Article Figures & Data
Figures
- Figure 1.
Overview of EZ-Root-VIS pipeline. A, EZ-Rhizo and Root-VIS software packages provide a convenient analysis pipeline transforming root images into a numerical and statistical data output describing root system architecture. B, A suitable image of Arabidopsis plants growing on a vertical agar plate can be acquired with a flatbed scanner at 200 dpi. C, Skeletonized roots obtained after image processing with EZ-Rhizo provide the basis for quantification of RSA features by EZ-Rhizo. The obtained data are saved in a searchable database. D, Root-VIS reconstructs the individual roots using the data extracted by EZ-Rhizo. E to J, Root-VIS generates visual reconstructions of root system architecture from a user-defined set of individual roots (replicates), including absolute (E) and binned (F) average RSA, alpha blends (G), flag plots (H), and LR profiles (I). The examples shown are based on data from the five individual Arabidopsis plants shown in B. Roots images were taken at 12 DAG. J, For subsequent generation of graphs, statistical analyses, and modeling, the numerical data obtained with Root-VIS are saved and can be displayed in Excel using the XL-Orate plug-in. The screenshot shows an example Excel output from a large data set. Data for each RSA parameter are provided in a separate datasheet. MRL, Main root path length; LRN, lateral root number; MRV, main root vector length.
- Figure 2.
Visual representation of RSA development over time. A, Change of selected RSA features over time displayed in a conventional bar graph. Plotted are plant age in days after germination (x axis), mean LRD-BZ (y axis), mean main root length (MRL; z axis), and mean LRL (color) of Arabidopsis Col-0 plants growing on control media. Numbers of roots analyzed at each time point are given in B. B to F, Root-VIS offers several options to visualize the RSA of many replicate plants, including absolute (B) and binned (C) average RSA reconstructions, superimposition of normalized RSAs in alpha blends (D), as well as shape reconstructions in the form of flag plots (E) and LRS profiles (F). All Root-VIS reconstructions shown were based on EZ-Rhizo data obtained from Arabidopsis Col-0 plants grown in control conditions. Plant age (in days) and numbers of replicate roots (n) are given in B.
- Figure 3.
Environment- and genotype-dependent growth investment into main root and lateral roots. LRS profiles (A) and average RSA reconstruction (B) of Arabidopsis accessions grown in control, low K, low P, and combined low P and low K (low PK) media. Vertical lines represent the mean main root path length. The main root path was divided into four equally sized sections and lengths of laterals were added within each section. The width of each square represents the mean LRS of three to six replicate plants.
- Figure 4.
RSA traits of Arabidopsis accessions grown in different nutrient conditions. Means and ses of selected RSA features of 12-d-old Arabidopsis accessions grown in control (black bars), low K (blue bars), low P (red bars), or low PK (green bars) media. The data were generated by EZ-Rhizo, and means across replicates (n = 3–6 plants) were calculated with Root-VIS for main root length (MRL; A), total LRS (B), LRD-BZ (C), and MRA (D). E, Means and SEs of LRL within four sections of the main root. Data were extracted from LRL profiles generated by Root-VIS and transferred to Excel using the XL-Orate plug-in.
- Figure 5.
Use of the EZ-Root-VIS pipeline for large-scale natural variation studies. A, Heat map of pairwise correlations (Pearson correlation coefficient) of 16 RSA traits in 147 Arabidopsis accessions. Plants were grown in control conditions. The correlations between different root features were calculated using means of five plants for each genotype. Stars indicate significance at P < 0.05 (Student’s t test). B, Hierarchical clustering of Arabidopsis accessions by genotype. Calculation of similarity was based on 15 mean RSA traits calculated by Root-VIS. See Supplemental Data Set 5 for the class assignment of the individual accessions. C, Visual reconstructions of RSA and LRS profiles of the central accession of each cluster. Accession names are colored according to B.
- Figure 6.
Genome-wide association studies for root system architecture traits. A, Manhattan plots for GWA mapping of three RSA traits; LRS over the basal quartile of the main root [LRS (0.25)], total LRS, and total root size (TRS). The horizontal dotted line corresponds to a 5% FDR threshold. Light-blue ticks labeled “GRF1” and “LRSL” indicate the location of the most significant associations. B,) LRS profiles of Arabidopsis Col-0 wild type and mutant lines. Plants were grown on control media in three independent experiments. The total number of replicate roots contributing to each LRS profile is given in parentheses. C, Means and SEs (n as shown in B) of some RSA traits in wild type Col-0 and mutant lines. Significant differences to the wild type are indicated by asterisks (P < 0.05, Student’s t test).
Additional Files
CCBY FREE ARTICLE Supplemental Data
Supplemental Figures and Data
Files in this Data Supplement:
- Supplemental Data - Supplemental Figures 1-6
- Supplemental Data - Supplemental Data 1
- Supplemental Data - Supplemental Data 2
- Supplemental Data - Supplemental Data 3
- Supplemental Data - Supplemental Data 4
- Supplemental Data - Supplemental Data 5
- Supplemental Data - Supplemental Data 6
