Identification of transcription-factor genes expressed in the Arabidopsis female gametophyte

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

Many signaling pathways regulate seed size through the development of endosperm and maternal tissues, which ultimately results in a range of variations in seed size or weight. Seed size can be determined through the development of zygotic tissues (endosperm and embryo) and maternal ovules. In addition, in some species such as rice, seed size is largely determined by husk growth. Transcription regulator factors are responsible for enhancing cell growth in the maternal ovule, resulting in seed growth. Phytohormones induce significant effects on entire features of growth and development of plants and also regulate seed size. Moreover, the vegetative parts are the major source of nutrients, including the majority of carbon and nitrogen-containing molecules for the reproductive part to control seed size. There is a need to increase the size of seeds without affecting the number of seeds in plants through conventional breeding programs to improve grain yield. In the past decades, many important genetic factors affecting seed size and yield have been identified and studied. These important factors constitute dynamic regulatory networks governing the seed size in response to environmental stimuli. In this review, we summarized recent advances regarding the molecular factors regulating seed size in Arabidopsis and other crops, followed by discussions on strategies to comprehend crops' genetic and molecular aspects in balancing seed size and yield.

Isolation of gametes and zygotes from Setaria viridis

Setaria viridis, the wild ancestor of foxtail millet (Setaria italica), is an effective model plant for larger C₄ crops because S. viridis has several desirable traits, such as short generation time, prolific seed production and a small genome size. These advantages are well suited for investigating molecular mechanisms in angiosperms, especially C₄ crop species. Here, we report a procedure for isolating gametes and zygotes from S. viridis flowers. To isolate egg cells, ovaries were harvested from unpollinated mature flowers and cut transversely, which allowed direct access to the embryo sac. Thereafter, an egg cell was released from the cut end of the basal portion of the dissected ovary. To isolate sperm cells, pollen grains released from anthers were immersed in a mannitol solution, resulting in pollen-grain bursting, which released sperm cells. Additionally, S. viridis zygotes were successfully isolated from freshly pollinated flowers. Isolated zygotes cultured in a liquid medium developed into globular-like embryos and cell masses. Thus, isolated S. viridis gametes, zygotes and embryos are attainable for detailed observations and investigations of fertilization and developmental events in angiosperms.

The SEEL motif and members of the MYB-related REVEILLE transcription factor family are important for the expression of LORELEI in the synergid cells of the Arabidopsis female gametophyte

Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a putative GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs ('TAATATCT') in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of cis-regulatory elements and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells.

The identification of type I MADS box genes as the upstream activators of an endosperm-specific invertase inhibitor in Arabidopsis

BACKGROUND

Nuclear endosperm development is a common mechanism among Angiosperms, including Arabidopsis. During nuclear development, the endosperm nuclei divide rapidly after fertilization without cytokinesis to enter the syncytial phase, which is then followed by the cellularized phase. The endosperm can be divided into three spatial domains with distinct functions: the micropylar, peripheral, and chalazal domains. Previously, we identified two putative small invertase inhibitors, InvINH1 and InvINH2, that are specifically expressed in the micropylar region of the syncytial endosperm. In addition, ectopically expressing InvINH1 in the cellularized endosperm led to a reduction in embryo growth rate. However, it is not clear what are the upstream regulators responsible for the specific expression of InvINHs in the syncytial endosperm.

RESULTS

Using protoplast transient expression system, we discovered that a group of type I MADS box transcription factors can form dimers to activate InvINH1 promoter. Promoter deletion assays carried out in the protoplast system revealed the presence of an enhancer region in InvINH1 promoter, which contains several consensus cis-elements for the MADS box proteins. Using promoter deletion assay in planta, we further demonstrated that this enhancer region is required for InvINH1 expression in the syncytial endosperm. One of the MADS box genes, AGL62, is a key transcription factor required for syncytial endosperm development. Using promoter-GFP reporter assay, we demonstrated that InvINH1 and InvINH2 are not expressed in agl62 mutant seeds. Collectively, our data supports the role of AGL62 and other type I MADS box genes as the upstream activators of InvINHs expression in the syncytial endosperm.

CONCLUSIONS

Our findings revealed several type I MADS box genes that are responsible for activating InvINH1 in the syncytial endosperm, which in turn regulates embryo growth rate during early stage of seed development.

ABA signalling promotes cell totipotency in the shoot apex of germinating embryos

Somatic embryogenesis (SE) is a type of induced cell totipotency where embryos develop from vegetative tissues of the plant instead of from gamete fusion after fertilization. SE can be induced in vitro by exposing explants to growth regulators, such as the auxinic herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). The plant hormone abscisic acid (ABA) has been proposed to be a downstream signalling component at the intersection between 2,4-D- and stress-induced SE, but it is not known how these pathways interact to induce cell totipotency. Here we show that 2,4-D-induced SE from the shoot apex of germinating Arabidopsis thaliana seeds is characterized by transcriptional maintenance of an ABA-dependent seed maturation pathway. Molecular-genetic analysis of Arabidopsis mutants revealed a role for ABA in promoting SE at three different levels: ABA biosynthesis, ABA receptor complex signalling, and ABA-mediated transcription, with essential roles for the ABSCISIC ACID INSENSITIVE 3 (ABI3) and ABI4 transcription factors. Our data suggest that the ability of mature Arabidopsis embryos to maintain the ABA seed maturation environment is an important first step in establishing competence for auxin-induced cell totipotency. This finding provides further support for the role of ABA in directing processes other than abiotic stress response.

