Genetic Regulation of Embryonic Pattern Formation
Thomas Laux,1 Tobias Wu¨ rschum, and Holger Breuninger
Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
INTRODUCTION
During plant embryogenesis, a simple body plan is established
that consists of shoot meristem, cotyledons, hypocotyl, root, and
root meristem along the apical–basal axis and a concentric
arrangement of epidermis, subepidermal ground tissue, and
central vascular cylinder along the radial axis. To establish this
organization, the cells of the embryo need to become speciﬁed
and must differentiate into cell types in an integrated manner.
The genetic regulation of this process is addressed here. We
focus on data from Arabidopsis but also refer to other species
where helpful. For information on other aspects of embryo
development, readers are referred to excellent reviews (Natesh
and Rau, 1984; Goldberg et al., 1994; Mordhorst et al., 1997;
Yadegari and Goldberg, 1997; Chaudhury et al., 2001).
REGIONALIZATION OF THE EARLY ARABIDOPSIS
EMBRYO INTO TRANSCRIPTIONAL DOMAINS
In addition to being widely used as a genetic model organism,
Arabidopsis lends itself to studies of embryonic development
because of a ﬁxed pattern of cell divisions in early stages, which
makes it possible to trace the origin of seedling structures back
to regions of the early embryo (Mansﬁeld and Briarty, 1991;
Ju¨ rgens and Mayer, 1994).
First, the egg cell and zygote display a polar organization, with
a large vacuole at the basal end and most of the cytoplasm and
the nucleus at the apical end (Mansﬁeld et al., 1991). Notably, in
maize, a fraction of egg cells appear nonpolarized and the
nucleus and cytoplasm shift toward the apical end only after
fertilization (Mol et al., 1994). In Arabidopsis, the zygote
elongates and then divides asymmetrically to form daughter
cells of different sizes and cytoplasmic densities (Figure 1). The
apical daughter cell after two rounds of longitudinal and one
round of transverse divisions gives rise to an eight-cell embryo
proper (Figure 1). At the same time, the descendants of the basal
daughter of the zygote divide transversely to form the suspensor
and the uppermost cell, the hypophysis. At the eight-cell stage,
four regions with different developmental fates can be recognized:
(1) the apical embryo domain, composed of the four most
apical cells of the embryo proper, will generate the shoot
meristem and most of the cotyledons; (2) the central embryo
domain, consisting of the four lower cells of the embryo proper,
will form the hypocotyl and root and contribute to cotyledons and
the root meristem; (3) the basal embryo domain (hypophysis) will
give rise to the distal parts of the root meristem, the quiescent
center, and the stem cells of the central root cap; and (4) the extra
embryonic suspensor pushes the embryo into the lumen of the
ovule and provides a connection to the mother tissue. The
boundary between the apical and the central embryo domains
can readily be recognized and serves as a histological reference
point throughout embryo development (Tykarska, 1976, 1979).
In agreement with the regular cell division pattern, clonal
analyses conﬁrm that the contribution of each cell to the seedling
body plan is highly predictable. However, rare variations in the
cell division pattern do occur. In such cases, each cell differentiates
according to its ﬁnal position, in agreement with the
well-established observation that developing plant cells are
ﬂexible and assume their fate corresponding to positional
information (Poethig et al., 1986; Saulsberry et al., 2002).
Gene expression studies indicate that already at the earliest
stages of embryogenesis, speciﬁc transcription programs are
initiated in single precursor cells of embryo pattern elements (Lu
et al., 1996; Weterings et al., 2001; Friml et al., 2003; Haecker
et al., 2004). For example, both the egg cell and the zygote
express a mixture of mRNAs encoding WUSCHEL HOMEOBOX2
(WOX2) and WOX8 transcription factors speciﬁc for early apical
and basal embryo development, respectively (Haecker et al.,
2004). The asymmetric division of the zygote separates these
mRNAs, thereby establishing two cells of different identities and
setting up the apical–basal axis of the embryo. At this stage,
additional genes are asymmetrically expressed, indicating that
both daughter cells of the zygote rapidly assume different
transcriptional proﬁles. Subsequently, the boundaries of transcriptional
domains are reﬁned by interregional communication,
resulting in the progressive elaboration of region-speciﬁc
expression programs. Thus, embryonic patterning is marked
by the early establishment and subsequent reﬁnement of
transcriptional domains.
MATERNAL INFLUENCES IN DEVELOPMENT
In animal embryogenesis, information from the mother is crucial
for embryonic patterning. Is this also the case in plants? The
observation that plants can form complete organisms from
cultured cells in a process that resembles zygotic embryogenesis
argues against a strict requirement for maternal information
(Backs-Hu¨ semann and Reinert, 1970; Nomura and Komamine,
1985; Mordhorst et al., 2002). Nevertheless, several ﬁndings
imply that in normal development maternal tissues do affect
embryo patterning. For example, the apical–basal axis of the
1 To whom correspondence should be addressed. E-mail laux@biologie.
uni-freiburg.de; fax 49-761-203-2745.
Article, publication date, and citation information can be found at
www.plantcell.org/cgi/doi/10.1105/tpc.016014.
The Plant Cell, Vol. 16, S190–S202, Supplement 2004, www.plantcell.org ª 2004 American Society of Plant Biologists
embryo is invariably aligned parallel to the chalazal–micropylar
axis of the ovule, suggesting that the polarity of the embryo
is guided by the surrounding maternal tissue (Esau, 1977;
Mansﬁeld and Briarty, 1991; Mansﬁeld et al., 1991). Below, we
discuss a number of genetic studies indicating that information
from the female sporophyte and the female gametophyte contributes
to zygotic embryogenesis.
