archiDART: an R package for the automated computation of plant root architectural traits
Background and aims
In order to analyse root system architectures (RSAs) from captured images, a variety of manual (e.g. Data Analysis of Root Tracings, DART), semi-automated and fully automated software packages have been developed. These tools offer complementary approaches to study RSAs and the use of the Root System Markup Language (RSML) to store RSA data makes the comparison of measurements obtained with different (semi-) automated root imaging platforms easier. The throughput of the data analysis process using exported RSA data, however, should benefit greatly from batch analysis in a generic data analysis environment (R software).
We developed an R package (archiDART) with five functions. It computes global RSA traits, root growth rates, root growth directions and trajectories, and lateral root distribution from DART-generated and/or RSML files. It also has specific plotting functions designed to visualise the dynamics of root system growth.
The results demonstrated the ability of the package’s functions to compute relevant traits for three contrasted RSAs (Brachypodium distachyon [L.] P. Beauv., Hevea brasiliensis Müll. Arg. and Solanum lycopersicum L.).
This work extends the DART software package and other image analysis tools supporting the RSML format, enabling users to easily calculate a number of RSA traits in a generic data analysis environment.
KeywordsPlant root system architecture Data Analysis of Root Tracings (DART) Root System Markup Language (RSML) 2D dynamic analysis Root trait
Delory B.M. (Research Fellow) and Lobet G. (Postdoctoral Researcher) are financially supported by the Belgian National Fund for Scientific Research. The authors would like to thank Jacques Le Bot (INRA, Centre PACA, UR 1115 PSH) for providing the vectorized root system of the tomato plant used in this paper, and Pierre Tocquin (University of Liège, PhytoSYSTEMS) and three anonymous reviewers for their helpful comments on the manuscript.
Conflict of interest
The authors declare that they have no conflict of interest.
- Cobb JN, DeClerck G, Greenberg A et al (2013) Next-generation phenotyping : requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor Appl Genet 126:867–887. doi: 10.1007/s00122-013-2066-0 CrossRefPubMedPubMedCentralGoogle Scholar
- R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.r-project.org/
- Delory BM, Baudson C, Brostaux Y et al (2015) archiDART: plant root system architecture analysis using DART and RSML files. R package version 1.1. http://CRAN.R-project.org/package=archiDART
- Diener J, Nacry P, Périn C et al (2013) An automated image-processing pipeline for high-throughput analysis of root architecture in OpenAlea. 7th Int. Conf. Funct. Plant Model. Saariselkä, Finland, pp 85–87Google Scholar
- Lobet G (2015) rsml: Plant Root System Markup Language (RSML) file processing. R package version 1.2. http://CRAN.R-project.org/package=rsml