Biology subjects

Guillaume Lobet

Publications and source records attributed to Guillaume Lobet.

3 recordsLinked to original sources

bioRxiv2016

Using a structural root system model for an in-depth assessment of root image analysis pipeline

Root system analysis is a complex task, often performed with fully automated image analysis pipelines. However, the outcome is rarely verified by ground-truth data, which might lead to underestimated biases.\n\nWe have used a root model, ArchiSimple, to create a large and diverse library of ground-truth root system images (10,000). For each image, three levels of noise were created. This library was used to evaluate the accuracy and usefulness of several image descriptors classically used in root image analysis softwares.\n\nOur analysis highlighted that the accuracy of the different traits is strongly dependent on the quality of the images and the type, size and complexity of the root systems analysed. Our study also demonstrated that machine learning algorithms can be trained on a synthetic library to improve the estimation of several root system traits.\n\nOverall, our analysis is a call to caution when using automatic root image analysis tools. If a thorough calibration is not performed on the dataset of interest, unexpected errors might arise, especially for large and complex root images. To facilitate such calibration, both the image library and the different codes used in the study have been made available to the community.

Plant Biology↗

bioRxiv2016

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana

Molecular data concerning the involvement of the roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutation was reported to alter flowering time are expressed in the roots but only few flowering integrators were found. Transcriptomic analysis of the roots during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. A delay in clock gene expression was observed upon extension of the photoperiod. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories and cis-regulatory elements converged towards sugar signaling. We inferred that roots are integrated in systemic signaling whereby carbon supply coordinates growth at the whole plant level during the induction of flowering.

Plant Biology↗

bioRxiv2015

GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown roots systems

Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multidimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

Plant Biology↗