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Plant Cell, Vol. 11, 407-416, March 1999, Copyright © 1999, American Society of Plant Physiologists
Mutations in FIE, a WD Polycomb Group Gene, Allow Endosperm Development without Fertilization
Nir Ohad1,a,
Ramin Yadegari1,b,
Linda Margossianb,
Mike Hannonb,
Daphna Michaelib,
John J. Haradac,
Robert B. Goldbergd, and
Robert L. Fischerb
a Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel
b Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
c Section of Plant Biology, Division of Biological Sciences, University of California, Davis, California 95616
d Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90024-1606
Correspondence to:
Robert L. Fischer, rfischer{at}uclink4.berkeley.edu (E-mail), 510-642-9017 (fax)
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ABSTRACT |
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A fundamental problem in biology is to understand how fertilization initiates reproductive development. Higher plant reproduction is unique because two fertilization events are required for sexual reproduction. First, a sperm must fuse with the egg to form an embryo. A second sperm must then fuse with the adjacent central cell nucleus that replicates to form an endosperm, which is the support tissue required for embryo and/or seedling development. Here, we report cloning of the Arabidopsis FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) gene. The FIE protein is a homolog of the WD motif–containing Polycomb proteins from Drosophila and mammals. These proteins function as repressors of homeotic genes. A female gametophyte with a loss-of-function allele of fie undergoes replication of the central cell nucleus and initiates endosperm development without fertilization. These results suggest that the FIE Polycomb protein functions to suppress a critical aspect of early plant reproduction, namely, endosperm development, until fertilization occurs.
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INTRODUCTION |
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The higher plant life cycle alternates between multicellular haploid (i.e., gametophyte) and diploid (i.e., sporophyte) generations. In Arabidopsis, the ovule generates the female gametophyte, which is composed of egg, central, synergid, and antipodal cells (Figure 1A). Surrounding and protecting the female gametophyte are maternal cell layers, which are called the integuments (Figure 1A). Double fertilization within the female gametophyte activates four reproductive developmental programs. (1) The fertilized egg initiates embryogenesis (Figure 1D). (2) The fertilized central cell generates the primary triploid endosperm nucleus that replicates to form the endosperm (Figure 1D), which is the tissue that supports the development of the embryo. (3) The maternal integument cell layers of the ovule become the seed coat (Figure 1D and Figure 1H). (4) The ovary differentiates and elongates to form the fruit, or silique (Figure 1F).
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Figure 1.
Phenotype of Wild-Type and fie-1 Plants.
(A) Wild-type ovule 6 days after anther removal.
(B) Wild-type silique 6 days after anther removal.
(C) fie-1 heterozygote silique 6 days after anther removal.
(D) Wild-type seed with globular embryo 2 days after pollination.
(E) fie-1 seedlike structure 6 days after anther removal.
(F) Self-pollinated wild-type silique.
(G) Self-pollinated silique from fie-1 heterozygote.
(H) Viable seed obtained from silique in (G).
(I) Defective seed from silique in (G).
AE, aborted embryo; CCN, central cell nucleus; ECN, egg cell nucleus; EM, embryo; EN, endosperm; ENN, one of the endosperm nuclei in the endosperm; FG, female gametophyte; I, integument; OV, ovule; SC, seed coat; SLS, seedlike structure. Bars in (B), (C), (F), and (G) = 1 mm; bars in (A), (D), (E), (H), and (I) = 0.1 mm.
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The two products of fertilization, embryo and endosperm, display distinct patterns of development. In Arabidopsis, the embryo proceeds through a series of stages that have been defined morphologically as preglobular, globular (Figure 1D), heart, cotyledon, and maturation (Figure 1H). During these stages, an axis of polarity is fixed, shoot and root meristems are formed, and storage organs are generated (Goldberg et al. 1994  ). In contrast, the fertilized central cell (i.e., the primary endosperm nucleus) divides mitotically to produce a syncytium of nuclei that fills an expanding central cell (Figure 1D). After cytokinesis occurs, endosperm cells produce storage proteins, starch, and lipids (Lopes and Larkins 1993 ).
Ultimately, the endosperm is absorbed by the developing embryo (Figure 1H). It is thought that endosperm evolved from a supernumerary fertilization event that originally produced multiple embryos and may represent a highly modified embryo that enhances the fitness of its sister embryo (Friedman 1992 , Friedman 1995 ).
