Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling by array of Nipponbare rice roots over a time course of potassium deprivation

ABSTRACT: Potassium (K+) is one of the most important nutrient ions in plant cells and play crucial roles in many plant physiological and developmental processes. K+ deficiency is the common abiotic stress in natural environment, which inhibits plant growth and reduces production of crops. We used microarrays to analyse the transcriptomic changes in rice roots after suffering K+ starvation at different times. The results of GO analysis showed that these transcriptionally changed genes mainly fell into the categories of metabolic process, membrane, cation binding, kinase activity, transport and so on. The two-week-old hydroponic rice seedlings were transferred to K+-free solution (-K) and K+-replete solution (+K, 1 mM K+) as treatment (LK) and control (CK) conditions respectively. The fresh roots of both control and treated rice seedlings were collected after K+-deficient treatment at indicated times (6 h, 3 d and 5 d). The roots were frozen immediately using liquid nitrogen and stored at -80℃ for further RNA extraction. Every RNA sample was derived from 5 independent seedlings. In sum, three time points were selected and three biological replicates were performed at each time point, totally 18 rice genome arrays were used.

ORGANISM(S): Oryza sativa japonica

SUBMITTER: Wei-Hua Wu

PROVIDER: E-GEOD-37161 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome analysis of rice root responses to potassium deficiency.

Ma Tian-Li TL Wu Wei-Hua WH Wang Yi Y

BMC plant biology 20120910

<h4>Background</h4>Potassium (K+) is an important nutrient ion in plant cells and plays crucial roles in many plant physiological and developmental processes. In the natural environment, K+ deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. Several microarray studies have been conducted on genome-wide gene expression profiles of rice during its responses to various stresses. However, little is known about the transcriptional changes in rice genes unde ...[more]

PMID: 22963580

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Project description:Internal aeration is crucial for root growth in waterlogged soil. A barrier to radial oxygen loss (ROL) can enhance long- distance oxygen transport via the aerenchyma to the root tip; a higher oxygen concentration at the apex enables root growth into anoxic soil. The ROL barrier is formed within the outer part of roots (OPR). Suberin and/or lignin depos- ited in cell walls are thought to contribute to the barrier, but it is unclear which compound is the main constituent. This study describes gene expression profiles during ROL barrier formation in rice roots to determine the relative responses of suberin and/or lignin biosyntheses for the barrier. OPR tissues were isolated by laser microdissection and their transcripts were analysed by microarray. A total of 128 genes were significantly up- or downregulated in the OPR during the barrier formation. Genes associated with suberin biosynthesis were strongly upregulated, whereas genes associated with lignin biosynthesis were not. By an ab initio analysis of the promoters of the upregulated genes, the putative cis-elements that could be associated with transcription factors, WRKY, AP2/ERF, NAC, bZIP, MYB, CBT/DREB, and MADS, were elucidated. They were particularly associated with the expression of transcrip- tion factor genes containing WRKY, AP2, and MYB domains. A semiquantitative reverse-transcription PCR analysis of genes associated with suberin biosynthesis (WRKY, CYP, and GPAT) confirmed that they were highly expressed during ROL barrier formation. Overall, these results suggest that suberin is a major constituent of the ROL barrier in roots of rice. 23-d-old plants were either continued in aerated solution or transplanted into N2-flushed or stagnant deoxygenated solution for 9 h. After treating the roots of plants in aerated, stagnant, or N2-flushed conditions for 9h, the basal parts (12.5 -22.5mm below the root - shoot junction) of the adventitious roots were collected. Cells in OPR (including exodermis and sclerenchyma) were isolated using laser microdissection. RNA extracted from the isolated OPR was analysed with a 44k rice oligo-DNA microarray. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturerM-bM-^@M-^Ys instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (10 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.

Dataset Information

Transcription profiling by array of Nipponbare rice roots over a time course of potassium deprivation

Publications

Transcriptome analysis of rice root responses to potassium deficiency.

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