Barley seeds miRNome stability during long-term storage and aging
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ABSTRACT:
PROVIDER: PRJNA691038 | ENA |
REPOSITORIES: ENA
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Project description:Seed aging is a complex biological process attracting the scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that despite the same genetic makeup differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families i.e. miR159, miR156, miR166 and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along to the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability was detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state. It might be responsible for the removal of (1-3.1-4)-beta-D-glucanase transcripts and lowering or completely blocking the synthesis of this key enzyme for seed germination.
2021-01-11 | GSE164512 | GEO
Project description: Not available
| S-EPMC8122619 | biostudies-literature
Project description:We analyzed the monsome and polysome associated transcripts of seeds and seedlings and identify transcripts specifically associated with monosome and polysome in both tissues The aim was to generate a global view about the state of mRNA storage in the seeds and the their fate during seed germination.
2019-09-18 | GSE76905 | GEO
Project description:We report the changes in transcriptome that results from RNAi suppression of 7S and 11S storage protein synthesis in soybean seeds, Proteomic results show that other proteins compensate for the storage protein shortfall. The transcriptome analysis show numerous changes result from suppressing storage proteins but compensating proteins are accumulated without parallel changes in the protein's transcription.
2010-05-01 | GSE21116 | GEO
Project description:We report the changes in transcriptome that results from RNAi suppression of 7S and 11S storage protein synthesis in soybean seeds, Proteomic results show that other proteins compensate for the storage protein shortfall. The transcriptome analysis show numerous changes result from suppressing storage proteins but compensating proteins are accumulated without parallel changes in the protein's transcription. Total RNA samples prepared from midmaturation wildtype and storage protein RNAi (SP-) soybeans were used to produce cDNA that was subjected to Illumina sequencing. The resulting sequences were assembled and analyzed to characterize the changes in transcriptome that results from suppressing storage protein synthesis/accumulation.
2010-05-01 | E-GEOD-21116 | biostudies-arrayexpress
Project description:Aim To identify genes specifically involved in the storage reserve mobilisation programme in Arabidopsis. Background: During germination and early post-germinative growth in Arabidopsis seed storage reserves are broken down to provide energy and nutrients for the developing seedling. Genes encoding enzymes involved in the mobilisation of both storage lipid and protein are expressed strongly 1-2 days following imbibition and then fall to very low levels. The regulatory mechanisms controlling expression of these genes are poorly understood. Although germination and reserve mobilisation occur at the same time we have obtained evidence using Abscisic Acid (ABA) treated seeds that the events are regulated by two separate programmes. Arabidopsis seeds treated with 10mM ABA still express genes involved in the mobilisation of storage reserves and break down storage lipid even though germination is blocked. ABA treated seeds therefore provide a powerful system for the identification of genes involved specifically in the reserve mobilisation programme. Microarray analysis will allow us to gain a global undertanding of the processes involved in storage reserve mobilisation and should also result in the identification of regulatory genes involved in this process. Experimental Set-up All seeds are Col-4 imbibed on plates containing 1/2 MS media for 4 days in the dark. All plant material will be grown in controlled environment growth rooms under defined light and temperature regimes. There are two parts to the experimental design. 1. Time course to identify genes involved in both seed storage reserve and germination programmes Comparison of mRNAs from seeds immediately after imbibition (storage reserve and germination programme genes being induced) with 2 day (storage reserve genes maximally expressed) and 7 day old seedlings (storage reserve and germination programme genes off, photoautotrophic genes on) will allow the identification of genes exclusively presentor present at enhanced levels at the peak of reserve mobilisation (day 2). 2. ABA treatment experiment to identify genes involved in the storage reserve programme ABA treatment blocks germination but does not block reserve mobilisation. Microarray analysis will be performed on RNA isolated from 2 day old seed imbibed in the presence of ABA. Comparison of the results of this experiment with those of the time course experiment should allow us to distinguish between genes involved in the two major programmes that we have uncovered.
2022-11-21 | E-NASC-47 | biostudies-arrayexpress
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines.
2012-11-06 | GSE34233 | GEO
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines. The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the microarray experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV M-bM-^@M-^S cotyledon, 25 mg seed weight; Stage V M-bM-^@M-^S cotyledon, 50 mg seed weight; Stage VI M-bM-^@M-^S maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII M-bM-^@M-^S maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for Stage IV and V and 3 biological replicates for Stage VI and VIII.
2012-11-06 | E-GEOD-34233 | biostudies-arrayexpress
Project description:4plex_barley_2017_01 - transcriptomic assay on embryos after barley seeds gamma_irradiation - Why radiation exposure on seeds at low doses causes stimulation of plant growth after germination? - Barley dry seeds of variety “Nur” were irradiated by gamma-rays (Co-60) at doses 20 Gy (stimulatory) and 100 Gy (inhibitory). Immediately after irradiation we put seeds for germination to Petri dishes containing water filter paper; embryos were taken 2h after irradiation, embryos with embrionic roots were taken 24 and 48h after irradiation. The following comparisons have been made: non-irradiated (0 Gy), 2h vs. 20 Gy, 2h; 0 Gy, 24h vs. 20 Gy, 24h; 0 Gy, 48h vs. 20 Gy, 48h; 0 Gy, 24h vs. 100 Gy, 24h. Three independent biological replicates were used.
2019-12-01 | GSE117356 | GEO
Project description:This series represents the complete series of the human 293h media depleted storage on agarose / rehydration condition course analysis. Samples include Control, monolayer; Control, monolayer/full recovery, antibiotics; Spheroid, no storage; two week storage/0hr recovery; two week storage/full recovery; four week storage/0hr recovery; six week storage/0hr recovery. Keywords = 293h cells Keywords = desiccation Keywords = rehydration Keywords = spheroid Keywords = stabilization Keywords = ambient temperature Keywords: other
2005-08-01 | GSE1364 | GEO