RNA-seq helps to analyze the regulation mechanism of maize roots under nutrient-deficiency conditions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA516341 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To increase crop yield without polluting the environment, improving crop nutrient efficiency is of great importance. The RSA of plants is centrally involved in nutrient use efficiency. Therefore, to uncover the molecular mechanisms that regulate RSA of maize under nutrient-deficiency conditions and to improve maize nutrient use efficiency based on this knowledge, we investigated the morphological changes and ribonucleic acid sequencing (RNA-seq) profiles of maize roots during growth under normal and N-, P-, and K-deficiency conditions. We analyzed the data in different aspects and verified the reliability of the RNA-seq data by real-time quantitative polymerase chain reaction (RT-qPCR). These results will provide theoretical support for improving plant nutrient use efficiency. The maize (Z. mays) inbred line DengHai 605 was used in this study. Provided for four treatment conditions: normal N, P, and K level (CK); potassium deficiency (K-DEF); nitrogen deficiency (N-DEF); and phosphorus deficiency (P-DEF). The experiments were carried out by combining sand culture with water culture. The standard for evaluating differential gene expression is fold change (FC) > 2 or FC < -2 and p value < 0.05.The numbers of DEGs under N-, P-, and K-deficiency conditions were 3494 (1801 up-regulated and 1693 down-regulated), 3424 (1761 up-regulated and 1663 down-regulated), and 1830 (827 up-regulated and 1003 down-regulated), respectively. A total of 1483, 1470, and 519 genes were specifically expressed under the N-, P-, and K-deficiency conditions, respectively.
2022-01-01 | GSE125417 | GEO
Project description:Iron deficiency is a yield-limiting factor and a worldwide problem for crop production in many agricultural regions, particularly in aerobic and calcareous soils. Graminaceous species, like maize, improve Fe acquisition through the release of phytosiderophores (PS) into the rhizosphere and the following uptake of Fe(III)-PS complexes through specific transporters. Transcriptional profile obtained by roots 12-d-old maize plants under Fe starvation for 1 week (Fe-deficient; 19-d-old plants) were compared with the transcriptional profile obtained by roots of 12-d-old maize plants grown in a nutrient solution containing 100 μM Fe-EDTA for 1 week (Fe-sufficient; 19-d-old plants).
2017-06-12 | GSE76829 | GEO
Project description:Microarrays were used to identify transcriptional responses in field-grown root material of wheat in order to dissect specific gene expression responses to limited macronutrient availability, particularly phosphate. This study fills the gap between the transcriptome studies on model plants and the lack of studies on soil-grown wheat aiming to identify candidate genes for enhancing nutrient uptake efficiency. The work at Rothamsted Research is supported via the 20:20 Wheat® Programme by the UK Biotechnology and Biological Sciences Research Council. The contribution was supported by BIONUT-ITN and the research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 264296. T. aestivum cv. Hereward root material was excavated in triplicates in May 2011 at booting stage from sections 0 and 1 plots representing continuous wheat plots of the “Broadbalk” field experiment at Rothamsted Research, UK (http://www.rothamsted.ac.uk/sample-archive/guide-classical-and-other-long-term-experiments-datasets-and-sample-archive). The distinct peculiarity of these plots, including a control plot with nutrient replete wheat plants, is the withdrawal of N, P, K, Mg and S fertilizers exposing the plants to multiple long-term nutrient deficiencies and representing 6 treatments ; 12 samples were analysed.
2015-04-01 | E-GEOD-61679 | biostudies-arrayexpress
Project description:Microarrays were used to identify transcriptional responses in field-grown root material of wheat in order to dissect specific gene expression responses to limited macronutrient availability, particularly phosphate. This study fills the gap between the transcriptome studies on model plants and the lack of studies on soil-grown wheat aiming to identify candidate genes for enhancing nutrient uptake efficiency. The work at Rothamsted Research is supported via the 20:20 Wheat® Programme by the UK Biotechnology and Biological Sciences Research Council. The contribution was supported by BIONUT-ITN and the research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 264296.
