Plants optimize carbon assimilation while limiting water loss by adjusting stomatal aperture. In grasses, a developmental innovation-the addition of subsidiary cells (SCs) flanking two dumbbell-shaped guard cells (GCs)-is linked to improved stomatal physiology. Here, we identify a transcription factor necessary and sufficient for SC formation in the wheat relative Unexpectedly, the transcription factor is an ortholog of the stomatal regulator, which defines GC precursor fate in The novel role of in specifying lateral SCs appears linked to its acquisition of cell-to-cell mobility in Physiological analyses on SC-less plants experimentally support classic hypotheses that SCs permit greater stomatal responsiveness and larger range of pore apertures. Manipulation of SC formation and function in crops, therefore, may be an effective approach to enhance plant performance.

Stomata, epidermal valves facilitating plant-atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix-loop-helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot's developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity.stomatal development | bHLH transcription factor | Brachypodium | grass S tomata are valves on the surface of plants with central roles in gas exchange and biosphere productivity. Stomata are both ancientthey appear on 400 million-year-old fossils-and nearly ubiquitously found in extant land plants. The diversity of stomatal morphologies and patterned distributions across different plant families coupled with rapidly advancing functional genomic resources offers a powerful opportunity to follow morphological innovation and gene regulatory network evolution simultaneously. In most plants, stomata consist of two kidney-shaped epidermal guard cells (GCs) surrounding a pore (Fig. 1A). Grass stomatal morphology is unique, featuring dumbbell-shaped GCs flanked by subsidiary cells (SCs) (Fig. 1A), and physiological measurements suggest this derived form is more efficient (1). The distribution of stomata on leaves is also species specific. Dicots such as Arabidopsis display a scattered distribution, with avoidance of direct contact being the most basic patterning rule; dispersed stem cell-like stomatal precursors divide throughout the leaf to produce this pattern and promote the typical "broadleaf" or radial growth characteristic of these plants (Fig. 1A). Grasses, in contrast, generate stomata, which are always oriented in the same direction, from specific cell files. These stomatal lineage files are established in a single zone at the leaf base with differentiation proceeding in a linear gradient toward the tip (Fig. 1A).Our understanding of the genetic underpinnings of stomatal fate and pattern is derived mostly from studies in the dicot Arabidopsis where the group Ia basic helix-loop-helix (bHLH) transcription factors SPEECHLESS (AtSPCH), AtMUTE, and AtFAMA establish stomatal lineage identity, regulate the transition to terminal precursor fate, and promote the differentiation of GCs, respectively (2-4). The function of these stage-specific factors requires heterodimerization with one of ...

Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis, we combined deep-sequencing-based RNA profiling and genetic analyses. At the 2-4 cell stage there is a strong, genome-wide dominance of maternal transcripts, although transcripts are contributed by both parental genomes. At the globular stage the relative paternal contribution is higher, largely due to a gradual activation of the paternal genome. We identified two antagonistic maternal pathways that control these parental contributions. Paternal alleles are initially downregulated by the chromatin siRNA pathway, linked to DNA and histone methylation, whereas transcriptional activation requires maternal activity of the histone chaperone complex CAF1. Our results define maternal epigenetic pathways controlling the parental contributions in plant embryos, which are distinct from those regulating genomic imprinting.

Summary Stomata are cellular breathing pores on leaves that open and close to absorb photosynthetic carbon dioxide and to restrict water loss through transpiration, respectively. Grasses (Poaceae) form morphologically innovative stomata, which consist of two dumbbell‐shaped guard cells flanked by two lateral subsidiary cells (SCs). This ‘graminoid’ morphology is associated with faster stomatal movements leading to more water‐efficient gas exchange in changing environments. Here, we offer a genetic and mechanistic perspective on the unique graminoid form of grass stomata and the developmental innovations during stomatal cell lineage initiation, recruitment of SCs and stomatal morphogenesis. Furthermore, the functional consequences of the four‐celled, graminoid stomatal morphology are summarized. We compile the identified players relevant for stomatal opening and closing in grasses, and discuss possible mechanisms leading to cell‐type‐specific regulation of osmotic potential and turgor. In conclusion, we propose that the investigation of functionally superior grass stomata might reveal routes to improve water‐stress resilience of agriculturally relevant plants in a changing climate.

Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner. It is achieved by the differential epigenetic marking of parental alleles. Over the past decade, studies in the model systems Arabidopsis thaliana and maize (Zea mays) have shown a strong correlation between silent or active states with epigenetic marks, such as DNA methylation and histone modifications, but the nature of the primary imprint has not been clearly established for all imprinted genes. Phenotypes and expression patterns of imprinted genes have fueled the perception that genomic imprinting is specific to the endosperm, a seed tissue that does not contribute to the next generation. However, several lines of evidence suggest a potential role for imprinting in the embryo, raising questions as to how imprints are erased and reset from one generation to the next. Imprinting regulation in flowering plants shows striking similarities, but also some important differences, compared with the mechanisms of imprinting described in mammals. For example, some imprinted genes are involved in seed growth and viability in plants, which is similar in mammals, where imprinted gene regulation is essential for embryonic development. However, it seems to be more flexible in plants, as imprinting requirements can be bypassed to allow the development of clonal offspring in apomicts.

Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner and is regulated by the differential epigenetic marking of the parental alleles. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a tissue nourishing the developing embryo that does not contribute to the next generation. In Arabidopsis, the genes MEDEA (MEA) and PHERES1 (PHE1), which are imprinted in the endosperm, are also expressed in the embryo; whether their embryonic expression is regulated by imprinting or not, however, remains controversial. In contrast, the maternally expressed in embryo 1 (mee1) gene of maize is clearly imprinted in the embryo. We identified several imprinted candidate genes in an allele-specific transcriptome of hybrid Arabidopsis embryos and confirmed parent-of-origin-dependent, monoallelic expression for eleven maternally expressed genes (MEGs) and one paternally expressed gene (PEG) in the embryo, using allele-specific expression analyses and reporter gene assays. Genetic studies indicate that the Polycomb Repressive Complex 2 (PRC2) but not the DNA METHYLTRANSFERASE1 (MET1) is involved in regulating imprinted expression in the embryo. In the seedling, all embryonic MEGs and the PEG are expressed from both parents, suggesting that the imprint is erased during late embryogenesis or early vegetative development. Our finding that several genes are regulated by genomic imprinting in the Arabidopsis embryo clearly demonstrates that this epigenetic phenomenon is not a unique feature of the endosperm in both monocots and dicots.

SUMMARYIn flowering plants, double fertilization of the female gametes, the egg and the central cell, initiates seed development to give rise to a diploid embryo and the triploid endosperm. In the absence of fertilization, the FERTILIZATION-INDEPENDENT SEED Polycomb Repressive Complex 2 (FIS-PRC2) represses this developmental process by histone methylation of certain target genes. The FERTILIZATION-INDEPENDENT SEED (FIS) class genes MEDEA (MEA) and FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) encode two of the core components of this complex. In addition, DNA methylation establishes and maintains the repression of gene activity, for instance via DNA METHYLTRANSFERASE1 (MET1), which maintains methylation of symmetric CpG residues. Here, we demonstrate that Arabidopsis MET1 interacts with MEA in vitro and in a yeast two-hybrid assay, similar to the previously identified interaction of the mammalian homologues DNMT1 and EZH2. MET1 and MEA share overlapping expression patterns in reproductive tissues before and after fertilization, a prerequisite for an interaction in vivo. Importantly, a much higher percentage of central cells initiate endosperm development in the absence of fertilization in mea-1/MEA; met1-3/MET1 as compared to mea-1/MEA mutant plants. In addition, DNA methylation at the PHERES1 and MEA loci, imprinted target genes of the FIS-PRC2, was affected in the mea-1 mutant compared with wild-type embryos. In conclusion, our data suggest a mechanistic link between two major epigenetic pathways involved in histone and DNA methylation in plants by physical interaction of MET1 with the FIS-PRC2 core component MEA. This concerted action is relevant for the repression of seed development in the absence of fertilization.

We present a generally applicable method allowing rapid identification of causal alleles in mutagenized genomes by nextgeneration sequencing. Currently used approaches rely on recovering homozygotes or extensive backcrossing. In contrast, SNP-ratio mapping allows rapid cloning of lethal and/or poorly transmitted mutations and second-site modifiers, which are often in complex genetic/transgenic backgrounds. FORWARD genetic screens are powerful in uncovering novel gene functions in genetic model organisms. While some mutant screens can be quick to perform, the identification of the causative mutation by map-based cloning is extremely labor-intensive. Large F 2 mapping populations of .1000 mutant individuals are required (Lukowitz et al. 2000;Jander et al. 2002) to fine-map a chromosomal region harboring a causative mutation. This number of mutant individuals can be difficult to obtain, especially when working with phenotypic traits that (i) are difficult to score, (ii) are weakly transmitted, or (iii) are in organisms that are hard to propagate. The recent development of next-generation sequencing (NGS) platforms has made sequencing of whole genomes quick and affordable. One application of NGS is to replace map-based cloning by the sequencing of mutagenized genomes to quickly identify causative mutations, a method successfully applied in many model organisms (Sarin et al. Here, we describe a generally applicable method, SNPratio mapping (SRM), which allows the rapid identification of lethal and/or poorly transmitted mutations and secondsite modifiers by NGS. It is based on the distinct segregation ratio of the causative (and linked) single-nucleotide polymorphism(s) (SNPs) from that of unlinked SNPs. SRM allows the mapping of lethal mutations after only two rounds of backcrossing via NGS. After backcrossing twice to the non-mutagenized parent, any unlinked SNP created by ethyl methanesulfonate (EMS) mutagenesis segregates 1:3 in a pool of individuals. By selecting only mutant individuals in the F 1 generation of the second backcross (BC2), the causative SNP is enriched and segregates 1:1 in a pool of mutant BC2 individuals (Figure 1). Thus, calculating the SNP/non-SNP segregation ratio allows the quick identification of the causative mutation. The method is applicable to any model organism and mutagen causing mostly point mutations or small indels. SRM is the method of choice when working with (i) lethal mutations, (ii) hard-to-score phenotypes, (iii) mutations with low transmission, and (iv) second-site modifiers in complex genetic/ transgenic backgrounds. Here, we demonstrate the power of