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32 results for “wheat root”
Data and statistical analysis scripts for manuscript on wheat root response to nitrate using X-ray CT and OpenSimRoot
<p>Data and statistical analysis scripts for manuscript on wheat root response to nitrate using X-ray CT and OpenSimRoot</p> <blockquote> <p><strong>X-ray CT reveals 4D root system development and lateral root responses to nitrate in soil </strong>- [<a href="https://doi.org/10.1002/ppj2.20036">https://doi.org/10.1002/ppj2.20036</a>]</p> </blockquote> <p>The ZIP file contains:</p> <ul> <li><code>MCT1_Rcode.R</code> - Statistics script for candidate single-timepoint experiment. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running.</li> <li><code>MCT1... .csv</code> - 3 CSV data files required by the R script.</li> <li><code>MCT2_Rcode.R</code> - Statistics script for time-series experiment. Requires all CSV data files in the directory. User needs to set working directory to location of this script and the CSV data files before running.</li> <li><code>MCT2... .csv</code> - 3 CSV data files required by the R script.</li> <li><code>R_RooThProcessing.R</code> - R code for aggregating root traits from RooTh software.</li> <li><code>Modelling folder</code> - OpenSimRoot with model parameters and root data used in manuscript.</li> </ul>
Raw data: Diversity in root architecture of durum wheat at stem elongation under drought stress
<p>Raw data on above and below ground traits from a greenhouse drought stress experiment with six durum wheat varieties performed at Tuscia University, Viterbo, Italy. Measurements were performed at stem elongation stage; recorded traits: plant shoot length, dry weight, number of leaves and tillers; total root length, root surface area, mean diameter, volume, number of tips, forks, crossings, root dry weight and root angle. Root measurments were performed on the whole root system and the topsoil area (upper 5 cm). </p>
Phenotypic diversity of root architecture and genotypic variation in durum wheat under salt stress
<p>Supplementary data consists of Principal Components values for traits detected under salt and control conditions (S1); Markers' locations onto the durum wheat reference genome associated with QTL (S2); Markers associated with genes from NCBI database (S4); PCR results and alleles distribrution</p>
Seminal Root Images of Wheat TILLING Mutants
<p>These files describe a forward genetic screen for variation in seminal root traits in a subset of an exome-sequenced wheat TILLING population in the UK bread wheat cultivar - Cadenza. The submission contains:</p> <ol> <li>readme.md: Contains detailed description of the dataset and experiment.</li> <li>List_of_Lines_Phenotyped.csv: Contains a list of the subset of the Cadenza TILLING population phenotyped.</li> <li>Cadenza_TILLING_Mutants_RootNav_Measurement.csv: Contains the original root trait measurements from RootNav (Root image analysis software).</li> <li>Wheat_TILLING_Seminal_Root_Images.tar.gz: An archive containing 6,240 root images of the mutant lines and control phenotyped.<br> </li> </ol>
Review of QTLs found in studies aimed at finding QTLs for bread wheat root traits (from 2005 to mid-2020)
<p>This list contains a number of articles that have been reviewed for QTLS for bread wheat root traits from 2005 to mid-2020 publication dates.</p>
Data and statistical analysis scripts for manuscript on high-throughput phenotyping of root economics in wheat
<p>This repository contains the root data, GEMMA files, and R code for generating the statistics and figures used in a preprint describing high-throughput phenotyping of root respiration in winter wheat.</p> <p><strong>Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture</strong></p> <p>Haichao Guo, Habtamu Ayalew, Anand Seethepalli, Kundan Dhakal, Marcus Griffiths, Xue-Feng Ma, Larry M. York</p> <p>bioRxiv 2020.11.12.380238; doi: <a href="https://doi.org/10.1101/2020.11.12.380238">https://doi.org/10.1101/2020.11.12.380238</a></p> <p><strong>analysis.R - </strong>A script for processing the included 4 CSV<em> </em>files of collected data. It is intended to run directly in RStudio and will automatically set the working directory in that case. The GEMMA folder includes files as output from GEMMA for genetic analysis, as described in the methods section of the preprint. These files are required by the R code for making Manhattan plots and other output. It will automatically create an output folder and the output text and figure files.</p> <p>The protocol for the respiration measurements are available in a separate Zenodo repository: <a href="https://doi.org/10.5281/zenodo.4247873">https://doi.org/10.5281/zenodo.4247873</a></p> <p>Please cite this repository and the preprint if any data or R code is used in your work.</p>
Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes
