Phiv-Rootcell: A supervised image analysis tool for rice root anatomical parameter quantification

Lartaud Marc, Perin Christophe, Courtois Brigitte, Thomas Emilie, Henry Sophia, Bettembourg Mathilde, Divol Malgoire Fanchon, Lanau Nadège, Artus Florence, Bureau Charlotte, Verdeil Jean-Luc, Sarah Gautier, Guiderdoni Emmanuel, Dievart Anne. 2015. Phiv-Rootcell: A supervised image analysis tool for rice root anatomical parameter quantification. Frontiers in Plant Science, 5 (790), 7 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : We developed the PHIV-RootCell software to quantify anatomical traits of rice roots transverse section images. Combined with an efficient root sample processing method for image acquisition, this program permits supervised measurements of areas (those of whole root section, stele, cortex, and central metaxylem vessels), number of cell layers and number of cells per cell layer. The PHIV-RootCell toolset runs under ImageJ, an independent operating system that has a license-free status. To demonstrate the usefulness of PHIV-RootCell, we conducted a genetic diversity study and an analysis of salt stress responses of root anatomical parameters in rice (Oryza sativa L.). Using 16 cultivars, we showed that we could discriminate between some of the varieties even at the 6 day-olds stage, and that tropical japonica varieties had larger root sections due to an increase in cell number. We observed, as described previously, that root sections become enlarged under salt stress. However, our results show an increase in cell number in ground tissues (endodermis and cortex) but a decrease in external (peripheral) tissues (sclerenchyma, exodermis, and epidermis). Thus, the PHIV-RootCell program is a user-friendly tool that will be helpful for future genetic and physiological studies that investigate root anatomical trait variations. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza sativa, Numération cellulaire, Analyse d'image, Bioinformatique, Racine adventive, Tissu végétal, Racine, Phénotype, Anatomie végétale, Stress osmotique, Physiologie végétale, Variation génétique, Variété

Mots-clés géographiques Agrovoc : France

Mots-clés complémentaires : Oryza sativa japonica, Histologie

Classification Agris : F62 - Plant physiology - Growth and development
U30 - Research methods
F50 - Plant structure
F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Lartaud Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Perin Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2469-310X
  • Courtois Brigitte, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-2118-7102
  • Thomas Emilie, CIRAD-BIOS-UMR AGAP (FRA)
  • Henry Sophia, CIRAD-BIOS-UMR AGAP (FRA)
  • Bettembourg Mathilde, CIRAD-BIOS-UMR AGAP (FRA)
  • Divol Malgoire Fanchon
  • Lanau Nadège, CIRAD-BIOS-UMR AGAP (FRA)
  • Artus Florence
  • Bureau Charlotte, CIRAD-BIOS-UMR AGAP (FRA)
  • Verdeil Jean-Luc, CIRAD-BIOS-UMR AGAP (FRA)
  • Sarah Gautier, INRA (FRA)
  • Guiderdoni Emmanuel, CIRAD-BIOS-UMR AGAP (FRA)
  • Dievart Anne, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9460-4638

Source : Cirad - Agritrop (

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