To understand the mechanisms controlling the onset of reproduction, we isolated gametophytic mutations in Arabidopsis, designated fie (for fertilization-independent endosperm), that initiate aspects of reproductive and maternal development in the absence of fertilization (Ohad et al. 1996 ). In this study, we extend our analysis of the mutant phenotype conferred by fie and report the cloning of the FIE gene. We show that the FIE gene encodes a polypeptide related to the family of WD Polycomb group proteins. Our results suggest that one function of the FIE gene is to suppress transcription of genes for central cell nuclear replication in the female gametophyte until fertilization occurs.
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RESULTS |
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Phenotype Conferred by fie
When fertilization was prevented in plants heterozygous for the fie-1 mutant allele, siliques elongated (Ohad et al. 1996 ) and contained seedlike structures (Figure 1C) composed of an endosperm surrounded by a seed coat (Figure 1E). No embryo development was observed (Figure 1E). In wild-type plants, when fertilization was prevented by the removal of pollen-producing anthers, no reproductive development was detected (Figure 1B). Genetic analysis suggested that the fie-1 mutation acts first in the female gametophyte to initiate endosperm development that in turn stimulates maternal seed coat and silique formation (Ohad et al. 1996 ).
The maternally derived FIE allele plays an essential role during embryo development (Ohad et al. 1996 ). Control wild-type siliques only rarely contained defective seeds (Figure 1F). However, inheritance of the fie-1 allele by the female gametophyte caused embryo abortion after fertilization. That is, heterozygous fie-1 plants, after self-pollination or when pollinated with wild-type pollen, displayed equal numbers (Figure 1G) of normal seeds with viable embryos (Figure 1H), and defective seeds with embryos aborted at the heart stage (Figure 1I). As shown in Figure 2, in wild-type embryos at 6 days after pollination, there was a dramatic increase in cell proliferation associated with growth and development of the embryo axis and cotyledons. In contrast, embryo cell proliferation was greatly reduced in embryos with a maternally derived mutant fie-1 allele, even though they inherited a wild-type paternally derived allele (Figure 2). These results indicate that the maternally derived fie mutant allele, directly or indirectly, inhibits embryo cell proliferation and morphogenesis.
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Figure 2.
Cell Proliferation in Wild-Type and Mutant Embryos.
The average number of cells (±SD; n > 10) is shown for each time point. Open circles indicate wild-type embryos; closed circles indicate heart-shaped embryos with a maternally derived fie-1 mutant allele and a paternally derived wild-type FIE allele. Stages of wild-type control embryos are as follows: 1 day after pollination (DAP), zygote; 2 DAP, two- to three-cell embryo proper; 3 DAP, four- to eight-cell embryo proper; 4 DAP, early- to mid-globular stage; 5 DAP, late-globular stage; 6 DAP, early-heart stage; 7 DAP, heart stage; 8 DAP, torpedo- to walking-stick stage.
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Cloning the FIE Gene
We used a map-based strategy to clone the FIE gene. As shown in Figure 3, the FIE gene was mapped between morphological markers emb29 (Meinke 1985 ) and axr2 (Timpte et al. 1994 ) and between molecular markers NDR (Century et al. 1997 ) and the end of yeast artificial chromosome clone CIC3D12 (Creusot et al. 1995 ). Fine-structure mapping localized the FIE gene between molecular markers CH18S and KN1N (Figure 3). To further define the position of the FIE gene, we introduced overlapping wild-type cosmid clones into heterozygous fie-1 plants by Agrobacterium-mediated transformation, and we observed genetic complementation for cosmids GM15, AD21, and pCLD36 (Figure 3). For lines homozygous for both the mutant fie-1 allele and the transgenic wild-type FIE allele, self-pollinated siliques contained viable seed, and the aborted embryos associated with the maternal fie-1 mutation (Figure 1I) were not observed (data not shown). When fertilization was prevented by the removal of anthers, fie-1 seedlike structures with an endosperm and seed coat were not formed, and the transgenic ovule resembled a wild-type ovule (Figure 1A). These complementation experiments suggest that the entire FIE gene resides within a 12-kb region delineated by the end points of cosmids AD21 and pCLD36 (Figure 3). Because fie is a gametophytic mutation, it was not possible to determine whether the mutant allele is dominant or recessive by using classic genetic procedures. However, these complementation experiments indicate that the mutant fie-1 allele is recessive to the wild-type FIE allele, suggesting that FIE represses endosperm development before fertilization.
