Genetic Regulation of Embryonic Pattern Formation

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). 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; Jürgens and Mayer, 1994). 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. 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. 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-Hüsemann 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 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. 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. 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 gene et al., et al., MEA is in the central the egg and the of the female but not in the gametophyte et al., the maternal of MEA to be in the developing the early and the but is of MEA be by an because mutations in the gene which results in to of the paternal MEA gene in the early embryo. MEA expression to be in the female gametophyte through the of in its by the suggesting that could through and in et al., 2002). expression is to the central cell and the suggesting that MEA expression in these cells expression of MEA in the egg cell be to a function of MEA expression be in the embryo and the establishment of a is in plants? of a of genes the to the paternal et al., However, also are in which both parental copies were not and each to zygotic expression et al., et al., 2001; et al., 2001). is to be a more it is a specific that the expression of but not genes plant embryo development. is the of of as as between of different suggest that gene from the results in the of and the However, when both copies are and on plant development is et al., is of the for which that to the of from the mother to the and and supports the that is not required for embryo development of the earliest patterning in plant embryogenesis is the establishment of the apical–basal which can be back to the egg cell and the Below, we discuss the mechanisms that this is the of the asymmetric division of the the transcriptional of the daughter cells to their different of the genes that is asymmetrically in the daughter cells of the encodes a member of the which presumably are of the et al., is to the basal daughter cell of the where it is at the apical cell and the of into the apical cell et al., In the to do to apical cell division in which is in the apical daughter results in similar (Haecker et al., 2004). the cell division pattern early Arabidopsis embryogenesis, the and of cell divisions is an of cell Thus, asymmetric and expression is to establish apical cell at this In both cases, marked defects can be the stage, and mutant The for this of embryo development is However, because defects are and the apical–basal of is if additional genes are genetic be an The phenotype of the mutant argues against the that the different of the daughter cells are for apical–basal the zygote is and more to daughter cells of et al., but the basal cell a and the apical cell an embryo in development, embryos can to of apical–basal in the et al., 1996). et al., encodes a that is required for the of from an to the at one of a cell et al., et al., of this is that the of the of and the of in the embryo. In this apical–basal embryo axis as an component of the However, because the of results in defects in function also be for the of additional factors involved in apical–basal such as other do descendants from the basal daughter cell of the zygote form a an as the descendants of the apical daughter Several observations indicate that it is the embryo itself that embryonic development in the suspensor. of the embryo can the of a embryo from the cells mutations in several genes result in the the embryo development or even if it to resulting in in the latter case (Schwartz et al., 1994; and 1994; and the apical–basal polarity of embryos in can be to that of the embryo and 1994), suggesting that polarity information to the embryo is not in of the Embryo The 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 of the stages as by the at central The expression domains of early genes in the apical are in as See text for details. The is by cell that are and more rapidly on gene However, the of is by and the cell to to to et al., 2002). in the precursor cells and the expression of genes is resulting in the of from the of the in the cells between the is the shoot established the is the of the from the of the embryo. the shoot meristem between the by its and and gene expression studies that shoot development is initiated and can be into of the apical of the cell and patterning into shoot meristem and in genes that are involved in the of the apical embryo are to both and shoot meristem development. is the case in the in which the shoot meristem form et al., 1996). However, the of is the Arabidopsis mutant a of embryonic the apical embryo can be the to a root even it already initiated shoot development et al., 2002). apical normal their from that of normal embryonic in that are not by the and do not express an Thus, it is possible that apical root in embryos mechanisms similar to the of for which also is and The of embryonic shoot meristem is the of expression in the subepidermal apical cells of the embryo et al., 1998). Subsequently, these cells asymmetrically several establishing the expression at its the developing shoot meristem function is required for embryonic shoot meristem and for the expression of or in embryos et al., 1996; et al., et al., 2002). expression in from the suggesting that the that meristem already is at this et al., The is is a model is that function the precursor cells of the cell from other embryonic et al., and The patterning of the apical embryo a central that the meristem from from which the In the of the apical is by and for the of the two of gene display only and In mutant the cells that the of which results in the of the and the of the shoot meristem et al., et al., The of the expression pattern are and are in of apical cells expression into a the embryo that it into a central and two et al., et al., 2001). that expression not a pattern but be involved in The genes putative transcription factors with the which also and shoot meristem et al., 1996). and show similar defects development, indicating mechanisms for in embryos and The expression and the of and and which are both in et al., 2002). a for in the patterning of the apical embryo with previous findings from et al., et al., 1998). on the other expression in the central the embryo et