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WIREs Dev Biol
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Patterning the primary root in Arabidopsis

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Abstract The Arabidopsis root, with its ordered cell divisons and straightforward patterning, is a tractable model for understanding organ formation during plant development. Regular cell divisions in the root tip produce consistent cell type arrangements that can be followed through time. Root development occurs through the precise spatiotemporal control of transcription factors and phytohormone signaling networks. In this article, we provide a broad overview of the major events controlling embryonic and post‐embryonic development within each major tissue and cell type in the primary root of Arabidopsis. WIREs Dev Biol 2012 doi: 10.1002/wdev.49 For further resources related to this article, please visit the WIREs website.

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Cell types and developmental zones of the Arabidopsis primary root. (a) Image of 5‐day‐old root showing developmental zones in the Arabidopsis root. Black oval outlines the stem cell niche (STN), meristematic zone (MZ), elongation zone (EZ), and differentiation zone (DZ). (b) Schematic of a longitudinal section through the root showing distinct cell types demarcated in colors. The STN is located at the center of the root tip and includes the quiescent center (QC) and initial cells (black oval), followed by the proximal meristem (PM) where initial cells divide and the transition zone (TZ) where cells begin to elongate. (c) Schematic of a transverse section of the root showing symmetry about the radial axis for the outer cell layers. There are approximately 15 cell types in the root including the lateral root cap, non‐hair epidermis, hair cell epidermis, cortex, endodermis, QC, phloem pole pericycle, xylem pole pericycle, metaphloem, protophloem, phloem companion cells, procambium, metaxylem, protoxylem, and columella. Vascular tissues are at the center with xylem cells in a line that cuts across the vasculature and phloem at the opposing poles. The vascular cylinder is surrounded by the pericycle (together they constitute the stele), then the endodermis, cortex, hair and non‐hair cell epidermis, and lateral root cap tissues. Dashed outline of root hair signifies possible location of emergence later in time.

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Asymmetric division of lateral root cap/epidermis initial cell. At left, a periclinal division results in self‐renewal of the lateral root cap/epidermis initial cell (magenta) and generation of a lateral root cap cell (light pink). At center, an anticlinal division of the lateral root cap/epidermis initial cell results in self‐renewal of the initial and generation of an epidermal cell (purple).

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Model of the transcriptional network responsible for epidermal patterning. SCRAMBLED (SCM) receptor‐like kinase transduces an unknown signal from the underlying cortex intercellular space that leads to repression of the WEREWOLF (WER) transcription factor complex, with TRANSPARENT TESTA GLABRA (TTG) and either GLABRA3 (GL3) or ENHANCER OF GLABRA3 (EGL3) basic helix‐loop‐helix (bHLH) transcription factors as interacting proteins, to allow root hair cells (light purple) to be specified. Conversely, without activation of SCM in the presumptive non‐hair cells (dark purple), WEREWOLF (WER), a bHLH transcription factor (GL3 or EGL3), and TTG work co‐operatively to activate the hair cell repressor gene GLABRA2 and the hair cell specification transcription factors CAPRICE (CPC) and TRIPTYCHON (TRY) which move to the presumptive hair cell for activity. Dotted outline of root hair shows location of elongation occurring later in time.

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Asymmetric division of cortex/endodermal initial cell (CEI) and cortex/endodermal intial daughter cell (CEID) gives rise to two layers of ground tissue. The CEI divides anticlinally (axis perpendicular to the axis of growth) to self‐renew and to generate a CEID. This division is coincident with CYCD6;1 (blue oval) expression. The CEID then divides along an axis parallel to the elongating root axis, or periclinally, to generate cells of the endodermis (dark purple) and the cortex (light purple), collectively termed the ground tissue. Model for activity of key patterning regulators with SHORTROOT (SHR; green), SCARECROW (SCR; white), MAGPIE (MGP; pink), and JACKDAW (JKD; purple) proteins as ovals and target genes expressed as ovals with bolded italic text.

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miR165/166 restricts PHABULOSA (PHB) expression domain in the root vasculature. (a) PHB expression in a gradient radiating from the center, with highest expression in metaxylem cells (red) and lowest in the endodermis (yellow). (b) miR165/166 expression as an opposing gradient with highest expression in the endodermis (dark blue), lower expression in the protoxylem and cortex (light blue), and lowest levels in the metaxylem.

