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Plant Physiol. 2018 Aug;177(4):1368-1381. doi: 10.1104/pp.18.00217. Epub 2018 Jun 12.

EZ-Root-VIS: A Software Pipeline for the Rapid Analysis and Visual Reconstruction of Root System Architecture.

Author information

1
Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
2
School of Computing Science, University of Glasgow, Glasgow G12 8QQ, United Kingdom.
3
Agrosphäre (IBG-3), Forschungszentrum Jülich, 52428 Jülich, Germany.
4
Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium.
5
Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom anna.amtmann@glasgow.ac.uk adrian.hills@glasgow.ac.uk.

Abstract

If we want to understand how the environment has shaped the appearance and behavior of living creatures, we need to compare groups of individuals that differ in genetic makeup and environment experience. For complex phenotypic features, such as body posture or facial expression in humans, comparison is not straightforward because some of the contributing factors cannot easily be quantified or averaged across individuals. Therefore, computational methods are used to reconstruct representative prototypes using a range of algorithms for filling in missing information and calculating means. The same problem applies to the root system architecture (RSA) of plants. Several computer programs are available for extracting numerical data from root images, but they usually do not offer customized data analysis or visual reconstruction of RSA. We developed Root-VIS, a free software tool that facilitates the determination of means and variance of many different RSA features across user-selected sets of root images. Furthermore, Root-VIS offers several options to generate visual reconstructions of root systems from the averaged data to enable screening and modeling. We confirmed the suitability of Root-VIS, combined with a new version of EZ-Rhizo, for the rapid characterization of genotype-environment interactions and gene discovery through genome-wide association studies in Arabidopsis (Arabidopsis thaliana).

PMID:
29895611
PMCID:
PMC6084667
[Available on 2019-08-01]
DOI:
10.1104/pp.18.00217

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