The miRNA822 loaded by ARGONAUTE9 modulates the monosporic female gametogenesis in Arabidopsis thaliana

KEY MESSAGE

The miR822 together with of AGO9 protein, modulates monosporic development in Arabidopsis thaliana through the regulation of target genes encoding Cysteine/Histidine-Rich C1 domain proteins, revealing a new role of miRNAs in the control of megaspore formation in flowering plants. In the ovule of flowering plants, the establishment of the haploid generation occurs when a somatic cell differentiates into a megaspore mother cell (MMC) and initiates meiosis. As most flowering plants, Arabidopsis thaliana (Arabidopsis) undergoes a monosporic type of gametogenesis as three meiotically derived cells degenerate, and a single one-the functional megaspore (FM), divides mitotically to form the female gametophyte. The genetic basis and molecular mechanisms that control monosporic gametophyte development remain largely unknown. Here, we show that Arabidopsis plants carrying loss-of-function mutations in the miR822, give rise to extranumerary surviving megaspores that acquire a FM identity and divides without giving rise to differentiated female gametophytes. The overexpression of three miR822 putative target genes encoding cysteine/histidine-rich C1 (DC1) domain proteins, At5g02350, At5g02330 and At2g13900 results in defects equivalent to those found in mutant mir822 plants. The three miR822 targets genes are overexpressed in ago9 mutant ovules, suggesting that miR822 acts through an AGO9-dependent pathway to negatively regulate DC1 domain proteins and restricts the survival of meiotically derived cells to a single megaspore. Our results identify a mechanism mediated by the AGO9-miR822 complex that modulates monosporic female gametogenesis in Arabidopsis thaliana.

Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation

Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.

Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs

Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons, if any, has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs (easiRNAs) in mutants in DECREASE IN DNA METHYLATION1 (DDM1), which promote histone H3 lysine-9 di-methylation (H3K9me2). Here, we show that mutants which lose both DDM1 and RNA dependent RNA polymerase (RdRP) have pleiotropic developmental defects and mis-segregation of chromosome 5 during mitosis. Fertility defects are epigenetically inherited with the centromeric region of chromosome 5, and can be rescued by directing artificial small RNAs to a single family of ATHILA5 retrotransposons specifically embedded within this centromeric region. easiRNAs and H3K9me2 promote pericentromeric condensation, chromosome cohesion and proper chromosome segregation in mitosis. Insertion of ATHILA silences transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs, promoting the selfish survival and spread of centromeric retrotransposons. Parallels are made with the fission yeast S. pombe, where chromosome segregation depends on RNAi, and with humans, where chromosome segregation depends on both RNAi and HELLSDDM1.

Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation

Epigenetic inheritance refers to the faithful replication of DNA methylation and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferases, unless they are remodeled by DECREASE IN DNA METHYLATION1 (DDM1 Lsh/HELLS ), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1 during the cell cycle. In ddm1 mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a disulfide bond in the helicase domain is essential for activity in vivo and in vitro . We show that differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo . DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1 Dnmt1 . DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome in the germline and contributes to epigenetic inheritance.

AGO104 is a RdDM effector of paramutation at the maize b1 locus

Although paramutation has been well-studied at a few hallmark loci involved in anthocyanin biosynthesis in maize, the cellular and molecular mechanisms underlying the phenomenon remain largely unknown. Previously described actors of paramutation encode components of the RNA-directed DNA-methylation (RdDM) pathway that participate in the biogenesis of 24-nucleotide small interfering RNAs (24-nt siRNAs) and long non-coding RNAs. In this study, we uncover an ARGONAUTE (AGO) protein as an effector of the RdDM pathway that is in charge of guiding 24-nt siRNAs to their DNA target to create de novo DNA methylation. We combined immunoprecipitation, small RNA sequencing and reverse genetics to, first, validate AGO104 as a member of the RdDM effector complex and, then, investigate its role in paramutation. We found that AGO104 binds 24-nt siRNAs involved in RdDM, including those required for paramutation at the b1 locus. We also show that the ago104-5 mutation causes a partial reversion of the paramutation phenotype at the b1 locus, revealed by intermediate pigmentation levels in stem tissues. Therefore, our results place AGO104 as a new member of the RdDM effector complex that plays a role in paramutation at the b1 locus in maize.

