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Oryza sativa strain:Nipponbare Transcriptome or Gene expression

ABSTRACT: To better understand the complex mechanisms regulating Pi homeostasis in rice (Oryza sativa L. cv. Nipponbare), a time course experiment was performed, where pre-germinated seedlings were grown hydroponically for two weeks on Pi-sufficient medium (0.32 mM Pi), before transferring half of the plants to Pi-deficient solution (0 mM Pi) for 21 days (d). After three weeks of Pi-starvation treatment, half of these plants where then re-supplied with Pi sufficient media for up to 24 hours (h). In total, nine time points were selected in order to cover short and long term responses to Pi starvation as well as the effects of Pi re-supply on Pi starved plants.

INSTRUMENT(S): Illumina HiSeq 1000

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: David Secco

PROVIDER: E-MTAB-4427 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.

Secco David D Jabnoune Mehdi M Walker Hayden H Shou Huixia H Wu Ping P Poirier Yves Y Whelan James J

The Plant cell 20131118 11

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvati ...[more]

PMID: 24249833

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Oryza sativa cultivar:Nipponbare Transcriptome or Gene expression

Project description:A comprehensive time-course experiment of Pi-starved plants was undertaken, spanning medium (3 and 7 days), and long-term (21 days up to 52 days) Pi deprivation (âPi), as well as both short term (1 and 3 days) and long-term (31 days) recovery. The 52 days time point consisting of 21 days starvation +31 days recovery enabled investigation of the effects of long term resupply on Pi starved plants, and coincided with the emergence of the first panicles and grains. Pre-germinated rice seedlings were grown for 14 days in Pi sufficient conditions (0.32 mM Pi) before being transferred to either Pi sufficient (0.32 mM Pi) or Pi deficient (0 mM Pi) media for 21 days. After 21 days of Pi deficient treatment, half of the plants were either maintained under Pi deficient conditions or re-supplied with Pi (0.32 mM) for 1, 3 or 31 days. To confirm the effectiveness of the Pi starvation and resupply treatments, physiological and molecular analyses were performed.

2015-07-31 | E-MTAB-4334 | biostudies-arrayexpress

Low P stress transcriptome of control rice variety (Dongjin-byeo) and NtPT1-trasngenic rice (PT 1-7-8)

Project description:To understand expression of candidate gene located on QTLs for phosphate sensitivity traits under low P using NtPT1-transgenic rice with increased Pi uptake efficiency and gene expression profile at the V3-stage seedling through the 60K Rice Whole Genome Microarray Uniformly germinated seedlings were transferred to a hydroponic system filled with aerated standard solution (normal P, 320 M Pi) and grown for 2 weeks in a glasshouse at 25°C/18°C (day/night) under a natural photoperiod (about 16 h). The composition and concentration of each element in the standard solution were as follows: N (1.43 mM), P (0.32 mM), K (0.51 mM), Ca (0.75 mM), Mg (1.64 mM), Fe (59.37 μM), B (18.92 μM), Mn (9.50 μM), Mo (0.10 μM), Zn (0.15 μM), Cu (0.16 μM), and citric acid (70.72 μM) (Yoshida et al., 1976). Some of the two-week-old seedlings were transferred to the low P solution (the same nutrient solution containing 32 M Pi) over a period of 5 days to expose them to P-deficiency condition. Control plants were maintained in the standard solution for the entire period.

2011-04-20 | E-GEOD-21377 | biostudies-arrayexpress

SHORT-ROOT Stabilizes PHOSPHATE1 to Regulate Phosphate Allocation in Arabidopsis

Project description:Coordinated distribution of Pi between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHR (SHORT-ROOT) is well-characterized for its function in root radial patterning1-3. Here, we demonstrate a new role of SHR in controlling phosphate (Pi) allocation from roots to shoots by regulating PHOSPHATE1 (PHO1) in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis which accumulates much less Pi in the shoot and shows constitutive Pi starvation response (PSR) under Pi-sufficient condition. Besides, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP Ⅲ transcription factor PHB. PHB accumulates and directly binds the promoter of PHO2 to upregulate its transcription, resulting in PHO1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants repress Pi translocation from roots to shoots in response to Pi starvation.

2022-06-24 | GSE199834 | GEO

Sugarcane transcriptome - Phosphate starvation

Project description:Rooted sugarcane plantlets, originated from in vitro meristem culture (genotype SP80-3280, CTC, Brazil), were greenhouse acclimatized by initial cultivation on 1/20th strength Hoagland and Arnon (1950) nutrient solution. Nutrient solutions were aired from an oil-less compressor and replaced every 7 days, increasing nutrient concentration to ¼ strength in 3 weeks. Plants were then individually transferred to 2.8 L pots filled with fresh ¼ strength nutrient solution. After one week, half of the plants were transferred to fresh solution containing 250 µM Pi, while the other half was transferred to nutrient solution deprived of phosphate (Pi), with H2PO4 being replaced by H2SO4 (Muchhal et al., 1996). Roots from six plants from each treatment (0 and 250 µM Pi) were harvested 6, 12, 24 and 48 h after exposure to phosphate starvation and immediately frozen in liquid nitrogen. For each time point and each treatment, root samples were aggregated in three pools of two samples each. Extraction of total RNA was performed separately on each sample pool. Keywords: time course of stress response

2007-05-20 | GSE4966 | GEO

Oryza sativa Japonica Group transcriptome sequencing

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2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress

Transcription profiling of Arabidopsis roots to investigate early phosphate-deficiency induced signal changes

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2009-04-18 | E-GEOD-15649 | biostudies-arrayexpress

Expression data from Col-0 and sp1,spx2 under phosphate starvation stress and recovery after resupplying phosphate

Project description:We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation.

2014-09-30 | GSE52046 | GEO

Expression data from Arabidopsis thaliana under phosphate starvation stress

Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.

2010-12-09 | GSE16722 | GEO

Early phosphate-deficiency induced signal changes in Arabidopsis roots

2009-04-14 | GSE15649 | GEO

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

Project description:Phosphate (Pi) starvation induces a suite of adaptive responses aimed at recalibrating cellular Pi homeostasis. Plants harboring a mutation in OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME5 (OTU5) showed altered DNA methylation of root hair-related genes and altered Pi-responsive root traits. Unlike the wild type, homozygous otu5 mutants did not respond to Pi starvation by increased lateral root formation and increased root hair length but formed very short root hairs when grown on low-Pi media. Under Pi-replete conditions, otu5 plants developed more root hairs than the wild type due to attenuated primary root growth, a phenotype that resembled that of Pi-deficient plants. Growth of plants on low-Pi media altered both H3K4 and H3K27 trimethylation levels at the transcriptional start site of a subset of genes encoding key players in Pi homeostasis, which was correlated with mRNA abundance changes of these genes. Pi starvation had a minor impact on DNA methylation. Differentially methylated regions were enriched in transposable elements, suggesting that DNA methylation associated with low Pi supply is required for maintaining genome integrity. It is concluded that DNA methylation and histone methylation constitute critical, interdependent regulatory components that orchestrate the activity of a subset of Pi-responsive genes.

2017-11-02 | GSE81407 | GEO

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