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Figure 3.
Positional Cloning of FIE.
A portion of yeast artificial chromosome CIC3D12 and an overlapping series of cosmid clones derived from this clone are shown. (-), no complementation; (+), complementation. After the name of each cosmid, the ratio of complementing fie-1 heterozygous T1 transgenic lines to total fie-1 heterozygous T1 transgenic lines is shown within parentheses. A genetic map indicating the position of FIE relative to morphological and molecular markers is shown at the bottom of the panel. ( ), number of upstream recombinant chromosomes between indicated marker and fie-1; ( ), number of downstream recombinant chromosomes between indicated marker and fie-1.
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As shown in Figure 4A, comparison of genomic and cDNA sequences revealed a gene with 13 exons in the region that complements the fie-1 mutation. When compared with the wild type, nine mutant alleles, each causing a similar mutant phenotype, were found to contain DNA sequence alterations in this gene, conclusively demonstrating that the FIE gene had been identified. For the fie-1, fie-2, and fie-3 alleles, a G residue was changed to an A residue at the 3' border of the first, third, and eighth introns, respectively (Figure 4A). This 3' intron border G residue is present in all wild-type Arabidopsis introns sequenced to date, and mutations that change the G to an A residue have been shown to disrupt the splicing reaction (Brown 1996 ). The fie-4, fie-5, fie-6, and fie-9 alleles have single-base changes that resulted in the formation of stop codons in the ninth, seventh, thirteenth, and fifth exons, respectively (Figure 4A). The fie-7 allele has a 27-bp deletion in the tenth exon, whereas the single-base change plus a two-base deletion associated with the fie-8 allele disrupted the reading frame in the seventh intron. All nine mutations are likely to represent loss-of-function alleles, which is consistent with fie being recessive to the wild type and further supports the idea that the wild-type FIE allele prevents the central cell from initiating endosperm development.
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Figure 4.
FIE Gene Structure and Sequence.
(A) Position of mutant fie alleles. Black and open boxes represent translated and untranslated sequences, respectively. The nucleotide change for mutations is shown. aa, amino acid; Stop, mutation created a stop codon.
(B) Comparison of the predicted FIE polypeptide to proteins with WD motifs encoded by the Extra sex combs (Esc) and Embryonic ectoderm development (Eed) genes. Optimal alignment of amino acid sequences was determined by using the Clustal V method (Higgins and Sharp 1989 ). WD repeats (Ng et al. 1997 ) are bracketed. Asterisks denote amino acids that comprise a potential bipartite nuclear localization signal (Jans and Hubner 1996 ). The gray bar shows the amino acids deleted in the fie-7 mutant allele. Positions of the fie-4, fie-5, fie-6, fie-7, fie-8, and fie-9 alleles are shown. Dashes were introduced to optimize alignment. Amino acids in black boxes are identical in at least two of the three Polycomb group proteins.
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As shown in Figure 4B, a search of the databases revealed that the FIE protein is related (i.e., ~40% amino acid sequence identity) to the family of WD Polycomb group proteins, which are encoded by genes such as Esc (for Extra sex combs) from Drosophila (Gutjahr et al. 1995 ; Sathe and Harte 1995 ) and Eed (for Embryonic ectoderm development) from mouse (Schumacher et al. 1996 ) and humans (Sewalt et al. 1998 ). The predicted FIE protein is a polypeptide with 369 amino acids and a molecular mass of 41 kD and displays sequence identity to Esc and Eed over its entire length. Like Esc and Eed, FIE contains seven predicted repeats of the WD motif (Ng et al. 1997 ). The WD repeats of the related heterotrimeric G protein and of insect Esc proteins are thought to form a propeller-like structure that functions in promoting protein–protein interactions (Wall et al. 1995 ; Sondek et al. 1996 ; Ng et al. 1997 ). The sequence identity displayed by the FIE Polycomb protein suggests that it also may form a similar tertiary structure that functions in protein–protein interactions. Gel blot hybridization experiments suggest that FIE is a single-copy gene in the Arabidopsis genome (data not shown).