<p>Trait plasticity (variation of a trait under environmental variability or gradients) and trait integration are both crucial for plant adaption to environmental change. Variations in different suite of root traits such as biomass allocation, morphology and physiology underlie diverse phosphorus (P) acquisition strategies among plants. Yet, how the intraspecific plasticity and integration of root traits influence plant adaptation to different P supply remains obscure. To characterize diverse adaptive strategies in relation to plant P acquisition, eight root traits were assessed in 20 wheat (<em>Triticum aestivum</em> L.) genotypes grown in a culture room with low and high P supply. High P supply increased shoot P accumulation and biomass of all wheat genotypes. The shoot P accumulation in genotypes with high P sensitivity (PS: calculated as shoot P content at low P / shoot P content at high P supply) was higher with high P supply and lower with low P supply compared with that in the genotypes with low PS. The high-PS genotypes exhibited larger variation in root length, root/shoot ratio and rhizosphere pH across P supplies than the low-PS genotypes, suggesting an integrated response at the whole-plant level. At low P supply, the high-PS genotypes had greater root length and specific root length, but lower acid phosphatase activity than the low-PS genotypes, which suggests contrasting P-acquisition strategies across the genotypes. Strong co-variation of root traits occurred across low-PS genotypes regardless of P supply; conversely, the high-PS genotypes only exhibited strong trait integration at low P supply, whereas high P supply sharply reduced root trait co-variation. Our findings suggest that P stress may strengthen root trait integration in wheat plants, and that both plasticity and integration of root traits drive plant adaptive strategies and tolerance to P-deficiency stress.</p>
A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease
<p>Datasets to accompany 'A fungal endophyte induces local cell-wall mediated resistance in wheat roots against take-all disease', <span>DOI: 10.3389/fpls.2024.1444271.</span></p> <p><span>These are datasheet 1 and table S2.</span></p> <p> </p>
Fig. 4 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 4. Phylogenetic analysis, gene structure, and conserved motifs in bZIP genes from T. Aestivum, Arabidopsis and O. sativa. A: The phylogenetic tree was constructed based on the full-length sequences of bZIP proteins using MEGA7 software. Different clusters are shown in different colours. B: The motif composition of bZIP proteins. Motifs 1 to 10 are displayed by different coloured boxes. C: Exon-intron structure of bZIP genes. Green boxes indicate untranslated 5′ and 3′ regions, and yellow boxes indicate exons. Black lines indicate introns, and the number indicates the phases of corresponding introns. The length of the protein can be estimated using the scale at the bottom. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 3. Phylogenetic analysis of bZIP genes from T. Aestivum, Arabidopsis and O. sativa. The different-coloured arcs indicate different groups (or subgroups) of bZIP genes. The black solid triangles represent bZIP genes with 'At' and 'Os' prefixes from Arabidopsis and rice, respectively. The coloured stars represent TabZIP genes differentially expressed under two concentrations of IAA.
Fig. 6 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 6. Statistical analysis of primary root elongation among wild-type (Ws), hy5 mutant, and TabZIP6D_147/hy5 complementary lines. Seeds were grown in 1/2 MS plates supplemented with 0, 1, and 50 μM IAA for 1 week. Three independent biological replicates for each genotype were performed. Asterisks indicate significant differences between wild-type and mutant or complementary lines at the p <0.01 level (t-test).
Fig. 1 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 1. Phenotypes and numbers of differentially expressed genes of T. aestivum cv. Chinese Spring roots under 1 and 50 μM IAA. A: Two-day wheat seedlings before treatments. B: Seven-day wheat seedlings under 1 and 50 μM IAA. C: Statistical data of root length in B. Double asterisks above bars indicate significant differences between the control and treatment groups at the p <0.01 level (t-test). D: Venn diagram of differentially expressed genes (DEGs) under 1 and 50 μM IAA.
Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes
Open the record for dataset details and reuse information.
Root crown images of soybean and wheat and statistical analysis for RhizoVision Crown
<p>This repository contains raw image data of root crowns imaged using the backlit RhizoVision Crown platform of soybean and wheat plants phenotyped in Missouri and Oklahoma, respectively, as described in the below manuscript. Data files and the R scripts are included for complete statistical analysis associated with the imaged root crown set as well as validation using images of copper wires and simulated root images. We request any reuse of this data to both cite this repository and also the publication given below.</p> <p><strong>Citation:</strong></p> <p>Seethepalli, A., Guo, H., Liu, X., Griffiths. M. G., Almtarfi, H., Li, Z., Liu, S., Zare, A., Fritschi, F., Blancaflor, E., Ma, X., and York, L. M. (2020). RhizoVision Crown: An integrated hardware and software platform for root crown phenotyping. <em>Plant Phenomics. doi:10.34133/2020/3074916</em></p> <p><strong>Link: </strong><a href="https://spj.sciencemag.org/plantphenomics/2020/3074916/">https://spj.sciencemag.org/plantphenomics/2020/3074916/</a></p> <p>Root crown images were acquired using the RhizoVision Imager software available at:</p> <p><a href="https://zenodo.org/record/2585882#.XWgOAeNKiUk">https://zenodo.org/record/2585882#.XWgOAeNKiUk</a></p> <p>Image analysis of physical wires, simulated dicot and monocot root systems, and soybean and wheat root crowns was originally conducted with RhizoVision Analyzer. However, Analyzer has been replaced by RhizoVision Explorer that uses the same underlying algorithms and the analysis can be recreated using the 'whole root' mode of Explorer, available here:</p> <p><a href="https://zenodo.org/record/4095629">https://zenodo.org/record/4095629</a></p> <p><strong>Image Files</strong></p> <p>physical_validation_wires.zip - A set for validation of physical units using 10 images of 2 individual wires of 5 gauges (10, 16, 22, 28, 32) in PNG format acquired using the RhizoVision Crown hardware platform. Includes a CSV file containing measured length and diameters as well as those from image analysis using RhizoVision Analyzer.