title: PHIV-RootCell: a supervised image analysis tool for rice root anatomical parameter quantification.
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.
authors: CIRAD, UMR AGAP Montpellier, France ; Plateforme Histocytologie et Imagerie Cellulaire Végétale, INRA-CIRAD Montpellier, France.
authors: Marc
authors: M
authors: Lartaud
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Christophe
authors: C
authors: Perin
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Brigitte
authors: B
authors: Courtois
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Emilie
authors: E
authors: Thomas
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Sophia
authors: S
authors: Henry
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Mathilde
authors: M
authors: Bettembourg
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Fanchon
authors: F
authors: Divol
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Nadege
authors: N
authors: Lanau
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Florence
authors: F
authors: Artus
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Charlotte
authors: C
authors: Bureau
authors: CIRAD, UMR AGAP Montpellier, France ; Plateforme Histocytologie et Imagerie Cellulaire Végétale, INRA-CIRAD Montpellier, France.
authors: Jean-Luc
authors: JL
authors: Verdeil
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Gautier
authors: G
authors: Sarah
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Emmanuel
authors: E
authors: Guiderdoni
authors: CIRAD, UMR AGAP Montpellier, France.
authors: Anne
authors: A
authors: Dievart
keywords: cell number; histological phenotype scoring; image analysis software; rice; root; tissue area; transverse histological section
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