Shoot and root of barley seeds
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
SUBMITTER: Shingo Nakamura
PROVIDER: E-GEOD-41518 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The combination of robust physiological models with “omics” studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. Here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (DT) in Arabidopsis thaliana seeds. We show that the incubation of desiccation-sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution re-induces the mechanisms necessary for expression of DT. Based on a SNP-tile array gene expression profile, our data indicates that the re-establishment of DT, in this system, is related to a programmed reversion from a metabolic active to a quiescent state similar to prior to germination. Our findings show that transcripts of germinated seeds after the PEG treatment are dominated by those encoding LEA, seed storage and dormancy-related proteins. On the other hand, a massive repression of genes belonging to many other classes such as photosynthesis, cell wall modification and energy metabolism occurs in parallel. Furthermore, comparison with a similar system for Medicago truncatula reveals a significant overlap between the two transcriptomes. Such overlap may highlight core mechanisms and key regulators of the trait DT. Taking into account the availability of the many genetic and molecular resources for Arabidopsis, the described system may prove useful for unraveling DT in higher plants. Desiccation-sensitive seeds vs. desiccation-tolerant seeds in the same developmental stage in triplicate.
2013-06-21 | E-GEOD-30853 | biostudies-arrayexpress
Project description:Transcriptomic study of the impact of osmopriming on rape seeds (Brassica napus L.; cv 'Libomir') during priming process and after germination. The assays were replicated twice on two independent priming and germination experiments. Seeds were osmoprimed in PEG solution (-1.2 MPa osmotic potential) during 7 days, dried to initial moisture content and then germinated for 7 hours on water. The analysis during different phases of priming procedure (soaking and drying), after whole osmopriming process and germination were done. 10 samples, four condition experiment; non dried primed seeds (Pnd) vs. dry unprimed seeds (UPd) (PEG soaking), non dried primed seeds (Pnd) vs dry primed seeds (Pd) (drying after soaking), dry primed seeds (Pd) vs. dry unprimed seeds (UPd) (full osmopriming process), primed seeds imbibed on water (P7h) vs unprimed seeds imbibed on water (UP7h) (germination after osmopriming). Biological replicates: 2 replicates for comparison PEG soaking, drying after soaking, full osmopriming process and germination after osmopriming.
2014-11-23 | E-GEOD-61702 | biostudies-arrayexpress
Project description:Sensing environmental cues is essential for plants in order to respond properly to, adapt to and survive changes in the environment and disturbances. Smoke-derived germination active compounds are important cues which provide a strong chemical signal to seeds in the soil seed bank about the available germination niche created by the passage of fire. The germination stimulatory activity can largely be attributed to the presence of the butenolide, 3-methyl-2H-furo[2,3-c]pyran-2-one (karrikinolide; KAR1). More recently, a related fire-borne butenolide, 3,4,5-trimethylfuran-2(5H)-one (inhibenolide A; InhA), was shown to have an inhibitory effect on germination. The aim of this study was to extensively characterize the interaction of these potent smoke-derived compounds in the highly KAR1-sensitive Lactuca sativa cv. M-bM-^@M-^XGrand RapidsM-bM-^@M-^Y achenes. A time course microarray analysis of KAR1- and InhA-treated achenes was performed using custom-made Agilent microarrays. Early time points for sampling the transcriptome were chosen by taking into account the fact that treatment with KAR1 is irreversible (by leaching with water) after 2 h, and that the KAR1-treated achenes enter an InhA-insensitive stage after 9 h. Therefore, samples were harvested after 2 and 10 h of initial exposure to 0.1 M-BM-5M KAR1 or 10 M-BM-5M InhA, and after 24 h, when germinated and non-germinating achenes could be distinguished visually. To assess the divergence between the expression patterns induced by the two compounds, a sample of achenes treated with 0.1 M-BM-5M KAR1 and 10 M-BM-5M InhA simultaneously, was harvested after 2 h. At 24 h, samples were collected from germinating and non-germinating achenes separately, and equal amounts of mRNA were pooled. Although this design implies that there is a small chance of losing data, our primary aim at 24 h was to screen for differences between the KAR1- and InhA-induced transcriptome. Achenes germinated in distilled water served as controls and were compared to the experimental samples treated as described above.
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