</p> <p>Soybean_RVC_RootCrowns.zip - 2,778 greyscale images in PNG format of field excavated soybean root crowns.</p> <p>Wheat_RVC_RootCrowns.zip - 1,754 greyscale images in PNG format of field excavated wheat root crowns.</p> <p>metadata_Analyzer_allImageSets.zip - CSV files with the metadata files output by the RhizoVision Analyzer software for the physical validation, validation of simulated dicots and monocots (described in preprint), and the soybean and wheat root crown images. Useful to see thresholding and physical resolution settings.</p> <p>The simulated monocot and dicot root systems images and associated data are described in the preprint and available from Lobet et al. here:</p> <p>Lobet, Guillaume, Koevoets, Iko, Noll, Manuel, Tocquin, Pierre, Meyer, Patrick E, Pagès, Loic, & Périlleux, Claire. (2016). Library of simulated root images, with different noise levels [Data set]. Zenodo.</p> <p><a href="https://zenodo.org/record/208214">https://zenodo.org/record/208214</a></p> <p><strong>Statistical Analysis</strong></p> <p>Rcode_allData.zip - Contains a single .R text file with code to reproduce all statistics and data figures. Contains several .CSV data files used by the R code. Assumption for running is that R code and data files are in the same working directory and setwd() is set there. Also, libraries needed are called at the top of the script and need to be previously installed.</p> <p><strong>Hardware Plans</strong></p> <p>RhizoVision_Crown_Hardware_Plans_Details.pdf - For completeness, hardware plans for the RhizoVision Crown platform as described in the manuscript are included. Currently, we recommend the following camera and lens to use in this system:</p> <p>Basler 5472 monochrome usb camera</p> <p><a href="https://graftek.biz/products/basler-aca5472-17um">https://graftek.biz/products/basler-aca5472-17um</a></p> <p>This Moritex 25 mm lens:</p> <p><a href="https://graftek.biz/products/moritex-ml-u2515sr-18c?">https://graftek.biz/products/moritex-ml-u2515sr-18c?</a></p> <p><br> <br> ⇒ Version 2 of this repository includes updates based on peer-review of the manuscript. New versions of physical_validation_wires.zip and Rcode_allData.zip were uploaded.</p> <p>⇒ Version 3 of this repository includes updates based on peer-review of the manuscript. A new version of Rcode_allData.zip was uploaded.</p>
RNA-seq based expression of DEGs in roots and leaves of bread wheat
<p><span>RNA from roots and leaves of twenty eight bread wheat genotypes was extracted, purified, quantified and sent to </span><span>Beijing Genomics Institute (BGI) for sequencing.<span> Briefly, </span><span>mRNAs were isolated and fragmented from total RNA using the oligo (dT) method for cDNA synthesis. The 75-bp single-end sequencing libraries were constructed, and sequencing was performed on HiSeq X Ten (Illumina, San Diego, USA) using standard protocols. Adapters with unknown bases (N's > 5%) and low quality were removed from raw reads to produce 'clean data' as FastQ data files using a quality control software, SOAPnuke version 2.1.6.</span><span> High quality single-end reads were mapped to the bread wheat reference genome </span><span>(IWGSC, INSDC Assembly <a href="http://www.ebi.ac.uk/ena/data/view/GCA_900519105.1" rel="noopener">GCA_900519105.1</a>) </span><span>using HISAT2 </span><span>(Hierarchical Indexing for Spliced Alignment of Transcripts) </span><span>software version 2.2.1. Alignment of the reference sequence with reads were performed using Bowtie. Quantification of the reads was performed using featureCounts software program. Differentially expressed genes (DEGs) were identified using DeSEQ2 in R version 4.1.1. DEGs were then filtered based on their adjusted p-value.</span><span> A total of 120744 DEGs were identified with varying expression in roots and leaves. </span><span>The threshold value for filtering was set at 0.1</span><span>.</span></span></p>
Fig. 2 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 2. Heatmap of auxin-responsive TabZIP genes from RNA-seq.
Fig. 5 in Identification of TabZIP family members with possible roles in the response to auxin in wheat roots
Fig. 5. Relative gene expression of 9 auxin-responsive TabZIP genes based on qPCR analysis.
RNA-seq based expression of DEGs in roots and leaves of bread wheat
Open the record for dataset details and reuse information.
Root transcriptional profile of wheat seedlings in response to Fe, S and dual (Fe and S) deficiencies.
GEO Series GSE98634. Triticum aestivum; Triticum turgidum subsp. durum. 12 samples. Type: Expression profiling by array.
Rhizoctonia solani AG8 infection of wheat seedling roots
GEO Series GSE74671. Triticum aestivum. 6 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.