Auxin regulates endosperm cellularization in Arabidopsis

Parental dialectic: Epigenetic conversations in endosperm

Endosperm is a major evolutionary innovation of flowering plants, and its proper development critically impacts seed growth and viability. Epigenetic regulators have a key function in parental control of endosperm development. Notably, epigenetic regulation of parental genome dosage is a major determinant of seed development success, and disruption of this balance can produce inviable seed, as observed in some interploidy and interspecific crosses. These postzygotic reproduction barriers are also a potent driver of speciation. The molecular machinery and regulatory architecture governing endosperm development is proposed to have evolved under parental conflict. In this review, we emphasize parental conflict as a dialectic conflict and discuss recent findings about the epigenetic molecular machinery that mediates parental conflict in the endosperm.

Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity

The endosperm, a product of double fertilization, is one of the keys to the evolution and success of angiosperms in conquering the land. While there are differences in endosperm development among flowering plants, the most common form is coenocytic growth, where the endosperm initially undergoes nuclear division without cytokinesis and eventually becomes cellularized. This complex process requires interplay among networks of transcription factors such as MADS-box, auxin response factors (ARFs), and phytohormones. The role of cytoskeletal elements in shaping the coenocytic endosperm and influencing seed growth also becomes evident. This review offers a recent understanding of the molecular and cellular dynamics in coenocytic endosperm development and their contributions to the final seed size.

Parental conflict driven regulation of endosperm cellularization by a family of Auxin Response Factors

The endosperm is a reproductive tissue supporting embryo development. In most flowering plants, the initial divisions of endosperm nuclei are not succeeded by cellularization; this process occurs only after a specific number of mitotic cycles have taken place. The timing of cellularization significantly influences seed viability and size. Previous research implicated auxin as a key factor in initiating nuclear divisions and determining the timing of cellularization. Here we uncover the involvement of a family of clustered auxin response factors (cARFs) as dosage-sensitive regulators of endosperm cellularization. cARFs, maternally expressed and paternally silenced, are shown to induce cellularization, thereby restricting seed growth. Our findings align with the predictions of the parental conflict theory, suggesting that cARFs represent major molecular targets in this conflict. We further demonstrate a recurring amplification of cARFs in the Brassicaceae, suggesting an evolutionary response to parental conflict by reinforcing maternal control over endosperm cellularization. Our study highlights that antagonistic parental control on endosperm cellularization converges on auxin biosynthesis and signalling.

Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.

Flowering plant reproduction

Flowering plants, also known as angiosperms, emerged approximately 150 to 200 million years ago. Since then, they have undergone rapid and extensive expansion, now encompassing around 90% of all land plant species. The remarkable diversification of this group has been a subject of in-depth investigations, and several evolutionary innovations have been proposed to account for their success. In this primer, we will specifically focus on one such innovation: the advent of seeds containing endosperm.

United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals

Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: (1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? (2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? (3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? (4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.

Evolutionary studies of the bHLH transcription factors belonging to MBW complex: their role in seed development

BACKGROUND AND AIMS

The MBW complex consist of proteins belonging to three major families (MYB, bHLH and WDR) involved in various processes throughout plant development: epidermal cell development, mucilage secretory cells and flavonoid biosynthesis. Recently, it has been reported that TT8, encoding a bHLH transcription factor, is involved in the biosynthesis of flavonoids in the seed coat and it also plays a role in bypassing the postzygotic barrier resulting from an unbalance in genetic loads of the parental lines. Here, we focus on the functional evolution, in seed development, of the bHLH proteins that are part of the MBW complex, complemented with a literature review.

METHODS

Phylogenetic analyses performed across seed plants and expression analyses in the reproductive tissues of four selected angiosperms (Arabidopsis thaliana, Brassica napus, Capsella rubella and Solanum lycopersicum) allow us to hypothesize on the evolution of its functions.

KEY RESULTS

TT8 expression in the innermost layer of the seed coat is conserved in the selected angiosperms. However, except for Arabidopsis, TT8 is also expressed in ovules, carpels and fruits. The homologues belonging to the sister clade of TT8, EGL3/GL3, involved in trichome development, are expressed in the outermost layer of the seed coat, suggesting potential roles in mucilage.