Because fie-conferred phenotypes are detected both without fertilization (Figure 1E) and after fertilization (Figure 1I), we analyzed the pattern of FIE gene expression in immature floral buds that contain developing female gametophytes, open flowers that are undergoing fertilization, and young siliques after fertilization that have seeds with preglobular- to heart-stage embryos. RNA gel blot experiments detected a low-abundance RNA of the expected length of 1.5 kb at all of the above-mentioned stages (data not shown). As shown in Figure 5, more-sensitive reverse transcription–polymerase chain reaction (RT-PCR) experiments also detected the presence of the FIE RNA. These results indicate that the FIE gene is expressed both before and after fertilization. Moreover, we also detected FIE RNA in cauline leaves, stems, and roots (Figure 5). Thus, the FIE gene is expressed in both reproductive and vegetative tissues.
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Figure 5.
RT-PCR Analysis of FIE RNA Accumulation during Vegetative and Reproductive Development.
CL, cauline leaf; ST, stem; R, root; IF, immature floral buds; OF, open flowers; SI, young siliques. As a control, glyceraldehyde-3-phosphate dehydrogenase C (GAPC) RNA was amplified.
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DISCUSSION |
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We have found that mutations in the maternally derived fie allele cause multiple phenotypes. In the absence of fertilization, the central cell replicates and initiates endosperm development (Figure 1E). After fertilization, embryonic cell proliferation and morphogenesis are inhibited (Figure 1I). We have cloned the FIE gene and showed that it is related to WD domain Polycomb group proteins that control pattern formation during embryogenesis in insects and mammals (Figure 4B). These results reveal new biological functions for Polycomb proteins in plant reproduction.
FIE Suppresses Endosperm Development in the Female Gametophyte
The higher plant life cycle alternates between morphologically distinct gametophyte and sporophyte generations. Regulatory proteins must exist that control gametophyte-specific and sporophyte-specific developmental pathways. We have found that mutations in the FIE gene allow for replication of the central cell nucleus without fertilization. Thus, the FIE gene prevents a sporophytic pattern of development, namely, endosperm formation, from occurring in the female gametophyte before fertilization.
In Drosophila and mammals, long-term repression of homeotic genes requires the activity of Polycomb group proteins (Pirrotta 1998 ). WD Polycomb proteins play an important role in the suppression of gene transcription during insect and mammal embryo development. As diagrammed in Figure 6A, by virtue of its multiple WD domains, this class of Polycomb group proteins has the capacity to bind simultaneously to various polypeptides and thereby contribute to the assembly of multiprotein complexes (Wall et al. 1995 ; Sondek et al. 1996 ; Ng et al. 1997 ). In this way, the Drosophila WD Polycomb group protein Esc is thought to inhibit transcription of homeotic genes by two mechanisms (Gutjahr et al. 1995 ). Initially recruited by interacting, either directly or indirectly, with a zinc finger transcription factor (i.e., Hunchback), Esc may interfere with the basal transcription machinery, TFIID. In addition, Esc recruits other Polycomb group proteins that form stable complexes at specific sites within the genome and most likely package chromatin into a condensed form that prevents gene transcription.
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Figure 6.
Models for the Silencing of Gene Transcription.
The T bars represent the inhibition of transcription by mechanisms described in the text.
(A) Proteins that may interact to silence homeotic gene transcription in Drosophila. Hb, hunchback transcription factor; Pc-G, Polycomb group protein complex; Ubx, ultrabithorax homeobox gene.
(B) Proteins that may interact to silence the transcription of genes needed to initiate endosperm development in Arabidopsis. Zinc Finger, zinc finger transcription factor; Endosperm, gene(s) required for endosperm formation.
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Our results suggest that in the female gametophyte, the FIE protein functions to repress the transcription of genes required for replication of the central cell nucleus and subsequent endosperm development. Most likely, FIE, like insect and animal WD Polycomb proteins (Pirrotta 1998 ), suppresses gene transcription by forming complexes with other Polycomb group proteins (Figure 6B). We propose that when fertilization occurs, alteration of complexes containing the FIE Polycomb protein may allow initiation of endosperm gene transcription. According to this model, loss-of-function mutations in the FIE gene prevent the formation of silencing complexes in the female gametophyte, resulting in fertilization-independent central cell nuclear replication and endosperm development. Finally, it is the developing endosperm that signals the maternal integuments and ovary to form the seed coat and fruit, respectively (Ohad et al. 1996 ).