al., in with and is for the expression of et al., 2002). In and genes assume expression that the of the shoot meristem the central with being to the shoot meristem and to the boundaries between the shoot meristem and the the expression of which is found in a the of the apical in to the and gene expression is initiated and 1998). these establish a of transcription factors the apical embryo a central in which genes are and a in which of the this process from that of in that the cells of the are not from the cell but are initiated is the of the shoot meristem Several lines of indicate that signals from surrounding the and the vascular are crucial for this their polarity by specific gene expression et al., et al., 2001; et al., 2001; et al., 2001). that into to the with shoot meristem a in that cell the of the embryonic shoot meristem and can in the mutant and 1998). these data suggest that cells of the signals signals from cells at the The of such signals is However, the of putative domains in and that signals be involved et al., 2001; et al., 2001). of the The and the at show of longitudinal the other in the show of through a 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. types are in as and cells are in See text for details. ground hy, hypophysis; lsc, lens-shaped cell; vascular of function this to be embryos display a of in which is and structures are in of the shoot meristem et al., 1994; and et al., et al., expression on the of in a results in the of into shoot with a meristem at its et al., 2002). In the is in cells of the early embryo and to the vascular and to the shoot and the of the encodes a member of the which is in animals and plants and several of which in et al., et al., 2002). that are mutant for and the which is involved in gene et al., display a suggesting that both et al., these data indicate that in surrounding cells a for meristem cell in the embryo In patterning the embryo the establishment of the cell and of the that to be initiated on expression studies of and but each the other for shoot meristem et al., 1998). through embryo development, the that meristem are in as by the of the the shoot meristem its The cells of the central embryo to apical descendants that contribute to the of the and basal descendants that form hypocotyl, embryonic root, and cells of the root meristem et al., 1994). of and indicate of for embryo development et al., 1997; et al., et al., et al., 2002). The earliest defects in the are the of cells in the central embryo to and to asymmetrically to form the vascular in development, mutant embryos also show in the apical and basal domains and form shoot and In which could be involved in embryo is that as by cell polarity and in for the of et al., molecules function as The that the and acts of to is in agreement with this et al., 2002). However, because acts of other genes involved in signals other could be involved in cell in the vascular In the root meristem, the quiescent a group of the of the surrounding cells by et al., 1997; et al., the to an function to that by the in the shoot The of the on the other on the of an in the which is by et al., Friml et al., cell to a of data the that it is not the but signals from more cells in each that the fate of the et al., and Thus, root meristem is by a between signals from the cell and signals from the more tissues During embryonic root meristem the cells are from the basal cells of the central embryo the and the cells of the central root are from the basal embryo the (Mansfield and Briarty, 1991; Jürgens and Mayer, 1994; et al., 1994). The establishment of the root meristem with an in the to establish this results in of root meristem cell et al., Friml et al., At the embryo stage, the an asymmetric cell an upper lens-shaped cell that form the and a lower daughter cell that to the asymmetric division is marked by the expression of and in the cell and only in the lens-shaped cell and the suggesting that is established at this et al., Haecker et al., 2004). defects in development are by of the cell et al., suggesting that the not only cell in the root meristem but also is crucial for the of cells in the embryo. observations suggest that the cell of the root and the shoot not only are but also and studies of two genes involved in and suggest that early root development on gene in the embryo encodes a putative transcription to factors and 1998). is to be by to the protein which is to its genes et al., 2002). The earliest defects in and in the apical daughter cell of the which of to mutant embryos of of two of cells and et al., in the expression to be from the to the central embryo as it is in the suggesting as a of (Haecker et al., 2004). the cells of the central and the to the lens-shaped resulting in the root, the root meristem, and the in the and are only in the embryo at the when the in the the and in embryo cells to be required for from the embryo to the to for normal root development. to be also in the basal cell for root development. In to and the defects in and embryos are cell divisions in the of the basal daughter cell of the root meristem is et al., et al., encodes a that in and animals is of an complex that through the of and show expression of an suggesting a between cell and et al., 2002). encodes a of the protein and could be involved in the of in to et al., The of a radial pattern of ground tissue, and is in embryos when cell divisions the from the cells Subsequently, divisions in the basal of cells in the central embryo establish concentric of tissue in the developing and The divisions the central vascular and a of ground tissue that the vascular into the central and a surrounding of and the ground tissue into an and an et al., radial pattern is at two along the apical–basal in the additional divisions result in two of and in the root meristem, the cell to the and the root The of root cell types is of the of the root meristem, with the that patterning information is on the root meristem cells by more cells et al., and the radial pattern is by cell The in radial patterning that can be are the cell divisions that from do the cells from these divisions different observation in is that the zygote and cell at the of the embryo are with a that as a for and from this observation that an as component fate to the is the cell of the zygote and to cell a cell to that of the cells assume subepidermal of cell in cell fate regulation also on in embryos et al., 1994). The early