An Optimized Whole-Mount Immunofluorescence Method for Shoot Apices

The localization of a protein provides important information about its biological functions. The visualization of proteins by immunofluorescence has become an essential approach in cell biology. Here, we describe an easy-to-follow immunofluorescence protocol to localize proteins in whole-mount tissues of maize (Zea mays) and Arabidopsis. We present the whole-mount immunofluorescence procedure using maize ear primordia and Arabidopsis inflorescence apices as examples, followed by tips and suggestions for each step. In addition, we provide a supporting protocol to describe the use of an ImageJ plug-in to analyze colocalization. This protocol has been optimized to observe proteins in 2-5 mm maize ear primordia or in developing Arabidopsis inflorescence apices; however, it can be used as a reference to perform whole-mount immunofluorescence in other plant tissues and species. © 2021 Wiley Periodicals LLC. Basic Protocol: Whole-mount immunofluorescence for maize and Arabidopsis shoot apices Support Protocol: Measure colocalization by JACoP plugin in ImageJ.

Organ geometry channels reproductive cell fate in the Arabidopsis ovule primordium

In multicellular organisms, sexual reproduction requires the separation of the germline from the soma. In flowering plants, the female germline precursor differentiates as a single spore mother cell (SMC) as the ovule primordium forms. Here, we explored how organ growth contributes to SMC differentiation. We generated 92 annotated 3D images at cellular resolution in Arabidopsis. We identified the spatio-temporal pattern of cell division that acts in a domain-specific manner as the primordium forms. Tissue growth models uncovered plausible morphogenetic principles involving a spatially confined growth signal, differential mechanical properties, and cell growth anisotropy. Our analysis revealed that SMC characteristics first arise in more than one cell but SMC fate becomes progressively restricted to a single cell during organ growth. Altered primordium geometry coincided with a delay in the fate restriction process in katanin mutants. Altogether, our study suggests that tissue geometry channels reproductive cell fate in the Arabidopsis ovule primordium.

DNA Methylation Readers in Plants

In plants, DNA methylation occurs in distinct sequence contexts, including CG, CHG, and CHH. Thus, plants have developed a surprisingly diverse set of DNA methylation readers to cope with an extended repertoire of methylated sites. The Arabidopsis genome contains twelve Methyl-Binding Domain proteins (MBD), and nine SET and RING finger-associated (SRA) domain containing proteins belonging to the SUVH clade, in addition to three homologs of UHRF1, namely VIM1-3, all containing SRA domains. In this review, we will highlight several research questions that remain unresolved with respect to the function of plant DNA methylation readers, which can have both de novo demethylase and maintenance activity. We argue that maintenance of CG methylation in plants likely involved actors not found in their mammalian counterparts, and that new evidence suggests significant reprogramming of DNA methylation during plant reproduction as an important new development in the field.

Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude

In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.

DNA methylation in Marchantia polymorpha

Methylation of DNA is an epigenetic mechanism for the control of gene expression. Alterations in the regulatory pathways involved in the establishment, perpetuation and removal of DNA methylation can lead to severe developmental alterations. Our understanding of the mechanistic aspects and relevance of DNA methylation comes from remarkable studies in well-established angiosperm plant models including maize and Arabidopsis. The study of plant models positioned at basal lineages opens exciting opportunities to expand our knowledge on the function and evolution of the components of DNA methylation. In this Tansley Insight, we summarize current progress in our understanding of the molecular basis and relevance of DNA methylation in the liverwort Marchantia polymorpha.