The FIE WD Polycomb protein may participate in a complex similar to that found in other organisms. The Drosophila WD Polycomb group protein physically interacts with a SET (Jenuwein et al. 1998 ) domain Polycomb group protein, Enhancer of Zeste (E(z)) (Jones et al. 1998 ; Figure 6A). Similarly, the mouse (van Lohuizen et al. 1998 ) and human (Sewalt et al. 1998 ) WD homologs have been shown to interact with their respective SET domain orthologs. In plants, the maternally derived allele of an Arabidopsis SET domain homolog, MEDEA (MEA), like FIE, has been shown to be necessary for embryo development (Grossniklaus et al. 1998 ). Moreover, we have found that central cells that inherit loss-of-function mea alleles display endosperm development without fertilization, although the phenotype is weaker than that observed with fie mutants (Kiyosue et al. 1999 ). Thus, the mechanism for establishing and maintaining Polycomb group complexes that silence gene transcription may be conserved during the evolution of insects, mammals, and plants (Figure 6B). Specifically, the molecular partnership of WD (i.e., FIE) and SET domain (i.e., MEA) Polycomb proteins may be utilized in plants to suppress precocious endosperm development in the female gametophyte. Other mutations that allow for fertilization-independent endosperm development have been isolated (Chaudhury et al. 1997 ; N. Ohad and R.L. Fischer, unpublished results) and may represent genes that encode additional proteins that participate in the formation of the silencing complex.
FIE Is Required for Proper Embryo Development
Loss-of-function mutations in the maternally derived FIE allele caused two phenotypes: fertilization-independent endosperm development (Figure 1E) and embryo abortion (Figure 1I). The relationship between these two phenotypes is not known. It is possible that the maternally derived FIE allele performs distinct functions essential for endosperm and embryo development. Alternatively, perturbations in endosperm development may be responsible for subsequent embryo abortion (Scott et al. 1998 ). Moreover, it is not understood why the paternally derived FIE allele has no effect on seed development after fertilization. Perhaps essential FIE gene expression for embryo development occurs before fertilization in the female gametophyte. Although this model cannot be ruled out, it is important to note that the FIE gene is expressed in siliques after fertilization and in vegetative tissues (Figure 5). Alternatively, the paternally derived allele may not produce active FIE protein, perhaps due to transcriptional silencing (Martienssen 1998 ).
Relation between Polycomb Proteins and Apomixis
Certain plant species display aspects of fertilization-independent reproductive development, including apomictic development of the embryo, endosperm, maternal seed coat, and fruit (Koltunow 1993 ). The fertilization-independent phenotype associated with mutations in genes, such as FIE, MEA, and FIS (for FERTILIZATION-INDEPENDENT SEED), reveals that Arabidopsis, a sexually reproducing plant, has the genetic potential for aspects of fertilization-independent reproductive development (Ohad et al. 1996 ; Chaudhury et al. 1997 ; Kiyosue et al. 1999 ). It is possible that alterations in the activity of Polycomb proteins are responsible, at least in part, for the fertilization-independent reproductive development observed in naturally occurring apomictic plant species.
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METHODS |
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Plant Material
Siliques, seedlike structures, and seeds were isolated, prepared, and photographed as described previously, except that whole-mount preparations were not stained with hematoxylin (Ohad et al. 1996 ). For counting embryonic cell number, wild-type or fertilization-independent endosperm (fie-1) heterozygous flowers were emasculated and pollinated with wild-type pollen. At the indicated time interval, seeds were harvested, cleared, and visualized with a Zeiss Axioskop microscope (Carl Zeiss, Inc., Thornwood, NY) by using Nomarski optics (Ohad et al. 1996 ). Each embryo was partitioned into optical sections, the number of cells per optical section was counted, and the total number of cells was determined by summing the values for the optical sections. Results for wild-type embryos were in good agreement with those obtained by others (Lindsey and Topping 1993 ).
