EZ-Root-VIS: A software pipeline for the rapid analysis and visual reconstruction of root system architecture

Shahzad, Z. , Kellermeier, F., Armstrong, E. M., Rogers, S. , Lobet, G., Amtmann, A. and Hills, A. (2018) EZ-Root-VIS: A software pipeline for the rapid analysis and visual reconstruction of root system architecture. Plant Physiology, 177(4), pp. 1368-1381. (doi:10.1104/pp.18.00217) (PMID:29895611)

Shahzad, Z. , Kellermeier, F., Armstrong, E. M., Rogers, S. , Lobet, G., Amtmann, A. and Hills, A. (2018) EZ-Root-VIS: A software pipeline for the rapid analysis and visual reconstruction of root system architecture. Plant Physiology, 177(4), pp. 1368-1381. (doi:10.1104/pp.18.00217) (PMID:29895611)

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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 make-up 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 have developed Root-VIS, a free software tool, which 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 have 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).

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Hills, Mr Adrian and Shahzad, Zaigham and Amtmann, Professor Anna and Rogers, Dr Simon
Authors: Shahzad, Z., Kellermeier, F., Armstrong, E. M., Rogers, S., Lobet, G., Amtmann, A., and Hills, A.
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Plant Physiology
Publisher:American Society of Plant Biologists
ISSN:0032-0889
ISSN (Online):1532-2548
Published Online:18 June 2018
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in Plant Physiology 177(4):1368-1381
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
716321Perception and integration of nutritional signals in plant root systems: Solving the mystery of K-Fe-P interactions.Anna AmtmannBiotechnology and Biological Sciences Research Council (BBSRC)BB/N018508/1RI MOLECULAR CELL & SYSTEMS BIOLOGY