Loss of CG Methylation in Marchantia polymorpha Causes Disorganization of Cell Division and Reveals Unique DNA Methylation Regulatory Mechanisms of Non-CG Methylation

DNA methylation is an epigenetic mark that ensures silencing of transposable elements (TEs) and affects gene expression in many organisms. The function of different DNA methylation regulatory pathways has been largely characterized in the model plant Arabidopsis thaliana. However, far less is known about DNA methylation regulation and functions in basal land plants. Here we focus on the liverwort Marchantia polymorpha, an emerging model species that represents a basal lineage of land plants. We identified MpMET, the M. polymorpha ortholog of the METHYLTRANSFERASE 1 (MET1) gene required for maintenance of methylation at CG sites in angiosperms. We generated Mpmet mutants using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9) system, which showed a significant loss of CG methylation and severe morphological changes and developmental defects. The mutants developed many adventitious shoot-like structures, suggesting that MpMET is required for maintaining differentiated cellular identities in the gametophyte. Even though numerous TEs were up-regulated, non-CG methylation was generally highly increased at TEs in the Mpmet mutants. Closer inspection of CHG methylation revealed features unique to M. polymorpha. Methylation of CCG sites in M. polymorpha does not depend on MET1, unlike in A. thaliana and Physcomitrella patens. Our results highlight the diversity of non-CG methylation regulatory mechanisms in plants.

Dividing a Maternal Pie among Half-Sibs: Genetic Conflicts and the Control of Resource Allocation to Seeds in Maize

Resource allocation to offspring is the battleground for various intrafamilial conflicts. Understanding these conflicts requires knowledge of how the different actors (mother, siblings with different paternal genotypes) influence resource allocation. In angiosperms, allocation of resources to seeds happens postfertilization, and the paternally inherited genome in offspring can therefore influence resource allocation. However, the precise mode of resource allocation-and, in particular, the occurrence of sibling rivalry-has rarely been investigated in plants. In this article, we develop a new method for analyzing the resource-allocation traits of the different actors (maternal sporophyte and half-sibs) using data obtained from a large-scale diallel cross experiment in maize involving mixed hand pollination and color markers to assess seed weight of known paternity. We found strong evidence for the occurrence of sibling rivalry: resources invested in an ear were allocated competitively, and offspring with different paternal genotypes aggressively competed for these resources, entailing a measurable direct cost to the mother. We also show how resource allocation can be described for each genotype by two maternal traits (source effect, average sink responsiveness) and two offspring traits (ability to attract maternal resources, competitive ability toward siblings). We will discuss how these findings help to understand how genetic conflicts shape resource-allocation traits in angiosperms.

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM

Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency and to prevent transgenerational inheritance of epimutations. However, the extent of DNA methylation reprogramming in plants remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis. Live imaging during reproduction revealed distinct and sex-specific dynamics for both contexts. We found that CHH methylation in the egg cell depends on DOMAINS REARRANGED METHYLASE 2 (DRM2) and RNA polymerase V (Pol V), two main actors of RNA-directed DNA methylation, but does not depend on Pol IV. Our sensors provide insight into global DNA methylation dynamics at the single-cell level with high temporal resolution and offer a powerful tool to track CG and non-CG methylation both during development and in response to environmental cues in all organisms with methylated DNA, as we illustrate in mouse embryonic stem cells.

An efficient method for quantitative, single-cell analysis of chromatin modification and nuclear architecture in whole-mount ovules in Arabidopsis

