Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform
- Department of Biology, Stanford University, United States
- Department of Plant Biology, Carnegie Institution for Science, United States
- Institute of Plant Sciences, University of Bern, Switzerland
- UCLouvain, Faculty of Bioengineering, Belgium
- Forschungszentrum Jülich, Agrosphere Institute, Germany
Figures
Figure 1 with 1 supplement
Growth and Luminescence Observatory for Roots (GLO-Roots) automation: GLO-Bot.
(A) Schematic of the GLO-Bot Cartesian gantry system includes: (1) The Growth and Luminescence Observatory 1 (GLO1) imaging system published in Rellán-Álvarez et al., 2015, which houses two cameras …
Figure 1—figure supplement 1
Detailed schematic of rhizotron design for automation.
(A) Rhizotron design changes between the original rhizotron design published in Rellán-Álvarez et al., 2015 (left) and new rhizotron for automation (right). The new design uses an acrylic top …
Figure 2
Workflow of image analysis pipeline that enables robust trait measurement.
(A) Sample workflow for processing time-series images from multiple days after sowing (das) starts by (1) combining raw images to merge front, back, upper, and lower images, (2) a blank image is …
Figure 3 with 3 supplements
Root system architecture (RSA) of six Arabidopsis accessions over time.
(A) Six accessions from diverse locations were imaged continuously from 9 to 31 days after sowing (DAS). *Col-0 location reflects where accession was originated, not collected. (B) Each accession …
Figure 3—figure supplement 1
Principal component analysis (PCA) plots of nine root system architecture (RSA) traits for the six accessions.PCA using raw trait values for nine traits. Left plots show PCA colored by time (red is 9 DAS and yellow is 31 DAS), center shows PCA colored by accessions, and the right shows the loading plot to demonstrate the traits influencing each PC.
Figure 3—figure supplement 2
Root system architecture (RSA) traits over time for the six accessions.
All nine root system raw traits for the six Arabidopsis accessions growing over time from 9 to 31 DAS. All raw data plotted on the left, trends of the raw data, plotted on the right, were plotted …
Figure 3—figure supplement 3
Continuous vs. single time point imaging.
Comparison between four raw traits measured on plants imaged and handled only once at 21 DAS (gray) and plants that were imaged and handled every day up until 21 DAS (black). Comparisons are shown …
Figure 4 with 3 supplements
Root system architecture (RSA) of the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel.
(A) Locations of all accessions used in this study. Inset highlights the concentration of accessions from the Swedish population. (B) RSAs of the GLO-Roots diversity panel used in the genome-wide …
Figure 4—figure supplement 1
Overview of the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel.
(A) Tracking of the transformation of 192 Arabidopsis accessions and final selection for the genome-wide association (GWA) population. (B) Both the extended GLO-Roots diversity panel and the …
Figure 4—figure supplement 2
Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel rhizotron positioning.
At the start of each replicate rhizotrons were placed in growth boxes (bins) at specific locations. The 96 rhizotrons were imaged in two parts on two consecutive days.
Figure 4—figure supplement 3
Raw vs. fitted values.
Raw (left) and fitted values (right) for all nine root traits. Colored by accession. Time represented in hours after the start of imaging: Hours 0, 48, 144, 192, 240, 288, and 336 are equivalent to …
Figure 5 with 1 supplement
Trait relationships among the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel.
(A) Principal component analysis (PCA) of nine fitted traits (i.e. fitted values) for the 93 accessions of the GLO-Roots diversity panel reveals traits influenced by time as the predominant source …
Figure 5—figure supplement 1
Principal component analysis (PCA) for nine root traits describing root system architecture (RSA).
(A–B) PCA of raw RSA traits for the 93 accessions in the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel shows time and traits correlated with time as the primary axis of …
Figure 6 with 1 supplement
Genome-wide association studies (GWAS) and climate correlations of root traits of the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel.
(A) Manhattan plot for average angle per day at 28 days after sowing (DAS). Black points indicate SNP positions that pass the Bonferroni threshold (solid line) at least once throughout the time …
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Figure 6—source data 1
Manhattan plots and SNP development of all nine root system architecture (RSA) traits.
(A) Manhattan plots of genome-wide association (GWA) run on each of the nine RSA traits at each time point with corresponding Q-Q plots (B). SNPs highlighted in black pass the threshold, gray indicates SNPs in linkage disequilibrium (LD). Genes in this region are reported in Supplementary file 4. (C) SNP development of the 29 unique SNPs that pass the Bonferroni threshold at least once throughout the time series.
- https://cdn.elifesciences.org/articles/76968/elife-76968-fig6-data1-v2.pdf
Figure 6—figure supplement 1
Correlations between average climatic variables and root traits.
Pearson correlations between average climatic traits and fitted root traits. We used minimum and maximum temperature for each month (1–12), total precipitation per month, and their composite Bio1–19 …
Author response image 1
Author response image 2
Videos
Video 1
GLO-Bot running.
Video 2
Root system architecture (RSA) growth of six Arabidopsis accessions over time.
Video 3
Root system architecture (RSA) growth of Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel over time.
Additional files
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Supplementary file 1
Analyzed root traits.
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp1-v2.xlsx
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Supplementary file 2
Accessions used for genome-wide association studies (GWAS).
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp2-v2.xlsx
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Supplementary file 3
Replicates with anomalies.
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp3-v2.xlsx
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Supplementary file 4
SNP list of 29 significant SNPs.
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp4-v2.xlsx
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Supplementary file 5
Broad-sense heritability of traits.
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp5-v2.xlsx
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Supplementary file 6
Removed images of the Growth and Luminescence Observatory for Roots (GLO-Roots) diversity panel.
- https://cdn.elifesciences.org/articles/76968/elife-76968-supp6-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/76968/elife-76968-transrepform1-v2.docx