Nuclear DNA replicates during zygote development in Arabidopsis and Torenia fournieri

The progression of the cell cycle is continuous in most cells, but gametes (sperm and egg cells) exhibit an arrest of the cell cycle to await fertilization to form a zygote, which then continues through the subsequent phases to complete cell division. The phase in which gametes of flowering plants arrest has been a matter of debate, since different phases have been reported for the gametes of different species. In this study, we reassessed the phase of cell-cycle arrest in the gametes of two species, Arabidopsis (Arabidopsis thaliana) and Torenia fournieri. We first showed that 4', 6-diamidino-2-phenylindole staining was not feasible to detect changes in gametic nuclear DNA in T. fournieri. Next, using 5-ethynyl-2'-deoxyuridine (EdU) staining that detects DNA replication by labeling the EdU absorbed by deoxyribonucleic acid, we found that the replication of nuclear DNA did not occur during gamete development but during zygote development, revealing that the gametes of these species have a haploid nuclear DNA content before fertilization. We thus propose that gametes in the G1 phase participate in the fertilization event in Arabidopsis and T. fournieri.

Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes

BACKGROUND

Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect.

RESULTS

To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization.

CONCLUSIONS

Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.

Gene Expression and Genome Editing Systems by Direct Delivery of Macromolecules Into Rice Egg Cells and Zygotes

Polyethylene glycol calcium (PEG-Ca2+)-mediated transfection allows rapid and efficient examination to analyze diverse cellular functions of genes of interest. In plant cells, macromolecules, such as DNA, RNA and protein, are delivered into protoplasts derived from somatic tissues or calli via PEG-Ca2+ transfection. To broaden and develop the scope of investigations using plant gametes and zygotes, a procedure for direct delivery of macromolecules into these cells has recently been established using PEG-Ca2+ transfection. This PEG-Ca2+-mediated delivery into rice egg cells/zygotes consists of four microtechniques, (i) isolation of gametes, (ii) production of zygotes by electrofusion of gametes, (iii) PEG-Ca2+-mediated delivery of macromolecules into isolated egg cells or produced zygotes, and (iv) culture and subsequent analyses of the transfected egg cells/zygotes. Because the full protocol for microtechniques (i) and (ii) have already been reported in Toda et al., 2016 , microtechniques (iii) and (iv) are mainly described in this protocol.

Development of a Heat-Inducible Gene Expression System Using Female Gametophytes of Arabidopsis thaliana

Female gametophyte (FG) is crucial for reproduction in flowering plants. Arabidopsis thaliana produces Polygonum-type FGs, which consist of an egg cell, two synergid cells, three antipodal cells and a central cell. Egg cell and central cell are the two female gametes that give rise to the embryo and surrounding endosperm, respectively, after fertilization. During the development of a FG, a single megaspore produced by meiosis undergoes three rounds of mitosis to produce an eight-nucleate cell. A seven-celled FG is formed after cellularization. The central cell initially contains two polar nuclei that fuse during female gametogenesis to form the secondary nucleus. In this study, we developed a gene induction system for analyzing the functions of various genes in developing Arabidopsis FGs. This system allows transgene expression in developing FGs using the heat-inducible Cre-loxP recombination system and FG-specific embryo sac 2 (ES2) promoter. Efficient gene induction was achieved in FGs by incubating flower buds and isolated pistils at 35�C for short periods of time (1-5 min). Gene induction was also induced in developing FGs by heat treatment of isolated ovules using the infrared laser-evoked gene operator (IR-LEGO) system. Expression of a dominant-negative mutant of Sad1/UNC84 (SUN) proteins in developing FGs using the gene induction system developed in this study caused defects in polar nuclear fusion, indicating the roles of SUN proteins in this process. This strategy represents a new tool for analyzing the functions of genes in FG development and FG functions.

Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis

Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatial-temporal activity of the NRPD1-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternal NRPD1 allele in the endosperm or seed coat. A group of maternally expressed NRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by the NRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales)

Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.

Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm

Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products, and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). Here, we mapped in vivo binding sites of O2 in B73 endosperm and compared the results with genes differentially expressed in B73 and B73o2 We identified 186 putative direct O2 targets and 1677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets revealed at least two distinct modes of O2-mediated gene activation. Two O2-activated genes, bZIP17 and NAKED ENDOSPERM2 (NKD2), encode transcription factors, which can in turn coactivate other O2 network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.

FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development

Early endosperm development presents a unique system in which to uncover epigenetic regulatory mechanisms because the contributing maternal and paternal genomes possess differential epigenetic modifications. In Arabidopsis (Arabidopsis thaliana), the initiation of endosperm coenocytic growth upon fertilization and the transition to endosperm cellularization are regulated by the FERTILIZATION-INDEPENDENT SEED (FIS)-Polycomb Repressive Complex 2 (PRC2), a putative H3K27 methyltransferase. Here, we address the possible role of the FIS-PRC2 complex in regulating the type I MADS-box gene family, which has been shown previously to regulate early endosperm development. We show that a subclass of type I MADS-box genes (C2 genes) was expressed in distinct domains of the coenocytic endosperm in wild-type seeds. Furthermore, the C2 genes were mostly up-regulated biallelically during the extended coenocytic phase of endosperm development in the FIS-PRC2 mutant background. Using allele-specific expression analysis, we also identified a small subset of C2 genes subjected to FIS-PRC2-dependent maternal or FIS-PRC2-independent paternal imprinting. Our data support a dual role for the FIS-PRC2 complex in the regulation of C2 type I MADS-box genes, as evidenced by a generalized role in the repression of gene expression at both alleles associated with endosperm cellularization and a specialized role in silencing the maternal allele of imprinted genes.

Prolonged Expression of a Putative Invertase Inhibitor in Micropylar Endosperm Suppressed Embryo Growth in Arabidopsis

Proper seed development requires coordinated growth among the three genetically distinct components, the embryo, the endosperm, and the seed coat. In Arabidopsis, embryo growth rate accelerates after endosperm cellularization, which requires a chromatin-remodeling complex, the FIS2-Polycomb Repressive Complex 2 (PRC2). After cellularization, the endosperm ceases to grow and is eventually absorbed by the embryo. This sequential growth pattern displayed by the endosperm and the embryo suggests a possibility that the supply of sugar might be shifted from the endosperm to the embryo upon endosperm cellularization. Since invertases and invertase inhibitors play an important role in sugar partition, we investigated their expression pattern during early stages of seed development in Arabidopsis. Two putative invertase inhibitors (InvINH1 and InvINH2) were identified as being preferentially expressed in the micropylar endosperm that surrounds the embryo. After endosperm cellularization, InvINH1 and InvINH2 were down-regulated in a FIS2-dependent manner. We hypothesized that FIS2-PRC2 complex either directly or indirectly represses InvINH1 and InvINH2 to increase invertase activity around the embryo, making more hexose available to support the accelerated embryo growth after endosperm cellularization. In support of our hypothesis, embryo growth was delayed in transgenic lines that ectopically expressed InvINH1 in the cellularized endosperm. Our data suggested a novel mechanism for the FIS2-PRC2 complex to control embryo growth rate via the regulation of invertase activity in the endosperm.