In flowering plants, the somatic-to-reproductive cell fate transition is marked by the specification of spore mother cells (SMCs) in floral organs of the adult plant. The female SMC (megaspore mother cell, MMC) differentiates in the ovule primordium and undergoes meiosis. The selected haploid megaspore then undergoes mitosis to form the multicellular female gametophyte, which will give rise to the gametes, the egg cell and central cell, together with accessory cells. The limited accessibility of the MMC, meiocyte and female gametophyte inside the ovule is technically challenging for cytological and cytogenetic analyses at single cell level. Particularly, direct or indirect immunodetection of cellular or nuclear epitopes is impaired by poor penetration of the reagents inside the plant cell and single-cell imaging is demised by the lack of optical clarity in whole-mount tissues. Thus, we developed an efficient method to analyze the nuclear organization and chromatin modification at high resolution of single cell in whole-mount embedded Arabidopsis ovules. It is based on dissection and embedding of fixed ovules in a thin layer of acrylamide gel on a microscopic slide. The embedded ovules are subjected to chemical and enzymatic treatments aiming at improving tissue clarity and permeability to the immunostaining reagents. Those treatments preserve cellular and chromatin organization, DNA and protein epitopes. The samples can be used for different downstream cytological analyses, including chromatin immunostaining, fluorescence in situ hybridization (FISH), and DNA staining for heterochromatin analysis. Confocal laser scanning microscopy (CLSM) imaging, with high resolution, followed by 3D reconstruction allows for quantitative measurements at single-cell resolution.

Chromatin reprogramming during the somatic-to-reproductive cell fate transition in plants

The life cycle of flowering plants is marked by several post-embryonic developmental transitions during which novel cell fates are established. Notably, the reproductive lineages are first formed during flower development. The differentiation of spore mother cells, which are destined for meiosis, marks the somatic-to-reproductive fate transition. Meiosis entails the formation of the haploid multicellular gametophytes, from which the gametes are derived, and during which epigenetic reprogramming takes place. Here we show that in the Arabidopsis female megaspore mother cell (MMC), cell fate transition is accompanied by large-scale chromatin reprogramming that is likely to establish an epigenetic and transcriptional status distinct from that of the surrounding somatic niche. Reprogramming is characterized by chromatin decondensation, reduction in heterochromatin, depletion of linker histones, changes in core histone variants and in histone modification landscapes. From the analysis of mutants in which the gametophyte fate is either expressed ectopically or compromised, we infer that chromatin reprogramming in the MMC is likely to contribute to establishing postmeiotic competence to the development of the pluripotent gametophyte. Thus, as in primordial germ cells of animals, the somatic-to-reproductive cell fate transition in plants entails large-scale epigenetic reprogramming.

Epigenetics and development in plants: green light to convergent innovations

Plants are sessile organisms that must constantly adjust to their environment. In contrast to animals, plant development mainly occurs postembryonically and is characterized by continuous growth and extensive phenotypic plasticity. Chromatin-level regulation of transcriptional patterns plays a central role in the ability of plants to adapt to internal and external cues. Here, we review selected examples of chromatin-based mechanisms involved in the regulation of key aspects of plant development. These illustrate that, in addition to mechanisms conserved between plants and animals, plant-specific innovations lead to particular chromatin dynamics related to their developmental and life strategies.

Epigenetic regulation of reproductive development and the emergence of apomixis in angiosperms

Apomictic plants reproduce asexually through seeds by avoiding both meiosis and fertilization. While apomixis is genetically controlled, individual loci contributing to its expression have yet to be identified. Here, we review recent results indicating that RNA-dependent DNA methylation pathways acting during female reproduction are essential for proper reproductive development in plants, and may represent key regulators of the differentiation between apomictic and sexual reproduction.

Production of viable gametes without meiosis in maize deficient for an ARGONAUTE protein

Apomixis is a form of asexual reproduction through seeds in angiosperms. Apomictic plants bypass meiosis and fertilization, developing offspring that are genetically identical to their mother. In a genetic screen for maize (Zea mays) mutants mimicking aspects of apomixis, we identified a dominant mutation resulting in the formation of functional unreduced gametes. The mutant shows defects in chromatin condensation during meiosis and subsequent failure to segregate chromosomes. The mutated locus codes for AGO104, a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob-repeat DNA. Digital gene expression tag profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis thaliana AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Our findings show that female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell-autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize.

