title: Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm.
abstract: Background and Aims The Arabidopsis thaliana root is a key experimental system in developmental biology. Despite its importance, we are still lacking an objective and broadly applicable approach for identification of number and position of developmental domains or zones along the longitudinal axis of the root apex or boundaries between them, which is essential for understanding the mechanisms underlying cell proliferation, elongation and differentiation dynamics during root development. Methods We used a statistics approach, the multiple structural change algorithm (MSC), for estimating the number and position of developmental transitions in the growing portion of the root apex. Once the positions of the transitions between domains and zones were determined, linear models were used to estimate the critical size of dividing cells (LcritD) and other parameters. Key Results The MSC approach enabled identification of three discrete regions in the growing parts of the root that correspond to the proliferation domain (PD), the transition domain (TD) and the elongation zone (EZ). Simultaneous application of the MSC approach and G2-to-M transition (CycB1;1DB:GFP) and endoreduplication (pCCS52A1:GUS) molecular markers confirmed the presence and position of the TD. We also found that the MADS-box gene XAANTAL1 (XAL1) is required for the wild-type (wt) PD increase in length during the first 2 weeks of growth. Contrary to wt, in the xal1 loss-of-function mutant the increase and acceleration of root growth were not detected. We also found alterations in LcritD in xal1 compared with wt, which was associated with longer cell cycle duration in the mutant. Conclusions The MSC approach is a useful, objective and versatile tool for identification of the PD, TD and EZ and boundaries between them in the root apices and can be used for the phenotyping of different genetic backgrounds, experimental treatments or developmental changes within a genotype. The tool is publicly available at www.ibiologia.com.mx/MSC_analysis.
authors.affiliation: Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico.
authors.forename: Mario A
authors.initials: MA
authors.lastname: Pacheco-Escobedo
authors.affiliation: Department of Root Physiology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow, 127276 Russia.
authors.forename: Victor B
authors.initials: VB
authors.lastname: Ivanov
authors.affiliation: Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico.
authors.forename: Iván
authors.initials: I
authors.lastname: Ransom-Rodríguez
authors.affiliation: Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, U.P. Adolfo López Mateos, México DF, México.
authors.forename: Germán
authors.initials: G
authors.lastname: Arriaga-Mejía
authors.affiliation: Escuela Superior de Física y Matemáticas, Instituto Politécnico Nacional, U.P. Adolfo López Mateos, México DF, México.
authors.forename: Hibels
authors.initials: H
authors.lastname: Ávila
authors.affiliation: Department of Root Physiology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, ul. Botanicheskaya 35, Moscow, 127276 Russia.
authors.forename: Ilya A
authors.initials: IA
authors.lastname: Baklanov
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México.
authors.forename: Arturo
authors.initials: A
authors.lastname: Pimentel
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Corkidi
authors.affiliation: Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Doerner
authors.affiliation: Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México.
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Dubrovsky
authors.affiliation: Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico.
authors.forename: Elena R
authors.initials: ER
authors.lastname: Álvarez-Buylla
authors.affiliation: Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM, México DF, Mexico.
authors.forename: Adriana
authors.initials: A
authors.lastname: Garay-Arroyo
keywords: 
            Arabidopsis thaliana
          ; 
            XAANTAL1
          ; breakpoints; cell differentiation; cell proliferation; critical size of dividing cells; elongation zone; longitudinal zonation pattern; multiple structural change model; proliferation domain; root apical meristem; transition domain