Maternal Effects from the Female Sporophyte
Evidence for effects of the diploid mother sporophyte on the
embryo were found by analyzing hypomorphic mutant alleles of
the DICER-LIKE1 (DCL1) gene (Ray et al., 1996; Golden et al.,
2002). Although putative null alleles of DCL1 (named sus1 in
previous studies) show a zygotic embryo-lethal phenotype
(Schwartz et al., 1994), 10% of embryos homozygous or
heterozygous for a weaker DCL1 allele (named sin1) display
various defects in apical development (Ray et al., 1996). The
latter can be rescued if the mother plant is heterozygous, but not
homozygous, for sin, indicating a maternal component of DCL1
function in embryo development. DCL1 localizes in the nucleus,
where it is required for the production of short micro-RNA
molecules that presumably are involved in gene-silencing
mechanisms (Papp et al., 2003), similar to the function of DICER
in animals (Bernstein et al., 2001; Ketting et al., 2001). Such
micro-RNAs produced in the mother plant then could affect
embryo development as direct signals or via a more indirect
mechanism.
Maternal Effects from the Female Gametophyte
Several observations suggest that the two parental gene copies
contribute differentially to early plant embryogenesis as a result
of parent-speciﬁc imprinting. For example, heterozygosity for
mutations in the MEDEA (MEA) gene results in 50% aborted
embryos that cannot be rescued by one or even two copies of the
paternal wild-type allele, indicating that MEA supports embryo
development only when supplied from the female gametophyte
(Chaudhury et al., 1997; Grossniklaus et al., 1998). MEA encodes
a member of a Polycomb group protein complex that acts largely
through transcriptional repression of the MADS box gene
PHERES1 (Vielle-Calzada et al., 1999; Kohler et al., 2003a,
2003b). MEA is expressed speciﬁcally in the central cell, the egg
cell, and the synergids of the female gametophyte, but not in the
male gametophyte (Vielle-Calzada et al., 1999). After fertilization,
the maternal copy of MEA continues to be expressed in the
developing endosperm, the early embryo, and the suspensor but
is repressed thereafter. Repression of MEA might be mediated
by an inhibitory chromatin structure, because mutations in the
chromatin remodeling factor gene DECREASE IN DNA METHYLATION1,
which results in genome-wide DNA hypomethylation,
lead to activation of the paternal MEA gene copy in the early
embryo. MEA expression appears to be induced again in the
female gametophyte through the introduction of nicks in its
promoter by the DNA glycosylase DEMETER (DEM), suggesting
that activation could occur through nucleosome sliding and
changes in chromatin structure (Choi et al., 2002). DEM
expression is restricted to the central cell and the synergids,
suggesting that DEM activates MEA expression in these cells
directly, whereas expression of MEA in the egg cell may be
attributable to a non-cell-autonomous function of DEM. Once
activated, MEA expression may be propagated after fertilization
in the embryo and the endosperm until renewed establishment of
a repressive imprint.
How common is imprinting in plants? Analysis of a set of
maternally expressed genes revealed the majority to have the
paternal copy silenced (Vielle-Calzada et al., 2000). However,
there also are examples in which both parental copies clearly
were not silenced and each contributed to zygotic expression
(Springer et al., 1995, 2000; Baroux et al., 2001; Weijers et al.,
2001). Therefore, imprinting is unlikely to be a general mechanism;
more likely, it is a speciﬁc mechanism that affects the
expression of some but not all genes during plant embryo
development.
What is the signiﬁcance of imprinting? Analysis of imprinted
loci as well as reciprocal crosses between individuals of different
ploidies suggest that increased gene activity from the maternally
derived genome results in the inhibition of mitosis and low seed
weight, whereas extra paternally derived activity causes the
opposite. However, when both copies are hypomethylated and
hence active, no pronounced effect on plant development is
observed (Adams et al., 2000). This is reminiscent of the
‘‘parental conﬂict’’ hypothesis proposed for mammals, which
holds that imprinting serves to balance the allocation of
Figure 1. Apical–Basal Arabidopsis Embryo Development.
Schemes of longitudinal median sections. The upper and lower thick
lines represent clonal boundaries between the descendants of the apical
and basal daughter cells of the zygote and between the apical and
central embryo domains, respectively. See text for details. a, antipodes;
ac, apical daughter cell; ad, apical embryo domain; bc, basal daughter
cell; cd, central embryo domain; cot, cotyledons; crc, central root cap;
ec, egg cell; hc, hypocotyl; hy, hypophysis; lsc, lens-shaped cell; pn,
polar nuclei; qc, quiescent center; rt, root; s, synergids; sm, shoot
meristem; su, suspensor.
Embryonic Patterning S191
resources from the mother to the offspring (Moore and Haig,
1991) and supports the notion that imprinting is not strictly
required for embryo development per se (Jaenisch, 1997).
APICAL–BASAL AXIS FORMATION
One of the earliest patterning events in plant embryogenesis is
the establishment of the apical–basal axis, which can be traced
back to the egg cell and the zygote. Below, we discuss our
current knowledge concerning the mechanisms that regulate this
process.
The First Division of the Zygote
What is the signiﬁcance of the asymmetric division of the zygote?
Are the morphological and/or transcriptional differences of the
daughter cells linked to their different developmental fates?
One of the genes that is expressed asymmetrically in the
daughter cells of the zygote, PINFORMED7 (PIN7), encodes
a member of the PIN family, which presumably are part of the
auxin efﬂux transport machinery (Ga¨ lweiler et al., 1998; Friml,
2003). PIN7 is restricted to the basal daughter cell of the zygote,
where it is localized at the apical cell wall and mediates the efﬂux
of auxin into the apical cell (Friml et al., 2003). In pin7 mutants, the
failure to do so appears to cause aberrant apical cell division
patterns. Mutations in WOX2, which is expressed speciﬁcally in
the apical daughter cell, results in similar phenotypes (Haecker
et al., 2004). Considering the invariant cell division pattern during
early Arabidopsis embryogenesis, the timing and orientation
of cell divisions is an important aspect of cell identity. Thus,
asymmetric PIN7 and WOX2 expression is important to establish
apical cell identity at this stage. In both cases, however, no
marked defects can be detected after the globular stage, and
mutant seedlings appear normal. The reason for this ‘‘rescue’’ of
embryo development is elusive. However, because pin7 defects
are enhanced and the apical–basal organization of seedlings is
severely disturbed if additional PIN genes are mutant, genetic
redundancy might be an explanation.