expression of two Arabidopsis and are with this mechanism. genes are at early stages in embryo cells that an cell with the cell of the zygote (Lu et al., 1996; et al., the cell divisions at the stage, the its the cells expression is to the of the shoot and Although the single are embryos an in the apical and the of the shoot the to an epidermis, resulting in with cells at the et al., and transcription factors a which is in factors to an that gene expression and that is also in the of and suggesting that both genes their expression in addition to that of other it is that cell is by a which the repression of both genes in the subepidermal cells mutant for one of cell divisions in the vascular resulting in a number of cells in the vascular cylinder of the root and cell differentiate into is et al., et al., encodes a that is in the vascular of the embryo and in the vascular cylinder and et al., is to et al., and is by and 2001). In to signals on the cell could the to the to the expression of genes that cell divisions in the vascular The vascular cylinder and the in the development of the surrounding ground tissue by a putative transcription et al., suggest that it is itself that into the ground tissue, where it the expression of the transcription et al., 1996; et al., 2001). The to be to cells to that only the of the but not the cell differentiate into and asymmetric cell divisions of the ground tissue, resulting in a single cell where and are the of a mutant to a pattern be to the to the cell fate information or the to the cells for that studies between radial patterning and the which an number of radial cell and 1994), this The is to the defects of and suggesting that is required for cell fate et al., et al., are to the number of cell In agreement with this the single cell in of both and et al., 1996). The of in could be by a in which the of one cell that of and in which the latter cannot if cells are by the rescued only the number of cell in but not cell fate et al., with the observation that the single in only this that acts both to the asymmetric cell divisions via and to cell fate via a et al., the stage, both the apical–basal and the radial of the embryo patterning between cell in root and with to their cells that are in with the of two cells differentiate into cells in the root and in the hypocotyl, cells that are in with only one cell differentiate into cells and cells The origin of this patterning information is but one is that signals from the between cells up the Subsequently, a of genes is that fate at the it in its of the of this the transcription used to patterning embryogenesis and 2001; and In is at the and fate to root cells and fate to the During embryogenesis, is in single cells at the root in At the stage, expression in the already is to the expression in the root through the and only to the position, indicating that cells become in to positional two mechanisms can be for different cell embryonic cell asymmetric divisions daughter cells that different and of different in daughter cells by positional of these mechanisms in plant embryo The polar of molecules cell division and their asymmetric into daughter cells to different in and animals and 1998). In the divisions of the the and the cells are of asymmetric divisions in the embryo that daughter cells with that into different cell In several cases, the division of cells mRNAs of such as and one daughter cell that to express the and one that its expression et al., et al., expression in both daughter cells is it is that mRNAs or of their expression in a polar in the cell and asymmetrically by its Thus, only indirect of molecules cell division in plants to and polar of such cell to be is that such a not imply a of cell fate because of the cell can on positional In cases, daughter cells of embryonic cell divisions and only to establish different gene expression do early embryo cells information that to different In signals and cell an in cell fate embryogenesis and the in embryo patterning are that as a an for in different of the embryo and at different stages, the of is in and embryogenesis. of the protein and of and the into this is established in the apical daughter cell of the zygote by of from the basal cell et al., At the embryo stage, the of to become from apical to establishing a in the is by the of and et al., Friml et al., in embryo development, to be the of the and other which supports a for as a and this is by et al., et al., 2003; et al., Although the of these results indicate that a of embryogenesis is by the of the can effects be by the of a simple such as is that cells are already to to in a and that the of this The and the specific expression of involved in the are with this and 2002). only a such as cell which in could direct the and of cell divisions and contribute to patterning. cells are via that the of even transcription factors et al., et al., the of is the of cells for cell fate and to a single cell or represent a in plant development. is in and that to form a cell resulting in embryos with cells et al., 1996; et al., 2001). genes of the suggesting a in the of to the of cell on gene the of and cell fate are in early embryos et al., 1996; et al., suggesting that cell is a for the of cell fate of that of cells is not but is specific and and and that through is possible for molecules but for et al., it is that and of embryo cells the of cell fate to cells a the of a fate different from that of an group of Although analyzing embryo development in plants is not because of the of the of the mechanisms plant embryogenesis the by Arabidopsis as a observation is that in embryonic patterning display cell divisions as their earliest In cases, these can be at in at stages when the embryo a cell number by the of that are to function in tissue is with observations from plant studies that the to into a body plan is a more of plant cells that is Arabidopsis embryogenesis in a but that can be in In this the embryonic cell division pattern that of cells are to for the and early establishment of the body plan that could an in to be as a result of or embryo and to to an In the and protein to the of in embryonic and of the used to in embryos the of the of be to the origin of patterning such as the mechanisms that establish specific transcriptional and cell fate and to that pattern information into cell We and the of the for We to excellent could not be because of We the of in by from the and the to