An Arabidopsis divergent pumilio protein, APUM24, is essential for embryogenesis and required for faithful pre-rRNA processing

Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization. Additionally, the mutant embryos displayed defects in cell patterning from pro-embryo through globular stages. The mutant embryos were marked by altered auxin maxima, which were substantiated by the mislocalization of PIN1 and PIN7 transporters in the defective embryos. Homozygous apum24 callus accumulates rRNA processing intermediates, including uridylated and adenylated 5.8S and 25S rRNA precursors. An RNA-protein interaction assay showed that the histidine-tagged recombinant APUM24 binds RNAin vitro with no apparent specificity. Overall, our results demonstrated that APUM24 is required for rRNA processing and early embryogenesis in Arabidopsis.

Development of gene expression system in egg cells and zygotes isolated from rice and maize

Polyethylene glycol calcium (PEG-Ca2+) transfection-mediated analysis allows rapid and efficient examination of gene function. To investigate the diverse cellular functions of genes of interest in plant cells, macromolecules, such as DNA, RNA, and proteins, are delivered into protoplasts prepared from somatic tissues or calli using a PEG-Ca2+ transfection procedure. To take advantage of this macromolecule delivery system in the reproductive and developmental biology of angiosperms, this study established a PEG-Ca2+ transfection system with isolated egg cells and zygotes. The conditions for PEG and plasmid DNA concentrations for transfection of rice egg cells were first addressed, and ~30% of PEG-Ca2+-transfected egg cells showed exogenous and transient expressions of fluorescent proteins from plasmid DNA delivered into the cells. Interestingly, a dual expression of two different fluorescent proteins in the same egg cell using two kinds of plasmid DNAs was also observed. For PEG-Ca2+ transfection with maize zygotes, ~80% of zygotes showed expression of GFP proteins from plasmid DNA. Importantly, PEG-transfected zygotes developed normally into cell masses and mature plants. These results suggest that the present PEG-Ca2+-mediated transient expression system provides a novel and effective platform for expressing and analyzing genes of interest in egg cells and zygotes. Moreover, combined with the CRISPR/Cas9 approach, the present transient expression system in zygotes will become a powerful and alternative tool for the preparation of gene-edited plants.

Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils

BACKGROUND

In rice, the pistil is the female reproductive organ, and it consists of two stigmas and an ovary. The stigma is capable of receiving pollen grains and guiding pollen tube growth. The ovary holds the embryo sac, which is fertilized with male gametes to produce seed. However, little is known about the gene function and regulatory networks during these processes in rice.

RESULTS

Here, using the RNA-Seq technique, we identified 3531 stigma-preferential genes and 703 stigma-specific genes within the rice pistils, and we verified 13 stigma-specific genes via qRT-PCR and in situ hybridization. The GO analysis showed that the transport-, localization-, membrane-, communication-, and pollination-related genes were significantly enriched in the stigma. Additionally, to identify the embryo sac-preferential/specific genes within the pistils, we compared a wild-type ovary with a mutant dst (defective stigma) ovary and found that 385 genes were down-regulated in dst. Among these genes, 122 exhibited an ovary-specific expression pattern and are thought to be embryo sac-preferential/specific genes within the pistils. Most of them were preferentially expressed, while 14 of them were specifically expressed in the pistil. Moreover, the rice homologs of some Arabidopsis embryo sac-specific genes, which played essential roles during sexual reproduction, were down-regulated in dst. Additionally, we identified 102 novel protein-coding genes, and 6 of them exhibited differences between the stigma and ovary in rice as determined using RT-PCR.

CONCLUSIONS

According to these rice ovary comparisons, numerous genes were preferentially or specifically expressed in the stigma, suggesting that they were involved in stigma development or pollination. The GO analysis indicated that a dry rice stigma might primarily perform its function through the cell membrane, which was different from the wet stigma of other species. Moreover, many embryo sac-preferential/specific genes within the pistils were identified and may be expressed in female rice gametophytes, implying that these genes might participate in the process of female gametophyte specialization and fertilization. Therefore, we provide the gene information for investigating the gene function and regulatory networks during female gametophyte development and fertilization. In addition, these novel genes are valuable for the supplementation and perfection of the existing transcriptome in rice, which provides an effective method of detecting novel rice genes.

RWP-RK domain-containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis

The formation of gametes is a prerequisite for any sexually reproducing organism in order to complete its life cycle. In plants, female gametes are formed in a multicellular tissue, the female gametophyte or embryo sac. Although the events leading to the formation of the female gametophyte have been morphologically characterized, the molecular control of embryo sac development remains elusive. We used single and double mutants as well as cell-specific marker lines to characterize a novel class of gene regulators in Arabidopsis thaliana, the RWP-RK domain-containing (RKD) transcription factors. Morphological and histological analyses were conducted using confocal laser scanning and differential interference contrast microscopy. Gene expression and transcriptome analyses were performed using quantitative reverse transcription-PCR and RNA sequencing, respectively. Our results showed that RKD genes are expressed during distinct stages of embryo sac development. Morphological analysis of the mutants revealed severe distortions in gametophyte polarity and cell differentiation. Transcriptome analysis revealed changes in the expression of several gametophyte-specific gene families (RKD2 and RKD3) and ovule development-specific genes (RKD3), and identified pleiotropic effects on phytohormone pathways (RKD5). Our data provide novel insight into the regulatory control of female gametophyte development. RKDs are involved in the control of cell differentiation and are required for normal gametophytic development.