The phenotype of the gnom (gn) mutant argues against the
possibility that the different sizes of the daughter cells per se are
important for apical–basal development: here, the zygote is less
elongated and divides more randomly to give daughter cells of
variable sizes (Mayer et al., 1993), but the basal cell nevertheless
generates a shortened suspensor and the apical cell forms an
embryo proper. Later in development, gn embryos can give rise
to ball-shaped seedlings without any signs of apical–basal
organization in the most extreme cases (Vroemen et al., 1996).
GN (also called EMB30; Shevell et al., 1994) encodes a guanine
nucleotide exchange factor that is required for the transport of
PIN1 from an endosomal compartment to the membrane at one
side of a cell (Steinmann et al., 1999; Geldner et al., 2001, 2003).
One interpretation of this ﬁnding is that the subcellular
localization of PIN1 determines the site of auxin efﬂux and thus
the direction of auxin ﬂow in the embryo. In this view, GN affects
apical–basal embryo axis formation as an essential component
of the vesicle transport machinery. However, because the loss of
PIN1 results in defects much less severe than those in gn, GN
function also might be important for the intracellular transport of
additional yet unknown factors involved in apical–basal patterning,
such as other PIN proteins.
Why do most descendants from the basal daughter cell of the
zygote form a suspensor rather than an embryo, as the
descendants of the apical daughter do? Several observations
indicate that it is the embryo itself that represses embryonic
development in the suspensor. Experimental abortion of the
embryo can induce the formation of a secondary embryo from
the suspensor cells (Gerlach-Cruse, 1969). Moreover, mutations
in several genes result in the same effect either after the primary
embryo arrests development or even if it continues to develop,
resulting in polyembryony in the latter case (Schwartz et al.,
1994; Vernon and Meinke, 1994; Zhang and Somerville, 1997).
Interestingly, the apical–basal polarity of suspensor embryos in
twin1 mutants can be reversed to that of the primary embryo
(Vernon and Meinke, 1994), suggesting that polarity information
available to the primary embryo is not functional in suspensor
cells.
Organization of the Shoot Apex
The shoot apical meristem is the center of postembryonic organ
formation in the shoot. It can be subdivided into regions with
different properties and functions (Figure 2). The central zone
(CZ) contains relatively slowly dividing cells that are slightly larger
and more vacuolated than the surrounding cells. It harbors the
stem cell niche, consisting of the stem cells in the outermost
three cell layers and the signaling niche cells, termed the
organizing center (OC) (Mayer et al., 1998). WUSCHEL (WUS)
activity in the OC maintains the stem cells in an undifferentiated
state. The stem cells in turn express CLAVATA3 (CLV3), the
putative ligand for the CLV1 receptor kinase signaling pathway
(Fletcher et al., 1999), which limits the size of the OC by restricting
WUS expression (Brand et al., 2000; Schoof et al., 2000). This
regulatory feedback loop between stem cells and the OC
provides a mechanistic framework to explain how the plant
could dynamically assess and adjust the size of the stem cell pool
(Schoof et al., 2000).
The CZ is surrounded by stem cell daughters that are
unvacuolated and divide more rapidly and, based on gene
expression, initiate differentiation. However, the outgrowth of
lateral organs is still suppressed by SHOOTMERISTEMLESS
(STM) (Long and Barton, 1998), possibly allowing the stem cell
daughters to amplify to sufﬁcient numbers before becoming
allocated to organ primordia (Lenhard et al., 2002). Eventually,
STM becomes downregulated in the organ precursor cells and
the expression of organ-speciﬁc genes is initiated, resulting in
the outgrowth of organ primordia from the ﬂanks of the meristem.
By contrast, outgrowth remains repressed in the cells between
the lateral organs.
How is the shoot apex established during embryogenesis?
Histologically, the ﬁrst sign is the outgrowth of the cotyledonary
primordia from the ﬂanks of the late globular embryo. Somewhat
later, the shoot meristem becomes apparent between
the cotyledons by its typical three-layered structure (Barton and
Poethig, 1993). Genetic and gene expression studies revealed,
however, that shoot apex development is initiated much earlier
and can be formally divided into three steps: (1) speciﬁcation of
S192 The Plant Cell
the apical domain, (2) initiation of the stem cell niche, and (3)
central–peripheral patterning into shoot meristem and cotyledonary
primordia.
Speciﬁcation of the Apical Domain
Mutations in genes that are involved in the speciﬁcation of the
apical embryo domain are predicted to disrupt both cotyledon
and shoot meristem development. This is the case in the gurke
(gk) mutant, in which neither the shoot meristem nor cotyledons
form properly (Torres-Ruiz et al., 1996). However, the precise role
of GK is unknown.
Elegant temperature-shift experiments using the temperaturesensitive
Arabidopsis mutant topless (tpl) demonstrated a remarkable
ﬂexibility of embryonic region identity: the apical
embryo domain can be respeciﬁed until approximately the
transition stage to make a root even after it had already initiated
shoot development (Long et al., 2002). These apical roots
morphologically resemble normal roots; however, their formation
differs from that of normal embryonic roots in that they are not
affected by the monopteros (mp) mutation (see below) and do not
express an auxin-responsive reporter gene. Thus, it is possible
that apical root formation in tpl embryos might use mechanisms
similar to the de novo induction of postembryonic roots, for
which MP also is dispensable (Berleth and Ju¨ rgens, 1993).
