events controlled by GA are not well characterised. Previous microarray studies have identified genes responsive to GA treatment in the whole seedling. The whole seedling represents many tissues where subtle effects of GA treatment in specific tissues may be masked. When treated with GA, an effect on the growth rate of roots was observed. More specifically, the shorter root of a GA-deficient plant can be rescued to wild-type length by the application of GA. This experiment was designed to identify GA-regulated genes in the root tips of Arabidopsis. The use of a GA-deficient mutant provides a greater potential to identify genes responding to GA treatment. Root tips are ideally suited for the quick uptake of the hormone treatment. There will be two biological replicates which will each consist of a control treatment at 0 minutes and 2 hours, as well as the experimental GA-treated 2 hour time point. This system provides an opportunity to compare gene expression between treated and non-treated root tips and allow the identification of early GA-responsive genes. 6 samples were used in this experiment.
2010-04-28 | E-GEOD-20223 | biostudies-arrayexpress