Patterning the Female Gametophyte of Flowering Plants

Intracellular and intercellular mechanisms govern the differentiation of female gametophytic cells.

Cytoskeleton dynamics control the first asymmetric cell division in Arabidopsis zygote

The asymmetric cell division of the zygote is the initial and crucial developmental step in most multicellular organisms. In flowering plants, whether zygote polarity is inherited from the preexisting organization in the egg cell or reestablished after fertilization has remained elusive. How dynamically the intracellular organization is generated during zygote polarization is also unknown. Here, we used a live-cell imaging system with Arabidopsis zygotes to visualize the dynamics of the major elements of the cytoskeleton, microtubules (MTs), and actin filaments (F-actins), during the entire process of zygote polarization. By combining image analysis and pharmacological experiments using specific inhibitors of the cytoskeleton, we found features related to zygote polarization. The preexisting alignment of MTs and F-actin in the egg cell is lost on fertilization. Then, MTs organize into a transverse ring defining the zygote subapical region and driving cell outgrowth in the apical direction. F-actin forms an apical cap and longitudinal arrays and is required to position the nucleus to the apical region of the zygote, setting the plane of the first asymmetrical division. Our findings show that, in flowering plants, the preexisting cytoskeletal patterns in the egg cell are lost on fertilization and that the zygote reorients the cytoskeletons to perform directional cell elongation and polar nuclear migration.

Marchantia MpRKD Regulates the Gametophyte-Sporophyte Transition by Keeping Egg Cells Quiescent in the Absence of Fertilization

Unlike in animals, the life cycle of land plants alternates between two multicellular generations, the haploid gametophyte and the diploid sporophyte [1]. Gamete differentiation initiates the transition from the gametophyte to the sporophyte generation and, upon maturation, the egg cell establishes a quiescent state that is maintained until fertilization. This quiescence represents a hallmark of the gametophyte-sporophyte transition. The underlying molecular mechanisms are complex and best characterized in the flowering plant Arabidopsis thaliana [2-4]. However, only few genes with egg cell-specific expression or defects have been identified [5-10]. Intriguingly, ectopic expression of members of a clade of RWP-RK domain (RKD)-containing transcription factors, which are absent from animal genomes [11-13], can induce an egg cell-like transcriptome in sporophytic cells of A. thaliana. Yet, to date, loss-of-function experiments have not produced phenotypes affecting the egg cell, likely due to genetic redundancy and/or cross-regulation among the five RKD genes of A. thaliana [10]. To reduce genetic complexity, we explored the genome of Marchantia polymorpha, a liverwort belonging to the basal lineage of extant land plants [14-17]. Based on sequence homology, we identified a single M. polymorpha RKD gene, MpRKD, which is orthologous to all five A. thaliana RKD genes. Analysis of the MpRKD expression pattern and characterization of lines with reduced MpRKD activity indicate that it functions as a regulator of gametophyte development and the gametophyte-sporophyte transition. In particular, MpRKD is required to establish and/or maintain the quiescent state of the egg cell in the absence of fertilization.

Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress

Drought stress has a negative impact on crop yield. Thus, understanding the molecular mechanisms responsible for plant drought stress tolerance is essential for improving this beneficial trait in crops. In the current study, a transcriptional analysis was conducted of gene regulatory networks in roots of soil-grown Arabidopsis plants in response to a drought stress treatment. A microarray analysis of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7, and 9 days. Results indicated that the expression of many drought stress-responsive genes and abscisic acid biosynthesis-related genes was differentially regulated in roots and shoots from days 3 to 9. The expression of cellular and metabolic process-related genes was up-regulated at an earlier time-point in roots than in shoots. In this regard, the expression of genes involved in oxidative signaling, chromatin structure, and cell wall modification also increased significantly in roots compared to shoots. Moreover, the increased expression of genes involved in the transport of amino acids and other solutes; including malate, iron, and sulfur, was observed in roots during the early time points following the initiation of the drought stress. These data suggest that plants may utilize these signaling channels and metabolic adjustments as adaptive responses in the early stages of a drought stress. Collectively, the results of the present study increases our understanding of the differences pertaining to the molecular mechanisms occurring in roots vs. shoots in response to a drought stress. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with increased drought tolerance.

Role of AINTEGUMENTA-like gene NtANTL in the regulation of tobacco organ growth

The Nicotiana tabacum AINTEGUMENTA-like gene (NtANTL), encoding one of AP2/ERF transcription factors, is a putative ortholog of the AtANT gene from Arabidopsis thaliana. In wild-type tobacco plants, the NtANTL gene was expressed in the actively dividing young flowers, shoot apices, and calluses, while the level of its mRNA increased considerably after treatment with exogenous 6-benzylaminopurine, indoleacetic acid and 24-epibrassinolide. We found a positive correlation among the expression levels of NtANTL, cyclin NtCYCD3;1 and cyclin-dependent kinase NtCDKB1-1 genes, suggesting possible molecular links between AINTEGUMENTA and cell cycle regulators in tobacco plants. However, no correlation was observed between NtANTL, NtCYCD3;1 and NtCDKB1-1 expression levels in response to NaCl and ABA. These observations indicate that the transcription factor NtANTL was not involved in the regulation of the cellular response to salinity nor did it affect the expression of NtCYCD3;1 and NtCDKB1-1 when tobacco plants were exposed to salt stress and ABA. In addition, we generated transgenic tobacco plants with both up-regulated and down-regulated expression of the NtANTL gene. Constitutive expression of the NtANTL gene contributed to an increase in the size of leaves and corolla of transgenic plants. Transgenic plants with reduced expression of the NtANTL gene had smaller leaves, flowers and stems, but showed a compensatory increase in the cell size of leaves and flowers. The results show the significance of the NtANTL gene for the control of organ growth by both cell division and expansion in tobacco plants.