Initiation of the Stem Cell Niche
The ﬁrst indication of embryonic shoot meristem initiation is the
onset of WUS expression in the four subepidermal apical cells of
the 16-cell embryo (Figure 2) (Mayer et al., 1998). Subsequently,
these cells divide asymmetrically several times, establishing
the WUS expression domain at its correct position within
the developing shoot meristem primordium. WUS function is
required for embryonic shoot meristem formation and for the
expression of CLV3 or STM in mature embryos (Laux et al., 1996;
Mayer et al., 1998; Brand et al., 2002). Correct spatial WUS
expression in turn requires CLV3 activity from the heart stage on,
suggesting that the feedback loop that regulates meristem
homeostasis already is functional at this stage (Schoof et al.,
2000). The reason why WUS is expressed earlier is unknown, yet
a plausible model is that WUS function prevents the precursor
cells of the stem cell niche from entering other embryonic
developmental pathways (Mayer et al., 1998; Grob-Hardt and
Laux, 2003).
Central–Peripheral Patterning of the Apical Domain
The central–peripheral patterning of the apical embryo domain
delineates a central region that includes the incipient meristem
primordium from peripheral regions, from which the cotyledonary
primordia grow out (Figure 2).
In the center of the apical domain, outgrowth is repressed
by CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3,
allowing for the separation of the two cotyledonary primordia.
Single mutants of either gene display only weak and infrequently
occurring aberrant phenotypes. In double mutant combinations,
however, the cells that normally separate the margins of opposite
cotyledons exhibit ectopic outgrowth, which results in the fusion
of the cotyledons and the loss of the shoot meristem (Aida et al.,
Figure 2. Development of the Apical Embryo Domain.
The top row shows schemes of longitudinal median sections. The upper and lower thick lines represent clonal boundaries between the descendants of
the apical and basal daughter cells of the zygote and between the apical and central embryo domains, respectively. The bottom row shows crosssections
of the same stages as indicated by the dashed line at left. CZ, central zone; PZ, peripheral zone; RZ, rib zone. The expression domains of early
genes in the apical region are shown in color as indicated. See text for details.
Embryonic Patterning S193
1997, 1999; Vroemen et al., 2003). The dynamics of the CUC
expression pattern are intriguing. CUC1 and CUC2 are ﬁrst
expressed in isolated patches of apical cells before expression
spreads into a stripe across the embryo apex that divides it into
a central and two peripheral zones (Aida et al., 1999; Takada
et al., 2001). This suggests that CUC expression does not simply
reﬂect a preexisting pattern but may be involved in generating
bilateral symmetry. The CUC genes encode putative transcription
factors homologous with the petunia NO APICAL MERISTEM
(NAM) protein, which also affects cotyledon separation
and shoot meristem formation (Souer et al., 1996). Both cuc and
nam mutants show similar defects during ﬂower development,
indicating related mechanisms for organ separation in embryos
and ﬂowers.
The spatial expression patterns and the functions of CUC1 and
CUC2 require MP and PIN1 activities, which are both implicated
in auxin signaling (Aida et al., 2002). This indicates a role for auxin
signaling in the patterning of the apical embryo domain,
consistent with previous ﬁndings from physiological experiments
(Liu et al., 1993; Hadﬁ et al., 1998). CUC functions, on the other
hand, activate STM expression in the central stripe across the
embryo (Aida et al., 1999). STM in turn promotes CUC1 activity
together with PIN1 and is necessary for the correct spatial
expression of CUC2 (Aida et al., 1999, 2002). In heart-stage
embryos, STM and CUC genes eventually assume complementary
expression patterns that reﬂect the delineation of the shoot
meristem primordium within the central stripe, with STM being
restricted to the incipient shoot meristem and CUC to the
boundaries between the shoot meristem and the cotyledons.
Concurrently, the expression of AINTEGUMENTA, which is
found in a ring around the circumference of the apical domain
in globular embryos, becomes restricted to the incipient
cotyledonary primordia, and organ-speciﬁc gene expression is
initiated (Long and Barton, 1998).
Together, these activities establish a regulatory network of
transcription factors within the apical embryo domain separating
a central stripe in which organ-promoting genes are repressed
and a peripheral zone in which outgrowth of the cotyledonary
primordia occurs. Even though many similarities exist, this
process differs from that of postembryonic leaf formation in that
the cells of the cotyledonary primordia are not derived from the
stem cell niche but are initiated simultaneously.
Competence to Form a Shoot Meristem
How is the position of the shoot meristem determined? Several
lines of evidence indicate that signals from surrounding cells, the
cotyledonary primordia and the underlying vascular primordium,
are crucial for this process.
Soon after cotyledonary primordia bulge out, their adaxial–
abaxial polarity becomes evident by speciﬁc gene expression
patterns (Siegfried et al., 1999; Kerstetter et al., 2001; McConnell
et al., 2001; Otsuga et al., 2001). Mutations that transform adaxial
fates into fates normally restricted to the abaxial side interfere
with shoot meristem formation. By contrast, a gain-of-function
mutation in PHABULOSA (PHB) that promotes adaxial cell fates
increases the size of the embryonic shoot meristem and can
partially rescue organ formation in the stm mutant (McConnell
and Barton, 1998). Together, these data suggest that adaxial
cells of the adjacent cotyledonary primordia provide meristempromoting
signals or, alternatively, block meristem-inhibiting
signals emanating from cells at the abaxial side. The nature of
such signals is unknown. However, the presence of putative
lipid/sterol binding domains in REVOLUTA and PHB suggests
that small-molecule signals might be involved (McConnell et al.,
2001; Otsuga et al., 2001).
The shoot meristem is localized on top of the developing
vasculature, which plausibly links the future transport of nutrients
to the apical growth point (Figure 3). Interestingly, during the
divisions of OC precursor cells, WUS expression always is
restricted to those daughter cells next to the vascular primordium.
This raises the question of whether communication
between the forming vasculature and the shoot meristem
coordinates their development.
Analysis of ZWILLE (ZLL; PINHEAD) function might allow this
question to be addressed. zll embryos display a range of
phenotypes in which STM is expressed aberrantly and differentiated
structures are formed in place of the shoot meristem
(Ju¨ rgens et al., 1994; McConnell and Barton, 1995; Moussian
Figure 3. Development of the Radial Pattern.
