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SRX10151459: GSM5100661: S_pH6_long rep 3; Hordeum vulgare; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 59.9M spots, 18G bases, 6.4Gb downloads

Submitted by: NCBI (GEO)
Study: Transcriptome analysis of barley root meristem under Al and low pH stress
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Aluminum (Al) is the most common metal in the Earth's crust and Al toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world's arable lands. The first symptom of Al toxicity is the reduction of root growth, resulting in decreased water and nutrients uptake, plant growth retardation, and finally, yield reduction. Barley (Hordeum vulgare L.), which is the fourth cereal crop in regards to cultivation area and production tonnage, belongs to crops most sensitive to toxic aluminum ions in low pH soils. We present the RNA-seq transcriptome analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 µM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. Interestingly, in the short-term experiment, more genes were differentially expressed between root meristems grown at pH=6.0 and pH=4.0, than between those grown at pH=4.0 with and without Al treatment. The upregulated genes that were overrepresented at conditions of low pH, compared to optimal pH, were associated with response to oxidative stress, cell wall organization, and iron ion binding. Among genes downregulated by low pH were mainly those related to chromatin organization. These results show that low pH itself is a severe stress for barley plants. Among genes upregulated by short Al treatment, overrepresented were those related to response to stress condition and calcium ion binding. After 7 days of hydroponics, the number of DEGs between hydroponics at pH=4.0 and 6.0 were still high but lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 day Al treatment caused massive changes in the transcriptome profile compared to the condition of low pH alone. Over 4 000 genes were upregulated and almost 2 000 genes were downregulated by long-term Al stress. These DEGs were related to e.g. stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants.Additionally, we phenotyped in detail the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH=6.0, pH=4.0, and pH=4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress facor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be underlined that in the acidic arable lands, plants are exposed simultaneously to both of these stresses (low pH and Al), as Al becomes soluble at pH below 5.5. The presented transcriptome analysis may help to find potential targets for breeding barley plants more tolerant to such conditions. Overall design: We examined the influence of low pH and aluminum on transcriptome of barley root meristems in two independent hydroponic experiments (short- and long-term). Root meristems from at least 8 plants from one hydroponic container were considered as one repetition (with an average of 5 root meristems per plant). Each experimental combination (optimal pH=6, low pH=4 and Al treated) was analyzed in three replicates in both experiments.
Sample: S_pH6_long rep 3
SAMN18028398 • SRS8303768 • All experiments • All runs
Organism: Hordeum vulgare
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: Root meristematic tissue was collected in RNAlater (Invitrogen). mRNA was isolated from root tips with the use of Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific). The RNA-seq libraries were prepared using the TruSeq Stranded mRNA kit (Illumina) according to the manufacturer's instructions. Indexed libraries were pooled, clustered with use the cBot and sequenced on the Illumina HiSeq 4000 platform.
Experiment attributes:
GEO Accession: GSM5100661
Runs: 1 run, 59.9M spots, 18G bases, 6.4Gb
Run# of Spots# of BasesSizePublished


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