Patterning of the angiosperm female gametophyte through the prism of theoretical paradigms

The FG (female gametophyte) of flowering plants (angiosperms) is a simple highly polar structure composed of only a few cell types. The FG develops from a single cell through mitotic divisions to generate, depending on the species, four to 16 nuclei in a syncytium. These nuclei are then partitioned into three or four distinct cell types. The mechanisms underlying the specification of the nuclei in the FG has been a focus of research over the last decade. Nevertheless, we are far from understanding the patterning mechanisms that govern cell specification. Although some results were previously interpreted in terms of static positional information, several lines of evidence now show that local interactions are important. In the present article, we revisit the available data on developmental mutants and cell fate markers in the light of theoretical frameworks for biological patterning. We argue that a further dissection of the mechanisms may be impeded by the combinatorial and dynamical nature of developmental cues. However, accounting for these properties of developing systems is necessary to disentangle the diversity of the phenotypic manifestations of the underlying molecular interactions.

Correlation between a loss of auxin signaling and a loss of proliferation in maize antipodal cells

The plant life cycle alternates between two genetically active generations: the diploid sporophyte and the haploid gametophyte. In angiosperms the gametophytes are sexually dimorphic and consist of only a few cells. The female gametophyte, or embryo sac, is comprised of four cell types: two synergids, an egg cell, a central cell, and a variable number of antipodal cells. In some species the antipodal cells are indistinct and fail to proliferate, so many aspects of antipodal cell function and development have been unclear. In maize and many other grasses, the antipodal cells proliferate to produce a highly distinct cluster at the chalazal end of the embryo sac that persists at the apex of the endosperm after fertilization. The antipodal cells are a site of auxin accumulation in the maize embryo sac. Analysis of different families of genes involved in auxin biosynthesis, distribution, and signaling for expression in the embryo sac demonstrates that all steps are expressed within the embryo sac. In contrast to auxin signaling, cytokinin signaling is absent in the embryo sac and instead occurs adjacent to but outside of the antipodal cells. Mutant analysis shows a correlation between a loss of auxin signaling and a loss of proliferation of the antipodal cells. The leaf polarity mutant Laxmidrib1 causes a lack of antipodal cell proliferation coupled with a loss of DR5 and PIN1a expression in the antipodal cells.

Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes

BACKGROUND

Plant gametophytes play central roles in sexual reproduction. A hallmark of the plant life cycle is that gene expression is required in the haploid gametophytes. Consequently, many mutant phenotypes are expressed in this phase.

RESULTS

We perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for annotated genes in both gametophytes, and novel transcripts were identified from de novo assembly of RNA-seq reads. Transposon-related transcripts are present in high levels in both gametophytes, suggesting a connection between gamete production and transposon expression in maize not previously identified in any female gametophytes. Two classes of small signaling proteins and several transcription factor gene families are enriched in gametophyte transcriptomes. Expression patterns of maize genes with duplicates in subgenome 1 and subgenome 2 indicate that pollen-expressed genes in subgenome 2 are retained at a higher rate than subgenome 2 genes with other expression patterns. Analysis of available insertion mutant collections shows a statistically significant deficit in insertions in gametophyte-expressed genes.

CONCLUSIONS

This analysis, the first RNA-seq study to compare both gametophytes in a monocot, identifies maize gametophyte functions, gametophyte expression of transposon-related sequences, and unannotated, novel transcripts. Reduced recovery of mutations in gametophyte-expressed genes is supporting evidence for their function in the gametophytes. Expression patterns of extant, duplicated maize genes reveals that selective pressures based on male gametophytic function have likely had a disproportionate effect on plant genomes.

Imaging sexual reproduction in Arabidopsis using fluorescent markers

Sexual reproduction in higher plants is a stealth process as most events occur within tissues protected by multiple surrounding cell layers. Female gametes are produced inside the embryo sac surrounded by layers of ovule integument cells. Upon double fertilization, two male gametes are released at one end of the embryo sac and migrate towards their respective female partner to generate the embryo and its feeding tissue, the endosperm, within a seed. Since the early discovery of plant reproduction, advances in microscopy have contributed enormously to our understanding of this process (Faure and Dumas, Plant Physiol 125:102-104, 2001). Recently, live imaging of double fertilization has been possible using a set of fluorescent markers for gametes in Arabidopsis. The following chapter will detail protocols to study male and female gametogenesis and double fertilization in living tissues using fluorescent markers.

DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis

Analysis of genome-scale gene networks (GNs) using large-scale gene expression data provides unprecedented opportunities to uncover gene interactions and regulatory networks involved in various biological processes and developmental programs, leading to accelerated discovery of novel knowledge of various biological processes, pathways and systems. The widely used context likelihood of relatedness (CLR) method based on the mutual information (MI) for scoring the similarity of gene pairs is one of the accurate methods currently available for inferring GNs. However, the MI-based reverse engineering method can achieve satisfactory performance only when sample size exceeds one hundred. This in turn limits their applications for GN construction from expression data set with small sample size. We developed a high performance web server, DeGNServer, to reverse engineering and decipher genome-scale networks. It extended the CLR method by integration of different correlation methods that are suitable for analyzing data sets ranging from moderate to large scale such as expression profiles with tens to hundreds of microarray hybridizations, and implemented all analysis algorithms using parallel computing techniques to infer gene-gene association at extraordinary speed. In addition, we integrated the SNBuilder and GeNa algorithms for subnetwork extraction and functional module discovery. DeGNServer is publicly and freely available online.