The top row and the illustration at bottom left show schemes of
longitudinal sections; the other illustrations in the bottom row show
schemes of cross-sections through a root. The upper and lower thick
lines represent clonal boundaries between the descendants of the apical
and basal daughter cells of the zygote and between the apical and
central embryo domains, respectively. Cell types are shown in color as
indicated. Vascular and pericycle cells are shown in lighter colors than
stem cells. See text for details. gt, ground tissue; hy, hypophysis; lsc,
lens-shaped cell; pc, pericycle; vp, vascular primordium.
S194 The Plant Cell
et al., 1998; Lynn et al., 1999). Ectopic ZLL expression on the
abaxial side of cotyledon primordia in a zll background results in
the transformation of cotyledons into shoot axes with a meristem
at its tip (Newman et al., 2002). In the wild type, ZLL is expressed
initially in all cells of the early embryo and later becomes
restricted to the vascular primordium (strong expression) and to
the shoot apex and the adaxial sides of the cotyledons (weak
expression). ZLL encodes a member of the PIWI ARGONAUTE
ZWILLE (PAZ) family, which is conserved in animals and plants
and several members of which have been implicated in RNA
interference (Cerutti et al., 2000; Carmell et al., 2002). Embryos
that are doubly mutant for ZLL and the ubiquitously expressed
related ARGONAUTE1 (AGO1), which is involved in posttranscriptional
gene silencing (Fagard et al., 2000), display
a synergistic phenotype, suggesting that both proteins have
partially overlapping functions (Lynn et al., 1999). Together, these
data indicate that ZLL activity in surrounding cells promotes
a favorable environment for meristem cell fates in the embryo
apex.
In summary, patterning the embryo apex involves the
successive establishment of the stem cell niche and of the
network that regulates organ formation. Both processes appear
to be initiated independently, based on expression studies of
WUS and STM, but each requires the other for ongoing shoot
meristem activity (Mayer et al., 1998). About halfway through
embryo development, the components that govern postembryonic
meristem activity are in place and, as judged by the
appearance of the ﬁrst leaf primordia, the shoot meristem
commences its activity.
The Central Embryo Domain
The cells of the central embryo domain ﬁrst divide horizontally to
give apical descendants that will contribute to the base of the
cotyledons and basal descendants that will form hypocotyl,
embryonic root, and proximal stem cells of the root meristem
(Figure 1) (Scheres et al., 1994).
Analysis of FACKEL (FK), HYDRA1, and STEROL METHYLTRANSFERASE1/CEPHALOPOD
activities indicate important
roles of sterols for proper embryo development (Topping et al.,
1997; Diener et al., 2000; Jang et al., 2000; Schrick et al., 2000,
2002). The earliest defects in the respective mutants are the
failure of cells in the central embryo domain to elongate and to
divide asymmetrically to form the vascular primordium. Later in
development, mutant embryos also show abnormalities in the
apical and basal domains and often form multiple shoot
meristems and cotyledons.
In which way could sterols be involved in embryo development?
One possibility is that they act as structural membrane
components, exempliﬁed by disturbed cell polarity and auxin
transport in mutants defective for the biosynthesis of major
membrane sterols (Willemsen et al., 2003). Alternatively, steroid
molecules may function as signaling molecules. The ﬁnding
that the brassinosteroid receptor BRASSINOSTEROID-INSENSITIVE1
(Sakurai and Fujioka, 1997) acts downstream of FK to
promote postembryonic growth is in agreement with this possibility
(Schrick et al., 2002). However, because FK acts independently
of other genes involved in brassinosteroid synthesis,
sterol signals other than brassinosteroids could be involved in cell
expansion in the vascular primordium.
The Basal Embryo Domain (Hypophysis)
In the root meristem, the quiescent center (QC), a group of
nondividing cells, maintains the undifferentiated state of the
surrounding stem cells by local signaling (Figure 3) (van den Berg
et al., 1997; Sabatini et al., 2003). Therefore, the QC appears to
fulﬁll an analogous function to that performed by the OC in the
shoot meristem. The position of the QC, on the other hand,
depends on the presence of an auxin maximum in the columella,
termed ‘‘distal organizer,’’ which is maintained by basipetal auxin
transport (Sabatini et al., 1999; Friml et al., 2002, 2003).
Each stem cell gives rise to a ﬁle of differentiating cells.
Accumulating data support the notion that it is not the stem cells,
but signals from adjacent more mature cells in each ﬁle, that
determine the fate of the differentiating daughters (van den Berg
et al., 1995; Malamy and Benfey, 1997). Thus, root meristem
activity is maintained by a balance between signals from the QC
inhibiting stem cell differentiation and opposing signals from the
more mature tissues instructing differentiating descendants.
During embryonic root meristem formation, the proximal stem
cells are derived from the most basal cells of the central embryo
domain, whereas the QC and the stem cells of the central root
cap are derived from the basal embryo domain, the hypophysis
(Figure 3) (Mansﬁeld and Briarty, 1991; Ju¨ rgens and Mayer, 1994;
Scheres et al., 1994). The establishment of the root meristem
coincides with an accumulating auxin maximum in the hypophyseal
region. Failure to properly establish this auxin maximum
results in aberrant speciﬁcation of root meristem cell fates
(Sabatini et al., 1999; Friml et al., 2002, 2003). At the globular
embryo stage, the hypophysis undergoes an asymmetric cell
division, producing an upper lens-shaped cell that will form the
QC and a lower daughter cell that will give rise to the columella
stem cells. This asymmetric division is marked by the expression
of SCARECROW (SCR) and WOX5, ﬁrst in the hypophyseal cell
and subsequently only in the lens-shaped cell and the QC,
suggesting that QC identity is established at approximately this
time (Wysocka-Diller et al., 2000; Haecker et al., 2004). Early
defects in QC development often are followed by abnormal
differentiation of the neighboring stem cell precursors (Willemsen
et al., 1998), suggesting that the QC signaling not only maintains
stem cell identity in the active root meristem but also is crucial for
the initiation of stem cells in the embryo. These observations
suggest that the stem cell niches of the root and the shoot pole
not only are functionally equivalent but also share molecular and
developmental similarities.