A role for CHROMOMETHYLASE3 in mediating transposon and euchromatin silencing during egg cell reprogramming in Arabidopsis

During embryogenesis there is a major switch from dependence upon maternally-deposited products to reliance on products of the zygotic genome. In animals, this so-called maternal-to-zygotic transition occurs following a period of transcriptional quiescence. Recently, we have shown that the early embryo in Arabidopsis is also quiescent, a state inherited from the female gamete and linked to specific patterns of H3K9 dimethylation and TERMINAL FLOWER2 (TFL2) localization. We also demonstrated that CHROMOMETHYLASE 3 (CMT3) is required for H3K9 dimethylation in the egg cell and for normal embryogenesis during the first few divisions of the zygote. Subsequent analysis of CMT3 mutants points to a key role in egg cell reprogramming by controlling silencing in both transposon and euchromatic regions. A speculative model of the CMT3-induced egg cell silencing is presented here, based on these results and current data from the literature suggesting the potential involvement of small RNAs targeted to the egg cell, a process conceptually similar to the division of labor described in the male gametophyte for which we show that H3K9 modifications and TFL2 localization are reminiscent of the female gametophyte.

Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis-like phenotypes

Apomictic plants reproduce asexually through seeds by avoiding both meiosis and fertilization. Although apomixis is genetically regulated, its core genetic component(s) has not been determined yet. Using profiling experiments comparing sexual development in maize (Zea mays) to apomixis in maize-Tripsacum hybrids, we identified six loci that are specifically downregulated in ovules of apomictic plants. Four of them share strong homology with members of the RNA-directed DNA methylation pathway, which in Arabidopsis thaliana is involved in silencing via DNA methylation. Analyzing loss-of-function alleles for two maize DNA methyltransferase genes belonging to that subset, dmt102 and dmt103, which are downregulated in the ovules of apomictic plants and are homologous to the Arabidopsis CHROMOMETHYLASEs and DOMAINS REARRANGED METHYLTRANSFERASE families, revealed phenotypes reminiscent of apomictic development, including the production of unreduced gametes and formation of multiple embryo sacs in the ovule. Loss of DMT102 activity in ovules resulted in the establishment of a transcriptionally competent chromatin state in the archesporial tissue and in the egg cell that mimics the chromatin state found in apomicts. Interestingly, dmt102 and dmt103 expression in the ovule is found in a restricted domain in and around the germ cells, indicating that a DNA methylation pathway active during reproduction is essential for gametophyte development in maize and likely plays a critical role in the differentiation between apomictic and sexual reproduction.

Control of female gamete formation by a small RNA pathway in Arabidopsis

In the ovules of most sexual flowering plants female gametogenesis is initiated from a single surviving gametic cell, the functional megaspore, formed after meiosis of the somatically derived megaspore mother cell (MMC). Because some mutants and certain sexual species exhibit more than one MMC, and many others are able to form gametes without meiosis (by apomixis), it has been suggested that somatic cells in the ovule are competent to respond to a local signal likely to have an important function in determination. Here we show that the Arabidopsis protein ARGONAUTE 9 (AGO9) controls female gamete formation by restricting the specification of gametophyte precursors in a dosage-dependent, non-cell-autonomous manner. Mutations in AGO9 lead to the differentiation of multiple gametic cells that are able to initiate gametogenesis. The AGO9 protein is not expressed in the gamete lineage; instead, it is expressed in cytoplasmic foci of somatic companion cells. Mutations in SUPPRESSOR OF GENE SILENCING 3 and RNA-DEPENDENT RNA POLYMERASE 6 exhibit an identical defect to ago9 mutants, indicating that the movement of small RNA (sRNAs) silencing out of somatic companion cells is necessary for controlling the specification of gametic cells. AGO9 preferentially interacts with 24-nucleotide sRNAs derived from transposable elements (TEs), and its activity is necessary to silence TEs in female gametes and their accessory cells. Our results show that AGO9-dependent sRNA silencing is crucial to specify cell fate in the Arabidopsis ovule, and that epigenetic reprogramming in companion cells is necessary for sRNA-dependent silencing in plant gametes.