Genetic Mapping
A heterozygous fie-1 mutant (Arabidopsis thaliana ecotype Landsberg erecta) was crossed as a male with a wild-type female plant (Columbia ecotype). Heterozygous progeny were crossed as males a second time to female wild-type (Columbia ecotype) plants, and 56 progeny were scored for the segregation of wild-type FIE and mutant fie-1 alleles and for molecular markers distinguishing Landsberg and Columbia chromosomes (Konieczny and Ausubel 1993 ; Bell and Ecker 1994 ). The FIE gene initially was mapped to the region between the left ends of yeast artificial chromosome clones CIC6F6 and CIC7B4. For fine structure mapping, we visually selected plants bearing recombinant chromosomes with break points between fie-1 and the downstream dominant morphological marker, axr2, that confers a dwarf phenotype (Timpte et al. 1994 ).
A fie-1 heterozygote (Landsberg erecta ecotype) was crossed as a male with female (Columbia ecotype) dwarf axr2 homozygotes. Dwarf F1 progeny that displayed 50% seed abortion in self-pollinated siliques (i.e., heterozygous for fie-1 and axr2) were self-pollinated. Three hundred F2 recombinant plants (i.e., normal-sized plants with 50% aborted seed in self-pollinated siliques) were identified among 15,600 nonrecombinant dwarf F2 progeny and used to map the fie-1 mutation relative to downstream molecular markers (Figure 3). We also visually selected plants bearing recombinant chromosomes with break points between fie-1 and the upstream morphological marker emb29. Self-pollinated siliques from heterozygous emb29 plants display 25% embryo abortion (Meinke 1985 ). A fie-1 heterozygote (Landsberg erecta ecotype) was crossed as a male with female (Columbia ecotype) emb29 heterozygotes. F1 progeny that displayed 75% seed abortion in self-pollinated siliques (i.e., heterozygous for fie-1 and emb29) were self-pollinated. Thirty-three recombinant F2 plants (i.e., self-pollinated siliques displayed 25 or 50% aborted seed) were identified among 3586 nonrecombinant (i.e., self-pollinated siliques displayed 75% aborted seed) F2 progeny, and they were used to map the fie-1 mutation relative to upstream molecular markers (Figure 3).
Genetic Complementation
A plant transformation-competent cosmid library of yeast artificial chromosome CIC3D12 (Columbia ecotype) was made in vector pCLD04541, a cosmid contig was constructed, and Agrobacterium tumefaciens–mediated transformation of fie-1 heterozygous plants (Landsberg erecta ecotype) was performed as described previously (Century et al. 1997 ). Siliques from kanamycin-resistant transgenic plants were harvested 10 days after self-pollination and were dissected, and the number of normal and aborted seeds was counted. Heterozygous fie T1 lines displaying 50% seed abortion (e.g., 58 normal/74 aborted 1:1;  2 = 1.94; P > 0.24) in self-pollinated siliques indicated lack of genetic complementation. T1 lines displaying 25% seed abortion (e.g., 97 normal/34 aborted 3:1; 2 = 0.064; P > 0.86) in self-pollinated siliques suggested that an unlinked transgenic FIE allele had complemented the mutant fie-1 allele.
To rule out the possibility that the observed 25% seed abortion in T1 plants was due to T-DNA disruption of a gene required for embryo viability (Meinke 1985 ), a representative T1 plant, heterozygous for fie-1 and hemizygous for cosmid GM15 (Figure 3), was self-pollinated, and the extent of T3 seed abortion in self-pollinated siliques from 171 T2 plants was determined. We observed a 7:3:2 segregation ratio (105:45:21; 2 = 2.4; P > 0.3) of T2 plants displaying 0:25:50% T3 seed abortion. These results are consistent with complementation of the mutant allele with the transgenic wild-type allele in the female gametophyte.
For lines homozygous for both the mutant fie-1 allele and the transgenic wild-type FIE allele on cosmid GM15 (Figure 3), 14 self-pollinated siliques containing 814 seeds displayed 0% seed abortion. After fertilization was prevented, all ovules (n = 48) displayed a central cell with a single nucleus. After fertilization was prevented in control fie-1 heterozygous plants, 44% (n = 110) of the ovules had central cells with two or more nuclei.