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Hormonal control of root meristem growth and development. (a) Approximate distributions of PINFORMED (PIN) protein auxin efflux transporters in the root meristem. PIN1 is found mainly in the basal plasma membrane of stele cells, and more weakly in the endodermis.27,28,30 PIN2 is localized apically in epidermal and lateral root cap cells and predominantly basally in cortex cells.27,28,32 PIN3 protein is found in an apolar manner in columella tiers 2 and 3, and laterally on the inner cell surface of pericycle cells in the transition and elongation zone (EZ).28,31 PIN4 is localized to the quiescent center (QC) and surrounding cells (initials and their daughters).31 PIN7 is found in the lateral and basal membranes of provascular cells in the meristem and EZ, and in an apolar manner in columella.27,28 Colors indicate the cell type in which each PIN is localized; multiple colors indicate that two or more PINs are localized to the same region. Note that colors are not meant to indicate how the PINs are localized within a cell (i.e., basal, apical, or lateral), (b) root tip of Arabidopsis expressing the auxin response reporter DR5::GFP showing the maxima in the QC. Auxin is transported rootward in the stele and reaches a maxima in the QC. In the columella, PIN3 and PIN7 redistribute the hormone flow laterally and bidirectionally into the lateral root cap, epidermis, and cortex, where auxin flows shootward due to the action of PIN2 (rootward movement of auxin in the cortex may also occur due to the action of PIN2).32 Auxin is directed back into the stele in the EZ, creating an auxin flux loop, (c) schematic showing PLT1, PLT2, SCARECROW (SCR), and SHORTROOT (SHR) protein expression domains.19,33–35 PLT1 is expressed in the QC, all surrounding initials, and the first layer of differentiated columella cells19; PLT2 has a very similar expression pattern. Note that PLT1/2 gene expression domains match the protein expression domains.33 SCR is expressed in the endodermis, cortex/endodermal initial cell (CEI), and QC. SHR is expressed in the stele and the protein moves one adjacent cell layer, (d) and (e) schematics of the players involved in the cytokinin, auxin, and GA control of root meristem size.5,36 (d) Prior to 5 dogs post‐germination (dpg), cell division predominates. Cytokinin signaling activates ARR12 expression, which results in low levels of the AUX/IAA repressor SHY2. SHY2 represses expression of PIN auxin transporters; low levels of SHY2 thus lead to higher auxin flow throughout the meristem and higher rates cell division. High levels of GA results in low levels of the GA‐responsive protein RGA, and repress cytokinin signaling through the ARR1. After 5 dpg, low levels of giberellin release repression of ARR1, allowing ARR1 activation by cytokinin. This results in SHY2 activation, which represses auxin flow through the PINs and leads to a balance between cell division and differentiation.5

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Schematic of major stages of Arabidopsis embryogenesis. Colors indicate clonal lineages for cotyledons (dark green), hypocotyl (light green), and root (yellow). Expression domains overlayed for WOX2 (vertical gray stripe), WOX8 (diagonal black stripe), WOX5/presumptive quiescent center (QC) (blue outline), WOL (red), and AHP6 (purple dashed outline). Embryonic stages are given below each image. The two stem cell niches of the embryo are shown as colored circles on the cotyledon stage embryo, with the shoot apical meristem (SAM) in black and the root apical meristem (RAM) in red.

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Auxin response in basal portion of globular stage embryo. (a) PINFORMED1 (PIN1; dark purple) is localized to the basal region of plasma membranes by GNOM (GN; orange) for directional auxin transport (dashed arrow indicates movement). In the absence of high levels of auxin, BODENLOS (BDL; blue) binds to MONOPTEROS (MP; green) and represses activity of the transcription factor. (b) Within provascular cells (lavender), auxin targets BDL for degradation, releasing MP to activate PIN1 and TARGET OF MONOPTEROS7 (TMO7; red) target genes (solid arrow). TMO7 then moves to the hypophyseal cell (yellow) to activate transcription of target genes.

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Gene Expression and Transcriptional Hierarchies > Cellular Differentiation
Early Embryonic Development > Development to the Basic Body Plan
Plant Development > Root Development