Embryo and endosperm inherit distinct chromatin and transcriptional states from the female gametes in Arabidopsis

Whether deposited maternal products are important during early seed development in flowering plants remains controversial. Here, we show that RNA interference-mediated downregulation of transcription is deleterious to endosperm development but does not block zygotic divisions. Furthermore, we show that RNA POLYMERASE II is less active in the embryo than in the endosperm. This dimorphic pattern is established late during female gametogenesis and is inherited by the two products of fertilization. This juxtaposition of distinct transcriptional activities correlates with differential patterns of histone H3 lysine 9 dimethylation, LIKE HETEROCHROMATIN PROTEIN1 localization, and Histone H2B turnover in the egg cell versus the central cell. Thus, distinct epigenetic and transcriptional patterns in the embryo and endosperm are already established in their gametic progenitors. We further demonstrate that the non-CG DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and DEMETER-LIKE DNA glycosylases are required for the correct distribution of H3K9 dimethylation in the egg and central cells, respectively, and that plants defective for CMT3 activity show abnormal embryo development. Our results provide evidence that cell-specific mechanisms lead to the differentiation of epigenetically distinct female gametes in Arabidopsis thaliana. They also suggest that the establishment of a quiescent state in the zygote may play a role in the reprogramming of the young plant embryo.

The maternal to zygotic transition in animals and plants

In the animal kingdom, maternal control of early development is a common feature. The onset of zygotic control over early development, defined as the maternal to zygotic transition (MZT), follows fertilization with a delay of a variable number of cell divisions, depending on the species. The MZT has been well defined in animals, but investigations remain in their infancy in plants. Recent evidence suggests, however, that in plants as in animals, the MZT also occurs several division cycles after fertilization. The likely convergent evolution of the MZT in the animal and plant kingdoms is fascinating and raises major questions regarding its biological significance, particularly with regard to its importance in genome reprogramming and the acquisition of totipotency by the embryo.

Timing of the maternal-to-zygotic transition during early seed development in maize

In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. Recent data in plants also suggest maternal control over early seed development, but the actual timing of zygotic genome activation is unclear. Here, we analyzed the timing of the maternal-to-zygotic transition during early Zea mays seed development. We show that for 16 genes expressed during early seed development, only maternally inherited alleles are detected during 3 d after fertilization in both the embryo and the endosperm. Microarray analyses of precocious embryonic development in apomictic hybrids between maize and its wild relative, Tripsacum, demonstrate that early embryo development occurs without significant quantitative changes to the transcript population in the ovule before fertilization. Precocious embryo development is also correlated with a higher proportion of polyadenylated mRNA in the ovules. Our data suggest that the maternal-to-zygotic transition occurs several days after fertilization. By contrast, novel transcription accompanies early endosperm development, indicating that different mechanisms are involved in the initiation of endosperm and embryo development.

Heterochronic Expression of Sexual Reproductive Programs During Apomictic Development in Tripsacum

Some angiosperms reproduce by apomixis, a natural way of cloning through seeds. Apomictic plants bypass both meiosis and egg cell fertilization, producing progeny that are genetic replicas of the mother plant. In this report, we analyze reproductive development in Tripsacum dactyloides, an apomictic relative of maize, and in experimental apomictic hybrids between maize and Tripsacum. We show that apomictic reproduction is characterized by an alteration of developmental timing of both sporogenesis and early embryo development. The absence of female meiosis in apomictic Tripsacum results from an early termination of female meiosis. Similarily, parthenogenetic development of a maternal embryo in apomicts results from precocious induction of early embryogenesis events. We also show that male meiosis in apomicts is characterized by comparable asynchronous expression of developmental stages. Apomixis thus results in an array of possible phenotypes, including wild-type sexual development. Overall, our observations suggest that apomixis in Tripsacum is a heterochronic phenotype; i.e., it relies on a deregulation of the timing of reproductive events, rather than on the alteration of a specific component of the reproductive pathway.