2015-04-01 | GSE61679 | GEO
Project description:Prospective single arm, single center observational study to assess the nutritional status and the nutrient supply during hospitalization for elective gastrointestinal surgery.
| 2293083 | ecrin-mdr-crc
Project description:METTL16 is a well-characterized m6A methyltransferase that has been reported to contribute to tumorigenesis in various types of cancer. However, the effect of METTL16 on tumor progression under restricted nutrient conditions, which commonly occur in tumor microenvironment, has yet to be elucidated. Herein, our study initially reported the inhibitory effect of METTL16 depletion on apoptosis under amino acid starvation conditions.
2023-11-11 | GSE244901 | GEO
Project description:Background: Since chemical assays of soil nutrients are unreliable the UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yields and quality. Excessive fertiliser applications are both costly and can lead to unnecessary pollution. A possible solution to this problem is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression profiles under incipient nutrient deficiency. The aim of this project is to identify genes upregulated in the early stages of nutrient depletion. Methods: Arabidopsis ecotype Col-5 (N1644) will be grown hydroponically using established techniques. In parallel experiments NP and K will be withdrawn individually after 21 d growth. RNA will be extracted from shoots of nutrient replete (control) and nutrient depleted plants 24 h after the removal of nutrients. Shoot nutrient content will be assayed by ICP-EMS as a reference. By comparing expression profiles we will be able to differentiate between genes that are upregulated by lack of specific nutrients and those upregulated by a universal stress-response system. Promoters and transcripts of these genes will underpin the development of novel sensor technologies and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition.
2022-11-21 | E-NASC-59 | biostudies-arrayexpress
Project description:We used Arabidopsis thaliana Col-0 for all experiments. The plants were grown hydroponically on nutrient solution as described previously [Plant J 1999, 18(5):509-519]. Briefly, plants were grown on sand, placed in custom-designed styrofoam rafts, in a growth chamber (EGC, Chagrin Falls, OH, USA) at 22°C with 60 mmol photons m-2s-1 light intensity and 8 h/16 h light/dark cycles. The seeds were initially germinated in tap water. After one week, the water was replaced with a complete nutrient solution [Plant J 1999, 18(5):509-519]. All the experiments were performed with 6 week old plants. Nutrient solutions were renewed weekly and on the day before the experiments. For treatments, individual rafts were transferred to containers with 300mL of nutrient solution supplemented with various concentrations of nitrate (as a mix of 2/1 KNO3/Ca(NO3)2) and/or sucrose. The N-free nutrient solutions contained 0.25 mM K2SO4 and 0.25 mM CaCl2 instead of KNO3 and Ca(NO3)2. Plants were transferred to treatments media at the beginning of the light period and were harvested 8h afterwards. Roots and leaves were harvested separately and quickly frozen in liquid N2.
2006-11-30 | E-MEXP-828 | biostudies-arrayexpress
Project description:Proton toxicity is one of the major environmental stresses limiting crop production, and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrient accumulation and global transcriptome changes in soybean (Glycine max) in response to long-term acid stress were investigated. Results showed that acid stress significantly inhibited soybean root growth, but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acid stress, mainly dependent on soybean organs and mineral nutrient types. The concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N) and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased, respectively. Whereas, the concentrations of calcium (Ca), sulfate (S) and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identifying 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrient transportation. Among them, all the detected five GmPTs and GmZIPs, two GmAMTs and GmKUP genes, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5 and GmHKT1, were significantly suppressed. Moreover, the genes encoding transcription factors (e.g., GmSTOP2s and a GmPHL1), and genes involved in pH stat metabolic pathways were significantly up-regulated by low pH stress in soybean roots. Taken together, it strongly suggested that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acid stress, which might be regulated by a complex signaling network.
2019-06-24 | GSE129320 | GEO
Project description:The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. The small RNA profile from phloem and inflorescence stems of plants grown under full nutrition conditions was also analyzed and compared. The study demonstrates that the phloem sap sRNA profile is distinct from that of the inflorescence stems, leaves and roots. Furthermore, we could identify phloem-enriched small RNAs and showed that some of them specifically accumulate in the phloem in response to nutrient deprivation.
2010-02-24 | GSE20263 | GEO