DNA Sequencing
Wild-type genomic DNA sequences were determined by Lark Technologies, Inc. (Houston, TX), using subcloned DNA fragments from cosmid clones that genetically complemented the fie-1 mutation (see above). Because it was not possible to obtain homozygous mutant fie plants, sequence alterations associated with mutant alleles were obtained as follows. To sequence the fie-1 mutant allele, we constructed a cosmid library using DNA from heterozygous Landsberg erecta ecotype fie-1/Columbia ecotype FIE+ plants. A cosmid clone was selected that contained a Landsberg erecta–specific polymorphism and the mutant fie-1 Polycomb gene. The fie-1 mutation was identified by comparing this sequence with that of the wild type (Landsberg erecta ecotype). The mutated sequence for the fie-1 allele was confirmed, and the fie-2, fie-3, fie-4, fie-5, fie-6, fie-7, fie-8, and fie-9 alleles were identified using a similar procedure in which heterozygous plant DNAs were polymerase chain reaction (PCR)-amplified, subcloned, and sequenced. Mutated sequences were confirmed within the genomes of each allele by converting them into a codominant cleaved amplified polymorphic sequence (Konieczny and Ausubel 1993 ).
FIE cDNA clones were isolated from a floral cDNA library (Weigel et al. 1992 ). The labeled probe, extending from the fourth exon to the 12th exon of FIE, was amplified from genomic DNA by PCR. Primers for the amplification reactions were 5'-TCCATCGACAGACATGGCTG-3' and 5'-CTCGCAAATGTGCAGAGTCT TGTG-3'. Seven FIE cDNA clones were identified among 200,000 plaques screened and were sequenced at the University of California, Berkeley, DNA Sequencing Facility. To obtain 5' cDNA sequences, we performed 5' rapid amplification of cDNA ends (RACE) by using the 5' RACE system, as described by the manufacturer (Life Technologies, Inc., Gaithersburg, MD). The FIE cDNA sequence is available as GenBank accession number
AF129516.
RNA Analysis
Cauline leaf, stem, root, and flower bud tissue containing stages 0 to 12 (Smyth et al. 1990 ) flowers and open flowers (stage 13) was harvested, and total RNA was isolated using the TRIZOL reagent as described by the manufacturer (Life Technologies, Inc.) and further purified by using the RNeasy minikit (Qiagen, Inc., Chatsworth, CA). Young silique (from preglobular- to late-heart-stage embryos) RNA was isolated using a modified hot borate extraction method (Wilkins and Smart 1996 ). Reverse transcription–PCRs (RT-PCRs) were performed using a RETROscript kit (Ambion, Inc., Austin, TX) and contained 2 µg of total RNA as starting material. Primers used to amplify FIE RNA were 5'-CGAGTCAT TGACGTCAACAGTG-3' and 5'-TCC-ATCGACAGACATGGCTG-3'. Primers used to amplify control GAPC (for glyceraldehyde-3-phosphate dehydrogenase C) RNA (Shih et al. 1991 ) were 5'-CACT TGAAGGGTGGTGCCAAG-3' and 5'-CCTGT T-GTCGCCAACGAAGTC-3'.
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FOOTNOTES |
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1 These authors contributed equally to this work. 
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ACKNOWLEDGMENTS |
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We thank Barbara Rotz for supplying excellent greenhouse services. We thank Karen Century, Douglas Dahlbeck, and Brian Staskawicz for providing us with cosmid clones and helpful advice on map-based cloning. We thank the Arabidopsis Biological Resource Center (Columbus, Ohio) for providing a floral cDNA library, yeast artificial chromosome libraries, and the emb29 and axr2 lines. We gratefully acknowledge support from Ceres, Inc. (Malibu, CA) for DNA sequencing. This work was funded by a grant to R.L.F. from the National Research Institute Competitive Grants Program of the U.S. Department of Agriculture (Grant No. 97-35304-4941), and a grant to N.O. from the Israel Science Foundation (Grant No. 677/97-1). R.Y. is a Department of Energy–Biosciences Research Fellow of the Life Sciences Research Foundation.
Received December 8, 1998; accepted January 26, 1999.
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NOTE ADDED IN PROOF |
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While this article was under review, Luo et al. (Luo, M., Bilodeau, P., Koltunow, A., Dennis, E.S., Peacock, W.J., and Chaudhury, A.M. [1999]. Genes controlling fertilization-independent seed development in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96, 296–301) showed that the FERTILIZATION-INDEPENDENT SEED2 (FIS2) gene encodes a C2H2 zinc-finger transcription factor and that the fertilization-independent seed1 (fis1) mutation is a medea allele.
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ABSTRACT
INTRODUCTION