Genetic studies of two genes involved in auxin response,
BODENLOS (BDL) and MP, suggest that early root development
depends on gene activities in the embryo proper. MP encodes
a putative transcription factor related to auxin response factors
(Hardtke and Berleth, 1998). MP is thought to be kept inactive
by binding to the indoleacetic acid (IAA) protein BDL, which
is degraded upon intracellular auxin signaling, allowing MP to
activate its target genes (Hamann et al., 2002). The earliest
defects in mp and bdl mutants appear in the apical daughter cell
of the zygote, which divides horizontally instead of vertically,
Embryonic Patterning S195
leading to octant-stage mutant embryos consisting of four
instead of two tiers of cells (Berleth and Ju¨ rgens, 1993; Hamann
et al., 1999). Additionally, in the eight-cell embryo, WOX9
expression fails to be shifted from the hypophysis to the central
embryo domain, as it is in the wild type, suggesting WOX9 as
a target of BDL/MP-dependent signaling (Haecker et al., 2004).
Later, the cells of the central domain divide abnormally and
the hypophysis fails to produce the lens-shaped cell, resulting
in seedlings lacking the root, the root meristem, and the hypocotyl
in the strongest phenotypes. Because MP and BDL are
expressed only in the embryo proper at the time when the
hypophysis develops aberrantly in the mutants, the MP- and
BDL-mediated auxin response in embryo proper cells appears to
be required for signaling from the embryo proper to the subjacent
hypophysis to allow for normal root development.
Not surprisingly, auxin response appears to be important also
in the basal cell lineage for root development. In contrast to mp
and bdl, the ﬁrst defects in hobbit (hbt) and auxin-resistant6 (axr6)
embryos are aberrantly orientated cell divisions in the derivatives
of the basal daughter cell of the zygote; subsequently, no root
meristem is formed (Willemsen et al., 1998; Hobbie et al., 2000).
HBT encodes a CDC27 homolog that in yeast and animals is part
of an anaphase-promoting complex that controls M-phase
progression through targeted proteolysis. hbt mutants accumulate
the IAA17 repressor of auxin response and show reduced
expression levels of an auxin-inducible reporter gene, suggesting
a functional link between proper cell cycle progression and
differentiation (Blilou et al., 2002). AXR6 encodes a subunit of
the ubiquitin protein ligase SKP1/CULLIN/F-BOX PROTEIN and
could be involved in the degradation of IAA proteins in response
to auxin signaling (Hellmann et al., 2003).
FORMATION OF THE RADIAL PATTERN
The ﬁrst manifestation of a radial (inner–outer) pattern consisting
of vasculature, ground tissue, and epidermis is apparent in
octant-stage embryos when tangential cell divisions delineate
the protoderm from the inner cells (Figure 3). Subsequently,
periclinal divisions in the basal tier of cells in the central embryo
domain successively establish concentric layers of tissue primordia
in the developing hypocotyl and root. The ﬁrst divisions
produce the central vascular primordium and a layer of ground
tissue that surrounds it. Later, the vascular primordium splits
into the central vasculature and a surrounding layer of pericycle
cells, and the ground tissue splits into an inner endodermis layer
and an outer cortex layer (Scheres et al., 1995). This radial
pattern is modiﬁed at two positions along the apical–basal axis:
in the hypocotyl region, additional periclinal divisions result in
two layers of cortex, and in the root meristem, the epidermal
stem cell divides periclinally to give the epidermis and the lateral
root cap.
The speciﬁcation of root cell types is independent of the
appearance of the root meristem, consistent with the view that
patterning information is imposed on the root meristem stem cells
by more differentiated cells (Scheres et al., 1995; Malamy and
Benfey, 1997). Once established, the radial pattern is precisely
maintained during postembryonic growth by orientated cell
divisions.
Establishment of the Radial Axis
The ﬁrst critical event in radial patterning that can be observed
are the cell divisions that separate protoderm from inner cells.
Why do the cells derived from these divisions enter different
pathways? One interesting observation made in Citrus jambhiri
is that the zygote and subsequently all cell walls at the surface
of the embryo are coated with a cuticle layer that serves as
a morphological marker for epidermal identity (Bruck and Walker,
1985). An attractive hypothesis derived from this observation
holds that an as yet unidentiﬁed component conferring epidermal
fate to the attached protoplasts is contained within the cell
wall of the zygote and propagated to every progeny cell having
a cell wall contiguous to that of the zygote, whereas all inner cells
assume subepidermal fates. A role of cell wall–located components
in cell fate regulation also has been proposed based on
ablation experiments in Fucus embryos (Berger et al., 1994).
The early expression patterns of two Arabidopsis homeobox
genes, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1)
and PROTODERMAL FACTOR2 (PDF2), are consistent with this
hypothetical mechanism. Both genes are expressed at early
stages in all embryo proper cells that possess an outer cell wall
contiguous with the cell wall of the zygote (Lu et al., 1996; Abe
et al., 2003). Upon the tangential cell divisions at the eight-cell
stage, the protoderm continues its expression, whereas the inner
cells gradually cease expression. Later expression is conﬁned to
the epidermis of the shoot apex and young primordia. Although
the single mutants are aphenotypic, double-mutant embryos
have an irregular surface in the apical domain and lack the
layered organization of the shoot meristem. Upon germination,
the double mutants appear to lack an epidermis, resulting in
leaves with mesophyll cells at the surface (Abe et al., 2003).
ATML1 and PDF2 encode homeodomain transcription factors
containing a START domain, which is implicated in lipid/sterol
binding. Both factors bind to an 8-bp cis-regulatory element that
confers epidermis-speciﬁc gene expression and that is present
also in the promoters of ATML1 and PDF2, suggesting that both
genes regulate their own expression in addition to that of other
target genes. Therefore, it is plausible that epidermal cell identity
is stably propagated by a positive feedback loop, which would
necessitate, however, the active repression of both genes in the
subepidermal cells after protoderm formation.
