Whole genome RNA-sequencing from roots of Arabidopsis thaliana wild-type and stop1 exposed to low pH, low phosphate (Pi), Aluminum and Iron excess conditions.
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE148457 | GEO | 2020/10/07
REPOSITORIES: GEO
Similar Datasets
Project description:Total mRNA was extracted from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and med16-2 mutants grown under low and high phosphate conditions 4 days after germination, using and sequenced by RNA-seq methodology.
2020-10-07 | GSE135778 | GEO
Project description:Phosphate limitation constrains plant development in natural and agricultural systems. Under phosphate-limiting conditions plants activate genetic, biochemical and morphological modifications to cope with phosphate starvation. One of the morphological modifications that plants induce under phosphate limitation is the arrest of primary root growth and it is induced by the root tip contact with low phosphate media. The sensitive to proton rhizotoxicity (stop1) and aluminium activate malate transporter 1 (almt1) mutants of Arabidopsis thaliana continue primary root growth under in vitro Pi-limiting conditions, thus, to get insight into the molecular components that control primary root growth inhibition under low phosphate conditions we extracted and sequenced mRNA from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and low-phosphate-insensitive mutants almt1 and stop1 grown under low and high phosphate conditions 5 days after germination using an RNA-seq methodology.
2017-08-22 | GSE90061 | GEO
Project description:For transcript analysis of aluminum tolerance responses in Medicago truncatula (A17) we compared transcripts from 2.5 µM Al-treated and control (-Al) root tips corresponding to 12 h after Al treatment. Keywords: One time point and one genotype
2007-02-22 | GSE7066 | GEO
Project description:For transcript analysis of aluminum tolerance responses in Medicago truncatula we compared transcripts from 2.5 µM Al-treated and control (-Al) root tips corresponding to 12 and 48 h after Al treatment in Al-tolerant (T32) and Al-sensitive (S70) lines. Keywords: 2 time points and 2 lines
2007-02-08 | GSE6946 | GEO
Project description:Gene expression profiling in soybean under aluminum stress: Transcriptome response to Al stress in roots of Al-tolerant genotype (PI 416937). Aluminum (Al) toxicity is a major constraint of crop production on acid soils. Many commercial soybean cultivars and advanced breeding lines have been evaluated for Al tolerance. Aluminum tolerance is quantitatively inherited trait in soybean making it difficult for genetic improvement. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient and effective programs aimed at improving Al tolerance trait The molecular mechanisms of Al tolerance is poorly understood in soybean. The objective of the research was to identify candidate aluminum tolerance genes in soybean Al-tolerant soybean genotype PI 416937 seedlings were exposed to zero or 10 µM Al in growth chamber under hydroponic conditions for four time span of 2, 12, 48 and 72 hrs in a randomized complete block design with three replications. Microarray analysis was made on mRNA isolated from 1 cm log tap root tips using Affymetrix soybean array with over 68,000 probe sets Glycine max L and wild soybean combined. Both novel and known genes were discovered in response to Al treatment. They include Al tolerance relevant proteins, families of transcription factors, zinc finger, bZIP, WRKY, MYB, ADR6, and NAC domain proteins were induced likely regulating Al tolerance downstream genes. Stress related proteins, cytochrome P450, glutathione-s transferase, glutaredoxin family and ascorbic acid biosynthesis protein were induced as signatures of cellular detoxification mechanisms. An ABC type multidrug resistance protein that could act as citrate transporter or Al exporter was up-regulated, a key Al tolerance mechanisms in several species. A cell wall loosening enzyme endoxylglucan hydrolases were also up-regulated probably reversing the wall rigidification caused by Al and promoting root growth under Al stress. Phytosulfokines growth factor involved in cell division and proliferation was up-regulated likely as a direct counter action to Al toxicity which inhibits root growth by limiting cell division and elongation. In conclusion, the Al tolerance candidate genes identified herein are potential targets for future genetic engineering and molecular breeding work on Al tolerance trait in soybean which in turn would contribute to gain in soybean productivity on acid soils.
2011-10-05 | GSE18423 | GEO
Project description:Gene expression profiling in soybean under aluminum stress: Transcriptome response to Al stress in roots of Al-tolerant genotype (PI 416937). Aluminum (Al) toxicity is a major constraint of crop production on acid soils. Many commercial soybean cultivars and advanced breeding lines have been evaluated for Al tolerance. Aluminum tolerance is quantitatively inherited trait in soybean making it difficult for genetic improvement. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient and effective programs aimed at improving Al tolerance trait The molecular mechanisms of Al tolerance is poorly understood in soybean. The objective of the research was to identify candidate aluminum tolerance genes in soybean Al-tolerant soybean genotype PI 416937 seedlings were exposed to zero or 10 µM Al in growth chamber under hydroponic conditions for four time span of 2, 12, 48 and 72 hrs in a randomized complete block design with three replications. Microarray analysis was made on mRNA isolated from 1 cm log tap root tips using Affymetrix soybean array with over 68,000 probe sets Glycine max L and wild soybean combined. Both novel and known genes were discovered in response to Al treatment. They include Al tolerance relevant proteins, families of transcription factors, zinc finger, bZIP, WRKY, MYB, ADR6, and NAC domain proteins were induced likely regulating Al tolerance downstream genes. Stress related proteins, cytochrome P450, glutathione-s transferase, glutaredoxin family and ascorbic acid biosynthesis protein were induced as signatures of cellular detoxification mechanisms. An ABC type multidrug resistance protein that could act as citrate transporter or Al exporter was up-regulated, a key Al tolerance mechanisms in several species. A cell wall loosening enzyme endoxylglucan hydrolases were also up-regulated probably reversing the wall rigidification caused by Al and promoting root growth under Al stress. Phytosulfokines growth factor involved in cell division and proliferation was up-regulated likely as a direct counter action to Al toxicity which inhibits root growth by limiting cell division and elongation. In conclusion, the Al tolerance candidate genes identified herein are potential targets for future genetic engineering and molecular breeding work on Al tolerance trait in soybean which in turn would contribute to gain in soybean productivity on acid soils. One genotype PI 416937 (p); four time points: (2, 12, 48, and 72 hrs), with replicates (2 or 3)
2011-10-04 | E-GEOD-18423 | biostudies-arrayexpress
Project description:Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice cultivars are naturally compatible to low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes - Dular (low Pi tolerant) and PB1 (low Pi sensitive) - have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes raised under Pi deficient and sufficient conditions revealed the potential low Pi tolerance mechanisms of traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) are highly induced in traditional rice genotype, Dular. Higher reserve of phospholipid and greater accumulation of galactolipids under low Pi in Dular indicated its better internal Pi utilization. Furthermore, Dular also maintained better root growth than PB1 under low Pi resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
2016-01-29 | GSE74795 | GEO
Project description:Barley shoot and root growing in low-Pi condition
| PRJNA607203 | ENA
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the full model described in the article.
2024-09-02 | BIOMD0000000413 | BioModels
Project description:The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer. Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer. Keywords: Genotype comparison, root impedance response
2008-03-19 | GSE10857 | GEO