Root-associated microbiota of field-grown maize
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ABSTRACT:
PROVIDER: PRJNA713997 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:These experiments were to investigate changes in gene expression associated with maize competition for light when grown at double normal population density or under 60% shaded conditions as opposed to when maize is grown under normal field conditions.
2008-12-04 | GSE13768 | GEO
Project description:These experiments were to investigate changes in gene expression associated with maize competition for light when grown at double normal population density or under 60% shaded conditions as opposed to when maize is grown under normal field conditions. Three biological replicates (collected from separate field plots) comprised of pooled samples of 4 plants from each treatment were hybridized in a rolling circle dye swap hybridization screen.
2008-12-04 | E-GEOD-13768 | biostudies-arrayexpress
Project description:This was a pilot project carried out by Dr Wojciech Majeran to determine the maize pollen proteome harvested from field-grown W22 (T43) plants in plots on the Musgrave Research Farm (Cornell CALS) in Aurora (NY). To enhance proteome coverage, the pollen were separated into soluble and membrane bound protein fractions, and separated by SDS-PAGE followed by in-gel digestion and shot-gun proteomics using a nanoLC-Orbitrap system.
2023-09-11 | PXD045274 | Pride
Project description:The root system is fundamental for maize growth and yield. The primary root system is the most important structure of maize seedlings and is the first organ that emerges at germination, providing water and nutrients for the growing seedlings. However, it is difficult to characterize them at single cell level, due to their complex and heterogeneous cell types. In this study, we profiled the transcriptomes of more than 7000 cells derived from maize root tips of seedlings grown on media with (nitrate+) or without nitrate (nitrate-).
2021-09-03 | GSE183171 | GEO
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance. Root tips from Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) maize genotypes were harvested after growing on acid or control soil for 1 or 3 days. Total RNA was extracted and hybridized to Affymetrix GeneChip Maize Genome Array. Three biological replicates were used for each sample.
2010-09-20 | E-GEOD-21070 | biostudies-arrayexpress
Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize
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Project description:Poly- and perfluorinated alkyl substances (PFAS) are a group of persistent organic pollutants. Plants can accumulate PFAS but their effect on plant physiology at the molecular level is not understood yet. We used hydroponically-grown maize plants treated with a combination of eleven different PFAS (each at 100 µg L-1) to investigate their bioaccumulation and effects on the growth, physiology and their impact on the root proteome. From the root proteome analysis, we identified 75 differentially abundant proteins, mostly involved in cellular metabolic and biosynthetic processes, translation and cytoskeletal reorganization. Results were validated using quantitative real-time PCR and further substantiated using amino acid and fatty acid profiling.
2023-02-08 | PXD029993 | Pride
Project description:Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality. We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance.
2010-09-20 | GSE21070 | GEO
Project description:Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.
2021-03-07 | GSE162312 | GEO
Project description:Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.
2021-03-07 | GSE162311 | GEO