Radial Organization of the Root and Hypocotyl
Embryos mutant for WOODEN LEG (WOL) omit one round of
tangential cell divisions in the vascular primordium, resulting in
a reduced number of cells in the vascular cylinder of the root and
hypocotyl. All cell ﬁles differentiate into protoxylem, whereas
phloem is missing (Scheres et al., 1995; Mahonen et al., 2000).
WOL encodes a two-component hybrid signal transducer that is
expressed in the vascular primordium of the embryo and later in
the vascular cylinder and pericycle (Mahonen et al., 2000). It is
allelic to CYTOKININ RECEPTOR1 (CRE1) (Inoue et al., 2001) and
is activated by extracellular cytokinin (Hwang and Sheen, 2001).
In analogy to bacterial two-component signaling pathways,
WOL/CRE1 after perceiving cytokinin signals on the cell surface
could transmit the signal to the nucleus to regulate the
S196 The Plant Cell
expression of genes that control cell divisions in the vascular
primordium.
The vascular cylinder and the pericycle in turn regulate the
development of the surrounding ground tissue by producing
SHORT ROOT (SHR), a putative transcription factor (Helariutta
et al., 2000). Elegant experiments suggest that it is SHR itself
that moves into the ground tissue, where it activates the expression
of the related transcription factor SCR (Di Laurenzio
et al., 1996; Nakajima et al., 2001). The movement appears to
be restricted to cells directly adjacent to those that transcribe
SHR, explaining why only the immediate neighbors of the
stele, but not the next cell layer, differentiate into endodermis.
scr and shr mutants lack asymmetric cell divisions of the
ground tissue, resulting in a single cell layer where normally
endodermis and cortex are formed.
Generally, the failure of a mutant to produce a given pattern
element may be attributable to either the inability to provide the
correct cell fate information or the failure to generate the cells
necessary for that element. Genetic studies between radial
patterning mutants and the fass (fs) mutant, which causes an
increased number of radial cell layers (Torres-Ruiz and Ju¨ rgens,
1994), address this issue. The fs mutation is able to rescue the
defects of scr and wol, suggesting that neither SCR nor WOL is
required for cell fate speciﬁcation (Scheres et al., 1995; Mahonen
et al., 2000); rather, they are needed to regulate the number of
cell layers. In agreement with this argument, the single cell layer
in scr expresses characteristics of both cortex and endodermis
(Di Laurenzio et al., 1996). The lack of phloem in wol mutants
could be explained by a hierarchical ﬁrst-come–ﬁrst-served
mechanism in which the speciﬁcation of one cell type (xylem)
precedes that of another (phloem) and in which the latter cannot
occur if all cells are consumed by the former. By contrast, fs
rescued only the reduced number of cell layers in shr mutants
but not endodermal cell fate (Scheres et al., 1995). Along with the
observation that the single layer in shr mutants has only cortex
identity, this ﬁnding indicates that SHR acts both to promote the
asymmetric cell divisions via SCR and to specify endodermal cell
fate via a yet unknown mechanism (Helariutta et al., 2000).
Patterning the Circumference
By the heart stage, both the apical–basal and the radial
organization of the embryo have been deﬁned. Yet another
patterning event distinguishes between epidermal cell fates in
root and hypocotyl with respect to their circumferential
position: cells that are in contact with the intercellular space
of two underlying cortex cells (the H position) will differentiate
into hair cells in the root and stomata in the hypocotyl,
whereas cells that are in contact with only one cortical cell (the
N position) differentiate into nonhair cells and nonstomatal
cells (Figure 3). The origin of this patterning information is
unknown, but one possibility is that signals emanating from
the intercellular space between cortex cells set up the initial
difference. Subsequently, a network of genes is activated that
speciﬁes non-root-hair fate while at the same time laterally
suppressing it in its neighbors (Schiefelbein, 2003). One of the
components of this network, the homeodomain transcription
factor GLABRA2 (GL2), has been used to monitor epidermal
patterning during embryogenesis (Lin and Schiefelbein, 2001;
Costa and Dolan, 2003). In seedlings, GL2 is expressed
speciﬁcally at the N position and confers nonhair fate to root
cells and nonstomata fate to the hypocotyl. During embryogenesis,
GL2 is expressed ﬁrst in single protodermal cells at
the root pole in heart-stage embryos. At the torpedo stage,
expression in the hypocotyl region already is conﬁned to the N
position. By contrast, expression in the root region expands
through the entire epidermis and only later becomes restricted
to the N position, indicating that initially equivalent cells
become diverse in response to positional cues.
MECHANISMS THAT ESTABLISH CELL FATE
IN THE EMBRYO
Generally, two mutually nonexclusive mechanisms can be
envisioned for how different cell fates segregate during embryonic
cell divisions: (1) asymmetric divisions generate daughter
cells that inherit different developmental determinants, and (2)
initiation of different developmental pathways in initially equal
daughter cells by differential positional cues. Which of these
mechanisms functions in plant embryo patterning?
Differential Inheritance of Determinants
The polar localization of molecules before cell division and their
asymmetric segregation into daughter cells have been demonstrated
to initiate different developmental fates in bacteria, fungi,
and animals (Jacobs and Shapiro, 1998). In plants, the divisions
of the zygote, the hypophysis, and the octant-stage cells are
examples of asymmetric divisions in the embryo that generate
daughter cells with morphological differences that develop into
different cell types. In several cases, the division of cells
expressing mRNAs of developmental regulators, such as WUS
and SCR, segregates one daughter cell that continues to express
the mRNA and one that lacks its expression (Mayer et al., 1998;
Wysocka-Diller et al., 2000). If initial symmetric expression in
both daughter cells is never observed, it is plausible that mRNAs
or regulators of their expression have been localized in a polar
manner in the dividing cell and subsequently inherited asymmetrically
by its daughters. Thus, only indirect evidence suggests
differential inheritance of molecules during cell division
in plants to date, and polar localization of such components
before cell separation has yet to be demonstrated. It is noteworthy
that such a mechanism would not imply a cell-autonomous
mode of cell fate speciﬁcation, because polarization of the
dividing cell conceivably can depend on positional cues.