MYB64 and MYB119 are required for cellularization and differentiation during female gametogenesis in Arabidopsis thaliana

In angiosperms, the egg cell forms within the multicellular, haploid female gametophyte. Female gametophyte and egg cell development occurs through a unique process in which a haploid spore initially undergoes several rounds of synchronous nuclear divisions without cytokinesis, resulting in a single cell containing multiple nuclei. The developing gametophyte then forms cell walls (cellularization) and the resulting cells differentiate to generate the egg cell and several accessory cells. The switch between free nuclear divisions and cellularization-differentiation occurs during developmental stage FG5 in Arabidopsis, and we refer to it as the FG5 transition. The molecular regulators that initiate the FG5 transition during female gametophyte development are unknown. In this study, we show using mutant analysis that two closely related MYB transcription factors, MYB64 and MYB119, act redundantly to promote this transition. MYB64 and MYB119 are expressed during the FG5 transition, and most myb64 myb119 double mutant gametophytes fail to initiate the FG5 transition, resulting in uncellularized gametophytes with supernumerary nuclei. Analysis of cell-specific markers in myb64 myb119 gametophytes that do cellularize suggests that gametophytic polarity and differentiation are also affected. We also show using multiple-mutant analysis that MYB119 expression is regulated by the histidine kinase CKI1, the primary activator of two-component signaling (TCS) during female gametophyte development. Our data establish a molecular pathway regulating the FG5 transition and implicates CKI1-dependent TCS in the promotion of cellularization, differentiation, and gamete specification during female gametogenesis.

Female gamete formation in angiosperms occurs through a unique process in which a haploid spore initially undergoes a series of free nuclear divisions without cytokinesis, resulting in a single cell containing multiple nuclei. The nuclei then differentiate and are partitioned with cell walls to generate the egg cell and several accessory cells. The molecular regulators that initiate the switch between free nuclear divisions and differentiation during female gametophyte development are unknown. In this study we show that two transcription factors, MYB64 and MYB119, redundantly act to promote this process in the model organism Arabidopsis. We also show that one of them, MYB119, is transcriptionally regulated by the histidine-kinase CKI1. Our data establish the framework of a gene regulatory network required to promote cellularization, differentiation, and gamete specification during female gametogenesis.

Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development

In angiosperms, the endosperm provides nutrients for embryogenesis and seed germination and is the primary tissue where gene imprinting occurs. To identify the imprintome of early developing maize (Zea mays) endosperm, we performed high-throughput transcriptome sequencing of whole kernels at 0, 3, and 5 d after pollination (DAP) and endosperms at 7, 10, and 15 DAP, using B73 by Mo17 reciprocal crosses. We observed gradually increased expression of paternal transcripts in 3- and 5-DAP kernels. In 7-DAP endosperm, the majority of the genes tested reached a 2:1 maternal versus paternal ratio, suggesting that paternal genes are nearly fully activated by 7 DAP. A total of 116, 234, and 63 genes exhibiting parent-specific expression were identified at 7, 10, and 15 DAP, respectively. The largest proportion of paternally expressed genes was at 7 DAP, mainly due to the significantly deviated parental allele expression ratio of these genes at this stage, while nearly 80% of the maternally expressed genes (MEGs) were specific to 10 DAP and were primarily attributed to sharply increased expression levels compared with the other stages. Gene ontology enrichment analysis of the imprinted genes suggested that 10-DAP endosperm-specific MEGs are involved in nutrient uptake and allocation and the auxin signaling pathway, coincident with the onset of starch and storage protein accumulation.

Gene expression profiles in rice gametes and zygotes: identification of gamete-enriched genes and up- or down-regulated genes in zygotes after fertilization

In angiosperms, fertilization and subsequent zygotic development occur in embryo sacs deeply embedded in the ovaries; therefore, these processes are poorly elucidated. In this study, microarray-based transcriptome analyses were conducted on rice sperm cells, egg cells, and zygotes isolated from flowers to identify candidate genes involved in gametic and/or early zygotic development. Cell type-specific transcriptomes were obtained, and up- or down-regulated genes in zygotes after fertilization were identified, in addition to genes enriched in male and female gametes. A total of 325 putatively up-regulated and 94 putatively down-regulated genes in zygotes were obtained. Interestingly, several genes encoding homeobox proteins or transcription factors were identified as highly up-regulated genes after fertilization, and the gene ontology for up-regulated genes was highly enriched in functions related to chromatin/DNA organization and assembly. Because a gene encoding methyltransferase 1 was identified as a highly up-regulated gene in zygotes after fertilization, the effect of an inhibitor of this enzyme on zygote development was monitored. The inhibitor appeared partially to affect polarity or division asymmetry in rice zygotes, but it did not block normal embryo generation.

Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations

Although the female gametophyte in angiosperms consists of just seven cells, it has a complex biological network. In this study, female gametophyte microarray data from Arabidopsis thaliana were integrated into the Arabidopsis interactome database to generate a putative interaction map of the female gametophyte development including proteome map based on biological processes and molecular functions of proteins. Biological and functional groups as well as topological characteristics of the network were investigated by analyzing phytohormones, plant defense, cell death, transporters, regulatory factors, and hydrolases. This approach led to the prediction of critical members and bottlenecks of the network. Seventy-four and 24 upregulated genes as well as 171 and 3 downregulated genes were identified in subtracted networks based on biological processes and molecular function respectively, including novel genes such as the pathogenesis-related protein 4, ER type Ca(2+) ATPase 3, dihydroflavonol reductase, and ATP disulfate isomerase. Biologically important relationships between genes, critical nodes, and new essential proteins such as AT1G26830, AT5G20850, CYP74A, AT1G42396, PR4 and MEA were found in the interactome's network. The positions of novel genes, both upregulated and downregulated, and their relationships with biological pathways, in particular phytohormones, were highlighted in this study.

