RNA-seq of germinating barley embryos in control and ABA
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PROVIDER: PRJEB74509 | ENA |
REPOSITORIES: ENA
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Project description:To address the lack of information on the function of CBC in the ABA signaling pathway during seed germination in barley, we employed TILLING to identify mutants of the genes hvcbp20.ab and hvcbp80.b and subsequently created the double mutant hvcbp20.ab/hvcbp80.b. We found that mutations in both CBC subunits resulted in a unique ABA response that differed from that of single mutants. Through transcriptomic analyses, we identified differential gene expression and alternative splicing patterns. Notably, the hvcbp20.ab/hvcbp80.b double mutant exhibited altered AS regulation and significant changes in brassinosteroid signaling following ABA exposure. Seeds were sterilized in 20% sodium hypochlorite solution for 20 min and washed with sterilized water for 5 min. They were then placed in Petri dishes with three layers of filters and treated with either sterilized water or sterilized water containing 75 μM ABA (cis-trans-abscisic acid; catalog no. 862169; Sigma-Aldrich). The seeds were stratified for 4 d at 4°C and then transferred to a growth chamber. Germination was defined as the visible emergence of the radicle through the seed coat and was assessed on 1 and 7 DAI (Days After Imbibition). The assay was performed in three biological replicates, each comprising 30 seeds of each genotype per petri dish. At 1 DAI, the embryos were isolated from the endosperm using a sharp scalpel blade, placed in microcentrifuge tubes (Eppendorf) containing RNAlater reagent, and stored at 4°C until RNA isolation. RNA was isolated using the mirVana™ Isolation Kit (Ambion, USA) following the manufacturer’s instructions. RNA was isolated in four biological replicates, each consisting of 20 embryos. In total, 32 RNA samples were extracted. RNA concentration and quality were assessed using a NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, USA) and Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA). We used grains and embryos of barley TILLING mutants: the hvcbp20.ab, in the CBP20 gene (CAP-BINDING PROTEIN 20; BaRT2v18chr6HG306340; 41,42), and hvcbp80.b, in the CBP80 gene (CAP-BINDING PROTEIN 80; BaRT2v18chr4HG195950), single mutants, the hvcbp20.ab/hvcbp80.b double mutant, and the 'Sebastian' wild-type (WT), all sourced from the HorTILLUS population 91. Single mutants were identified through TILLING in the M2 generation (then backcrossed with WT to clean the genetic background), and the double mutant was isolated from the F2 progeny following crossbreeding of the single mutants
2024-07-08 | E-MTAB-13989 | biostudies-arrayexpress
Project description:Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h
2016-02-18 | E-GEOD-66024 | biostudies-arrayexpress
Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.
2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress
Project description:Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos
2016-02-18 | GSE66024 | GEO
Project description:Transcriptional profiling of barley shoot and root with ABA
2014-04-01 | GSE41511 | GEO
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to ABA treatment, at two time points, each including triplicated measurements Experiment Overall Design: Plants were grown at 20ºC for seven days.
2009-05-11 | E-GEOD-10328 | biostudies-arrayexpress
Project description:A Spatial Transcriptome for Germinating Barley Grain
| PRJNA906477 | ENA
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to ABA treatment, at two time points, each including triplicated measurements Keywords: ABA response
2009-04-29 | GSE10328 | GEO
Project description:During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, and the global RNA profile of rice genes can be affected by their availabilities. In the aerobically germinating rice embryos, most sugar-regulated genes are responsive to low energy and anaerobic conditions, indicating that sugar-regulation is closely associated with energy and anaerobic signaling. The interference pattern of sugar-regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for the alteration in the expression of sugar-regulated genes in aerobically germinating rice embryos. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar-regulated gene expression. Anaerobically responsive genes are highly overlapped with low-energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those induced by low energy-conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It was noted that abscisic acid (ABA)-responsive genes were over-representative of the genes upregulated under low energy conditions, in contrast to the downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.
2021-03-16 | GSE168915 | GEO
Project description:ABA INSENSITIVE 5 (ABI5) is a basic leucine zipper (bZIP) transcription factor which acts in the abscisic acid (ABA) signaling and is activated in response to abiotic stresses. It was shown that ABI5 binds ABA RESPONSIVE ELEMENTs (ABRE cis-elements) present in the promoters of regulated genes and activates or represses their transcription in response to stress. However, the precise role of barley (Hordeum vulgare) ABI5 in ABA signaling is still not well understood. We have identified a hvabi5.d mutant using barley TILLING (Targeted Induced Local Lesions IN Genomes) platform. hvabi5.d showed drought tolerant phenotype. To identify molecular mechanisms responsible for hvabi5.d response to drought, we perform drought-related gene expression analysis in barley in two genotypes: the wild-type (WT) barley cultivar 'Sebastian’ and hvabi5.d mutant; in two time points: (1) optimal water conditions, and (2) after 10 days of drought stress in the second leaf; analyses were performed in three biological replicates. Global transcriptome analysis (Agilent Barley Microarray) of the mutant and parent cultivar ‘Sebastian’ exposed to drought enabled to identify genes in hvabi5.d which were associated with better response of the mutant to drought. These data increase our understanding of HvABI5-dependent modulation of plant response to the drought stress.
2020-07-22 | E-MTAB-9072 | biostudies-arrayexpress