Pathways of Cell–Cell Communication
In many cases, daughter cells of embryonic cell divisions initially
appear equal and only subsequently seem to establish different
gene expression patterns. How do early embryo cells perceive
information that enables them to enter different developmental
pathways?
In animals, cell–cell communication involving extracellular
signals and cell surface–bound receptors plays an important role
in cell fate decisions during embryogenesis (Johnston and
Embryonic Patterning S197
Nu¨ sslein-Volhard, 1992). Probably the best characterized signaling
events in embryo patterning are those that involve auxin as
a signaling molecule. Many examples demonstrate an important
role for cellular auxin response in different parts of the embryo
and at different stages, raising the question of how auxin is
distributed in space and time during embryogenesis. Recent
analysis of the PIN protein family and monitoring of auxin and the
auxin response provided signiﬁcant novel insights into this issue.
A ﬁrst auxin maximum is established in the apical daughter cell of
the zygote by PIN7-mediated transport of auxin from the basal
cell (Friml et al., 2003). At the globular embryo stage, the direction
of net auxin ﬂow appears to become reversed from apical to
basipetal, establishing a new auxin maximum in the hypophysis.
This step is accomplished by the dynamic localization of PIN1,
PIN4, and PIN7 (Steinmann et al., 1999; Friml et al., 2002, 2003).
Later in embryo development, auxin ﬂow appears to be directed
toward the tips of the cotyledons and other organs, which
supports a role for auxin as a general distal organizer, and this
accumulation is reﬂected by apically orientated PIN1 localization
(Sabatini et al., 1999; Benkova et al., 2003; Reinhardt et al.,
2003). Although the source of auxin often remains elusive, these
results indicate that a dynamic distribution of auxin during
embryogenesis is accomplished by the changing localization of
the cellular auxin efﬂux machinery.
How can diverse effects be explained by the action of a simple
molecule such as auxin? One possibility is that cells are already
predetermined to respond to auxin in a cell-speciﬁc manner and
that the presence of auxin triggers this preset pathway. The large
variety and the speciﬁc expression patterns of proteins involved
in the auxin response are consistent with this hypothesis
(Kepinski and Leyser, 2002). Alternatively, auxin may induce
only a few generic primary cellular responses, such as cell
elongation, which in turn could direct the timing and orientation of
cell divisions and thus contribute to patterning.
Stable Separation of Cell Fates
Plant cells are effectively coupled via plasmodesmata that permit
the facilitated exchange of molecules, including even transcription
factors (Lucas et al., 1995; Wu et al., 2003). This poses the
question of how important is the separation of cells for cell fate
segregation and to what extent does a single cell or nucleus
represent a functional unit in plant development.
Cellular separation is disturbed in knolle (kn) and keule mutants
that fail to properly form a cell plate during cytokinesis, resulting
in embryos with multinucleate cells (Lukowitz et al., 1996;
Assaad et al., 2001). Both genes encode components of the
vesicle fusion apparatus, suggesting a role in the transport of
material to the site of cell wall formation during cytokinesis.
Based on marker gene expression, the segregation of protoderm
and inner cell fate are affected in early kn embryos (Lukowitz
et al., 1996; Vroemen et al., 1996), suggesting that cell separation
is a prerequisite for the stable segregation of cell fate
determinants. Studies of cell–cell transport demonstrated that
plasmodesmal coupling of cells is not always present but is
region speciﬁc and dynamic (van der Schoot and Rinne, 1999)
and that movement through plasmodesmata is possible for
some molecules but excluded for others (Lucas et al., 1995).
Therefore, it is conceivable that preferential and selective
coupling of embryo cells restricts the movement of cell fate
determinants to cells within a given group, allowing the acquisition
of a developmental fate different from that of an adjacent
group of cells.
PERSPECTIVES
Although analyzing embryo development in plants is not easy
because of the inaccessibility of the embryo, our understanding
of the mechanisms underlying plant embryogenesis has been
enhanced considerably during the last decades by using
Arabidopsis as a model.
A curious observation is that many mutants disturbed in
embryonic patterning display abnormal cell divisions as their
earliest defect. In many cases, however, these can be compensated
for, at least in part, at later stages when the embryo has
reached a higher cell number by the activation of alternative
pathways that are known to function in postembryonic tissue
regeneration. This is consistent with long-standing observations
derived from plant regeneration studies that the ability to
organize into a body plan is a more general property of plant
cells that is executed during Arabidopsis embryogenesis in
a stereotypic manner but that can be reached in many alternative
ways. In this view, the stereotypic embryonic cell division pattern
might simply ensure that sufﬁcient numbers of cells are present
to allow for the most rapid and early establishment of the body
plan that could provide an advantage in natural habitats.
Many important functions likely remain to be detected as
a result of functional redundancy or embryo lethality. Molecular
and reverse genetics approaches have begun to add new
players to an increasingly comprehensive regulatory network. In
the future, global RNA and protein proﬁling will enable us to
assess the molecular basis of cellular states (i.e., in embryonic
versus differentiated cells), and improvement of the tools used
to visualize intracellular processes in embryos will allow the
assessment of the dynamics of regulatory processes. Future
challenges will be to identify the origin of patterning information,
such as the mechanisms that establish speciﬁc transcriptional
zones and regulate cell fate segregation, and to identify effector
processes that translate pattern information into cell types.
ACKNOWLEDGMENTS
We thank Kathrin Schrick and the members of the Laux laboratory for
critical comments. We apologize to all colleagues whose excellent work
could not be cited because of space constraints. We gratefully
acknowledge the support of research in our laboratory by grants from
the Deutsche Forschungsgemeinshaft and the European Union to T.L.
Received August 5, 2003; accepted December 26, 2003.
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