DART: a software to analyse root system architecture and development from captured images

Bot, Jacques Le; Serra, Valérie; Fabre, José; Draye, Xavier; Adamowicz, Stéphane; Pagès, Loïc

doi:10.1007/s11104-009-0005-2

Cited by 119 publications

(40 citation statements)

References 37 publications

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“…increased tracing automation). Following the root tracing protocol described by [26] the method could also be extended to the temporal analysis of root growth and its merging with relevant local soil conditions (e.g. soil water content and mechanical impedance).…”

Section: Resultsmentioning

confidence: 99%

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

2013

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This paper presents an original spit-and-combine imaging procedure that enables the complete vectorization of complex root systems grown in rhizotrons. The general principle of the method is to (1) separate the root system into a small number of large pieces to reduce root overlap, (2) scan these pieces one by one, (3) analyze separate images with a root tracing software and (4) combine all tracings into a single vectorized root system. This method generates a rich dataset containing morphological, topological and geometrical information of entire root systems grown in rhizotrons. The utility of the method is illustrated with a detailed architectural analysis of a 20-day old maize root system, coupled with a spatial analysis of water uptake patterns.

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Section: Resultsmentioning

confidence: 99%

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

2013

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“…Even with automated analysis algorithms that have been thoroughly tested, it is necessary for the experimenter to manually check and validate the system outputs regularly. Along those same lines, incorporating user-guided processes into the phenotyping pipeline can also provide a useful compromise that improves the flexibility while maintaining the efficiency needed to perform large experiments (Clark et al 2012; Le Bot et al 2010; Lobet et al 2011). …”

Section: Development Of Technology and Phenotyping Toolsmentioning

confidence: 99%

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

et al. 2013

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More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties.

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“…At the second and third harvests, the same measurements were made using the same procedure on a sample of thirdorder lateral roots. The measurements on the images were made using DART software (Le Bot et al 2010; http://www6.paca.inra.fr/psh/ Modeles-et-logiciels/Dart) for lengths, and ImageJ (http://rsbweb.nih. gov/ij/) for diameters.…”

Section: Measurementsmentioning

confidence: 99%

Root system development and architecture in various genotypes of the Solanaceae family

Bui

Serra

Pagès

2015

Botany

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We present an extensive, dynamic, and quantitative study of the root system architecture of Solanaceae based on 29 genotypes from three important groups (aubergines, capsicums, and tomatoes). Quantitative traits were essentially obtained from measurements made on high resolution images of different plant parts at several stages. The developmental schema was common to all genotypes. Several traits showed significant genetic variations: root apical diameter (reflecting meristem size), interbranch distances, slopes of the regression lines of elongation rate versus apical diameter, and ratios of diameters of laterals to mother roots. On all genotypes, the initial root system was complemented by a strong adventitious system emerging near the plant collar, made up of a set of fast growing roots with large apical diameters. Correlations between traits were evidenced within the root systems on one hand (e.g., interbranch distance and diameter ratio of laterals to their mother) and between shoot and root on the other hand (e.g., leaf area growth rate and root elongation rate). They revealed both trade-offs in developmental processes and coordination between plant parts. Beyond these results, we demonstrated the importance of characterizing phenotypes through multiple criteria, considering the whole plant and including late stages.Résumé : Nous présentons une étude dynamique et quantitative de l'architecture racinaire des Solanaceae conduite sur 29 génotypes parmi trois groupes (aubergines, piments et tomates). Les traits quantitatifs ont été obtenus essentiellement à partir de mesures faites sur des images haute-résolution de différentes parties de la plante. Le schéma de développement est commun à tous les génotypes. Plusieurs traits présentent des variations génétiques significatives : diamètres apicaux des racines (reflétant la taille des méristèmes), ratio des diamètres entre racines latérales et racines mères, distances inter-ramification et pentes des régressions entre diamètre apical et vitesse d'élongation. Sur l'ensemble des génotypes, le système racinaire initial est complété par un système adventif puissant composé de multiples racines ayant de gros méristèmes apicaux. Des corrélations existent entre traits racinaires d'une part (p. ex. entre distance inter-ramification et ratio de diamètres des latérales sur leur mère) et entre traits aérien et racinaire d'autre part (p. ex. vitesse relative de croissance des feuilles et vitesse d'élongation de racines individuelles). Ces corrélations révèlent des compromis de développement et des coordinations entre parties de la plante. Au-delà des résultats, nous avons démontré l'intérêt de caractériser les phénotypes racinaires à travers de multiples critères, en considérant aussi la plante entière et en intégrant des stades avancés.

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DART: a software to analyse root system architecture and development from captured images

Cited by 119 publications

References 37 publications

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

Root system development and architecture in various genotypes of the Solanaceae family

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