High-throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

Next generation sequencing (NGS) technologies have revolutionized the pace and scale of genomics- and transcriptomics-based SNP discovery across different plant and animal species. Herein, 72-base paired-end Illumina sequencing was employed for high-throughput, parallel and large-scale SNP discovery in 41 growth-related candidate genes in Eucalyptus camaldulensis. Approximately 100 kb of genome from 96 individuals was amplified and sequenced using a hierarchical DNA/PCR pooling strategy and assembled over corresponding E. grandis reference. A total of 1191 SNPs (minimum 5% other allele frequency) were identified with an average frequency of 1 SNP/83.9 bp, whereas in exons and introns, it was 1 SNP/108.4 bp and 1 SNP/65.6 bp, respectively. A total of 75 insertions and 89 deletions were detected of which approximately 15% were exonic. Transitions (Tr) were in excess than transversions (Tv) (Tr/Tv: 1.89), but exceeded in exons (Tr/Tv: 2.73). In exons, synonymous SNPs (Ka) prevailed over the non-synonymous SNPs (Ks; average Ka/Ks ratio: 0.72, range: 0-3.00 across genes). Many of the exonic SNPs/indels had potential to change amino acid sequence of respective genes. Transcription factors appeared more conserved, whereas enzyme coding genes appeared under relaxed control. Further, 541 SNPs were classified into 196 'equal frequency' (EF) blocks with almost similar minor allele frequencies to facilitate selection of one tag-SNP/EF-block. There were 241 (approximately 20%) 'zero-SNP' blocks with absence of SNPs in surrounding ±60 bp windows. The data thus indicated enormous extant and unexplored diversity in E. camaldulensis in the studied genes with potential applications for marker-trait associations.

Endosperm: food for humankind and fodder for scientific discoveries

The endosperm is an essential constituent of seeds in flowering plants. It originates from a fertilization event parallel to the fertilization that gives rise to the embryo. The endosperm nurtures embryo development and, in some species including cereals, stores the seed reserves and represents a major source of food for humankind. Endosperm biology is characterized by specific features, including idiosyncratic cellular controls of cell division and epigenetic controls associated with parental genomic imprinting. This review attempts a comprehensive summary of our current knowledge of endosperm development and highlights recent advances in this field.

Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing

The life cycle of flowering plants alternates between a predominant sporophytic (diploid) and an ephemeral gametophytic (haploid) generation that only occurs in reproductive organs. In Arabidopsis thaliana, the female gametophyte is deeply embedded within the ovule, complicating the study of the genetic and molecular interactions involved in the sporophytic to gametophytic transition. Massively parallel signature sequencing (MPSS) was used to conduct a quantitative large-scale transcriptional analysis of the fully differentiated Arabidopsis ovule prior to fertilization. The expression of 9775 genes was quantified in wild-type ovules, additionally detecting >2200 new transcripts mapping to antisense or intergenic regions. A quantitative comparison of global expression in wild-type and sporocyteless (spl) individuals resulted in 1301 genes showing 25-fold reduced or null activity in ovules lacking a female gametophyte, including those encoding 92 signalling proteins, 75 transcription factors, and 72 RNA-binding proteins not reported in previous studies based on microarray profiling. A combination of independent genetic and molecular strategies confirmed the differential expression of 28 of them, showing that they are either preferentially active in the female gametophyte, or dependent on the presence of a female gametophyte to be expressed in sporophytic cells of the ovule. Among 18 genes encoding pentatricopeptide-repeat proteins (PPRs) that show transcriptional activity in wild-type but not spl ovules, CIHUATEOTL (At4g38150) is specifically expressed in the female gametophyte and necessary for female gametogenesis. These results expand the nature of the transcriptional universe present in the ovule of Arabidopsis, and offer a large-scale quantitative reference of global expression for future genomic and developmental studies.

Somatic small RNA pathways promote the mitotic events of megagametogenesis during female reproductive development in Arabidopsis

Female gamete development in Arabidopsis ovules comprises two phases. During megasporogenesis, a somatic ovule cell differentiates into a megaspore mother cell and undergoes meiosis to produce four haploid megaspores, three of which degrade. The surviving functional megaspore participates in megagametogenesis, undergoing syncytial mitosis and cellular differentiation to produce a multicellular female gametophyte containing the egg and central cell, progenitors of the embryo and endosperm of the seed. The transition between megasporogenesis and megagametogenesis is poorly characterised, partly owing to the inaccessibility of reproductive cells within the ovule. Here, laser capture microdissection was used to identify genes expressed in and/or around developing megaspores during the transition to megagametogenesis. ARGONAUTE5 (AGO5), a putative effector of small RNA (sRNA) silencing pathways, was found to be expressed around reproductive cells during megasporogenesis, and a novel semi-dominant ago5-4 insertion allele showed defects in the initiation of megagametogenesis. Expression of a viral RNAi suppressor, P1/Hc-Pro, driven by the WUSCHEL and AGO5 promoters in somatic cells flanking the megaspores resulted in a similar phenotype. This indicates that sRNA-dependent pathways acting in somatic ovule tissues promote the initiation of megagametogenesis in the functional megaspore. Notably, these pathways are independent of AGO9, which functions in somatic epidermal ovule cells to inhibit the formation of multiple megaspore-like cells. Therefore, one somatic sRNA pathway involving AGO9 restricts reproductive development to the functional megaspore and a second pathway, inhibited by ago5-4 and P1/Hc-Pro, promotes megagametogenesis.

Double fertilization on the move

Double fertilization is a flowering plant mechanism whereby two immotile sperm cells fertilize two different female gametes. One of the two sperm cells fertilizes the egg cell to produce the embryo and the other fertilizes the central cell to produce the endosperm. Despite the biological and agricultural significance of double fertilization, the mechanism remains largely unknown owing to difficulties associated with the embedded structure of female gametes in the maternal tissue. However, molecular genetic approaches combined with novel live-cell imaging techniques have begun to clarify the actual behavior of the sperm cells, which is different from that described by previous hypotheses. In this review article, we discuss the mechanism of double fertilization based on the dynamics of the two sperm cells in Arabidopsis.

