Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform
Abstract
The plant kingdom contains a stunning array of complex morphologies easily observed above-ground, but more challenging to visualize below-ground. Understanding the magnitude of diversity in root distribution within the soil, termed root system architecture (RSA), is fundamental to determining how this trait contributes to species adaptation in local environments. Roots are the interface between the soil environment and the shoot system and therefore play a key role in anchorage, resource uptake, and stress resilience. Previously, we presented the GLO-Roots (Growth and Luminescence Observatory for Roots) system to study the RSA of soil-grown Arabidopsis thaliana plants from germination to maturity (Rellán-Álvarez et al. 2015). In this study, we present the automation of GLO-Roots using robotics and the development of image analysis pipelines in order to examine the temporal dynamic regulation of RSA and the broader natural variation of RSA in Arabidopsis, over time. These datasets describe the developmental dynamics of two independent panels of accessions and reveal highly complex and polygenic RSA traits that show significant correlation with climate variables of the accessions' respective origins.
Data availability
GLORIAv2 is available through Zenodo, DOI: https://doi.org/10.5281/zenodo.5574925Image analysis pipelines and scripts are available through Zenodo, DOI: https://doi.org/10.5281/zenodo.5708430RShiny App for exploring root system architecture of accessions is available through Zenodo, DOI: https://doi.org/10.5281/zenodo.5708422Imaging data and images are available through Zenodo, DOI: https://doi.org/10.5281/zenodo.5709009General code for software operating robotics available: GitHub: https://github.com/rhizolab/rhizo-serverRhizotron laser cutting files are available through Zenodo, DOI: https://doi.org/10.5281/zenodo.6694558)Previously published datasets used: WORLCLIM2: Fick SE, Hijmans RJ, 2017, https://worldclim.org/, https://doi.org/10.1002/joc.5086
Article and author information
Author details
Funding
U.S. Department of Energy (DE-SC0008769)
- José R Dinneny
U.S. Department of Energy (DE-SC0018277)
- José R Dinneny
National Institutes of Health (T32GM007276)
- Therese LaRue
Deutsche Forschungsgemeinschaft (LI 2776/1-1)
- Heike Lindner
National Institutes of Health (1DP5OD029506-01)
- Moises Exposito-Alonso
U.S. Department of Energy (DE-SC0021286)
- Moises Exposito-Alonso
Deutsche Forschungsgemeinschaft (EXC-2070 - 390732324)
- Guillaume Lobet
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, LaRue et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Further reading
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Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.