Developmental genetics of gametophytic apomixis

Some higher plants reproduce asexually by apomixis, a natural way of cloning through seeds. Apomictic plants produce progeny that are an exact genetic replica of the mother plant. The replication is achieved through changes in the female reproductive pathway such that female gametes develop without meiosis and embryos develop without fertilization. Although apomixis is a complex developmental process, genetic evidence suggests that it might be inherited as a simple mendelian trait - a paradox that could be explained by recent data derived from apomictic species and model sexual organisms. The data suggest that apomixis might rely more on a global deregulation of sexual reproductive development than on truly new functions, and molecular mechanisms for such a global deregulation can be proposed. This new understanding has direct consequences for the engineering of apomixis in sexual crop species, an application that could have an immense impact on agriculture.

Non-Mendelian transmission of apomixis in maize-Tripsacum hybrids caused by a transmission ratio distortion

Apomixis is a mode of asexual reproduction through seeds. The apomictic process bypasses both meiosis and egg cell fertilization, producing offspring that are exact genetic replicas of the mother plant. In the Tripsacum agamic complex, all polyploids reproduce through the diplosporous type of apomixis, and diploids are sexual. In this paper, molecular markers linked with diplospory were used to analyse various generations of maize-Tripsacum hybrids and backcross derivatives and to derive a model for the inheritance of diplosporous reproduction. The results suggest that the gene or genes controlling apomixis in Tripsacum are linked with a segregation distorter-type system promoting the elimination of the apomixis alleles when transmitted through haploid gametes. Hence, this model offers an explanation of the relationship between apomixis and polyploidy. The evolutionary importance of this mechanism, which protects the diploid level from being invaded by apomixis, is discussed.

Mapping diplosporous apomixis in tetraploid Tripsacum: one gene or several genes?

Polyploids in Tripsacum, a wild relative of maize, reproduce through the diplosporous type of apomixis, an asexual mode of reproduction through seeds. Diplosporous apomixis involves both the failure of meiosis and the parthenogenetic development of the unreduced gametes, resulting in progenies that are exact genetic copies of the mother plant. Apomixis is believed to be controlled by one single dominant allele, responsible for the whole developmental process. Construction of a linkage map for the chromosome controlling diplosporous apomixis in Tripsacum was carried out in both tetraploid-apomictic and diploid-sexual Tripsacum species using maize restriction fragment length polymorphism (RFLP) probes. A high level of collinearity was observed between the Tripsacum chromosome carrying the control of apomixis and a duplicated segment in the maize genome. In the apomictic tetraploid, there was a strong restriction to recombination, as compared to the corresponding genomic segment in sexual plants and maize. This suggests that apomixis, although inherited as a single Mendelian allele, might really be controlled by a cluster of linked loci. The analysis also revealed the tetrasomic nature of the inheritance of the chromosomal segment controlling apomixis, which contradicts the usually accepted hypothesis of an allopolyploid origin of apomictic species. The implications of these data for the transfer of apomixis into cultivated crops are discussed, and a new approach to studying the genetics of apomixis, based on comparative mapping, is proposed.

Detection of the apomictic mode of reproduction in maize-Tripsacum hybrids using maize RFLP markers

Polyploid plants in the genus Tripsacum, a wild relative of maize, reproduce through gametophytic apomixis of the diplosporous type, an asexual mode of reproduction through seed. Moving gene(s) responsible for the apomictic trait into crop plants would open new areas in plant breeding and agriculture. Efforts to transfer apomixis from Tripsacum into maize at CIMMYT resulted in numerou intergeneric F1 hybrids obtained from various Tripsacum species. A bulk-segregant analysis was carried out to identify molecular markers linked to diplospory in T. dactyloides. This was possible because of numerous genome similarities among related species in the Andropogoneae. On the basis of maize RFLP probes, three restriction fragments co-segregating with diplospory were identified in one maize-Tripsacum dactyloides F1 population that segregated 1∶1 for the mode of reproduction. The markers were also found to be linked in the maize RFLP map, on the distal end of the long arm of chromosome 6. These results support a simple inheritance of diplospory in Tripsacum. Manipulation of the mode of reproduction in maize-Tripsacum backcross generations, and implications for the transfer of apomixis into maize, are discussed.