Identification of genes expressed in the angiosperm female gametophyte

Until recently, identification of gene regulatory networks controlling the development of the angiosperm female gametophyte has presented a significant challenge to the plant biology community. The angiosperm female gametophyte is fairly inaccessible because it is a highly reduced structure relative to the sporophyte and is embedded within multiple layers of the sporophytic tissue of the ovule. Moreover, although mutations affecting the female gametophyte can be readily isolated, their analysis can be difficult because most affect genes involved in basic cellular processes that are also required in the diploid sporophyte. In recent years, expression-based approaches in multiple species have begun to uncover gene sets expressed in specific female gametophyte cells as a means of identifying regulatory networks controlling cell differentiation in the female gametophyte. Here, recent efforts to identify and analyse gene expression programmes in the Arabidopsis female gametophyte are reviewed.

Imaging fertilization in flowering plants, not so abominable after all

Although the discovery of double fertilization in flowering plants took place at the end of the nineteenth century little progress had been made in understanding the cellular and molecular mechanisms involved until the end of the twentieth century. After attempts to study fertilization with isolated male and female gametes, researchers turned to Arabidopsis thaliana as a model for genetic analysis and in vivo imaging. The development of confocal imaging and fluorescent proteins, coupled with new molecular insights into cell fate specification of plant gametes, allowed the development of robust markers for cells participating in double fertilization. These markers enabled the imaging of double fertilization in vivo in Arabidopsis. These studies have been coupled with the identification and molecular characterization of genes controlling fertilization in Arabidopsis. Live imaging has already provided new insights on sperm cell delivery, the equivalence of the fate of the sperm cells, gamete fusion, and re-initiation of the zygotic life. This review covers these topics and outlines many important aspects of double fertilization that remain unknown.

Nuclear behavior, cell polarity, and cell specification in the female gametophyte

In flowering plants, the haploid gamete-forming generation comprises only a few cells and develops within the reproductive organs of the flower. The female gametophyte has become an attractive model system to study the genetic and molecular mechanisms involved in pattern formation and gamete specification. It originates from a single haploid spore through three free nuclear division cycles, giving rise to four different cell types. Research over recent years has allowed to catch a glimpse of the mechanisms that establish the distinct cell identities and suggests dynamic cell-cell communication to orchestrate not only development among the cells of the female gametophyte but also the interaction between male and female gametophytes. Additionally, cytological observations and mutant studies have highlighted the importance of nuclei migration- and positioning for patterning the female gametophyte. Here we review current knowledge on the mechanisms of cell specification in the female gametophyte, emphasizing the importance of positional cues for the establishment of distinct molecular profiles.

Distinct gene expression profiles in egg and synergid cells of rice as revealed by cell type-specific microarrays

Double fertilization in flowering plants refers to a process in which two sperm cells, carried by the pollen tube, fertilize both the egg and the central cell after their release into a synergid cell of the female gametophyte. The molecular processes by which the female gametophytic cells express their unique functions during fertilization are not well understood. Genes expressed in egg and synergid cells might be important for multiple stages of the plant reproductive process. Here, we profiled genome-wide gene expression in egg and synergid cells in rice (Oryza sativa), a model monocot, using a nonenzymatic cell isolation technique. We found that the expression profiles of the egg and synergid cells were already specified at the micropylar end of the female gametophyte during the short developmental period that comprises the three consecutive mitotic nuclear divisions after megaspore generation. In addition, we identified a large number of genes expressed in the rice egg and synergid cells and characterized these genes using Gene Ontology analysis. The analysis suggested that epigenetic and posttranscriptional regulatory mechanisms are involved in the specification and/or maintenance of these cells. Comparisons between the rice profiles and reported Arabidopsis (Arabidopsis thaliana) profiles revealed that genes enriched in the egg/synergid cell of rice were distinct from those in Arabidopsis.

The female gametophyte

The angiosperm female gametophyte is critical for plant reproduction. It contains the egg cell and central cell that become fertilized and give rise to the embryo and endosperm of the seed, respectively. Female gametophyte development begins early in ovule development with the formation of a diploid megaspore mother cell that undergoes meiosis. One resulting haploid megaspore then develops into the female gametophyte. Genetic and epigenetic processes mediate specification of megaspore mother cell identity and limit megaspore mother cell formation to a single cell per ovule. Auxin gradients influence female gametophyte polarity and a battery of transcription factors mediate female gametophyte cell specification and differentiation. The mature female gametophyte secretes peptides that guide the pollen tube to the embryo sac and contains protein complexes that prevent seed development before fertilization. Post-fertilization, the female gametophyte influences seed development through maternal-effect genes and by regulating parental contributions. Female gametophytes can form by an asexual process called gametophytic apomixis, which involves formation of a diploid female gametophyte and fertilization-independent development of the egg into the embryo. These functions collectively underscore the important role of the female gametophyte in seed and food production.

Germline specification and function in plants

The flowering plant germline is produced during the haploid gametophytic stage. Defining the germline is complicated by the extreme reduction of the male and female gametophytes, also referred to as pollen and embryo sac, respectively. Both male and female gamete progenitors are segregated by an asymmetric cell division, as is the case for the germline in animals. Genetic studies and access to the transcriptome of isolated gametes have provided a regulatory framework for the mechanisms that define the male germline. What specifies female germline identity remains unknown. Recent evidence indicates that an auxin gradient provides positional information and plays a role in defining the identity of the female gamete lineage. The animal germline is also marked by production of small RNAs, and recent evidence indicates that this trait might be shared with the plant gamete lineage.

A comprehensive and universal method for assessing the performance of differential gene expression analyses

The number of methods for pre-processing and analysis of gene expression data continues to increase, often making it difficult to select the most appropriate approach. We present a simple procedure for comparative estimation of a variety of methods for microarray data pre-processing and analysis. Our approach is based on the use of real microarray data in which controlled fold changes are introduced into 20% of the data to provide a metric for comparison with the unmodified data. The data modifications can be easily applied to raw data measured with any technological platform and retains all the complex structures and statistical characteristics of the real-world data. The power of the method is illustrated by its application to the quantitative comparison of different methods of normalization and analysis of microarray data. Our results demonstrate that the method of controlled modifications of real experimental data provides a simple tool for assessing the performance of data preprocessing and analysis methods.