CONCLUSIONS

The ancestral function of these genes appears to be flavonoid biosynthesis, and the conservation of TT8 expression patterns in the innermost layer of the seed coat in angiosperms suggests that their function in postzygotic barriers might also be conserved. Moreover, the literature review and the results of the present study suggest a sophisticated association, linking the mechanisms of action of these genes to the cross-communication activity between the different tissues of the seed. Thus, it provides avenues to study the mechanisms of action of TT8 in the postzygotic triploid block, which is crucial because it impacts seed development in unbalanced crosses.

Winners take all: competition for carbon resource determines grain fate

As an evolutionary strategy, plants overproduce ovaries as a safety net for survival, with those losing in the competition for resources being aborted. Grain abortion is, however, highly detrimental agronomically. The molecular basis of selective abortion of grain siblings remains unknown. In this opinion article we assess the current understanding of the molecular players controlling carbon resource import into ovaries and young grains, followed by an evaluation of the spatial hierarchy of sink capacity among grain siblings, focusing on the roles exerted by sugar transporters and enzymes. We argue that, upon sequential pollination and fertilization, robust activation of the carbon import and sugar signaling system plays a key role in establishing the capacity of grain siblings to acquire enough carbon resources to survive and thrive.

[First evidence of nitrilase enzymatic activity of Xylaria sp. and its relationship with the biosynthesis of indole-3-acetic acid]

Endophytic fungi inhabit plant tissues internally and asymptomatically, and many of them are involved in the synthesis of bioactive metabolites of antifungal and therapeutic nature, as well as other compounds of biotechnological importance including indole derivatives, among many others. Ecologically, they provide some benefits to plants including protection against phytopathogens and promotion of root growth. In this sense, Xylaria sp. is a cellulose-decomposing fungus with biotechnological potential. It is worth mentioning that indole-3-acetic acid (IAA) also plays an extremely important role in plant-micro-organism interactions, as it is essential for physiology and proper plant morphological development. It is known that nitrile-hydrolytic enzymes (nitrilases) are involved in the synthesis of plant indole compounds; however, relatively little information is available concerning the nature of these enzymes in the fungal kingdom. In view of the above, through a biochemical and molecular-genetic approach, it has been demonstrated for the first time that Xylaria sp. carries out nitrile-hydrolytic enzyme activity using nitrogen and carbon-rich compounds as substrate. The studied strain increased its relative gene expression levels and showed mycelial growth, both in the presence of chemical compounds such as cyanobenzene and KCN. Thus, the results of this work suggest that the micro-organism is capable of degrading complex nitrogenous molecules. On the other hand, through fungal biofertilization, it was observed that Xylaria sp. promotes the development of the root system of Arabidopsis thaliana seedlings, in addition to synthesizing IAA.

Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley

Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.

Biosynthesis- and transport-mediated dynamic auxin distribution during seed development controls seed size in Arabidopsis

Auxin is indispensable to the fertilization-induced coordinated development of the embryo, endosperm, and seed coat. However, little attention has been given to the distribution pattern, maintenance mechanism, and function of auxin throughout the process of seed development. In the present study, we found that auxin response signals display a dynamic distribution pattern during Arabidopsis seed development. Shortly after fertilization, strong auxin response signals were observed at the funiculus, chalaza, and micropylar integument where the embryo attaches. Later, additional signals appeared at the middle layer of the inner integument (ii1') above the chalaza and the whole inner layer of the outer integument (oi1). These signals peaked when the seed was mature, then declined upon desiccation and disappeared in the dried seed. Auxin biosynthesis genes, including ASB1, TAA1, YUC1, YUC4, YUC8, and YUC9, contributed to the accumulation of auxin in the funiculus and seed coat. Auxin efflux carrier PIN3 and influx carrier AUX1 also contributed to the polar auxin distribution in the seed coat. PIN3 was expressed in the ii1 (innermost layer of the inner integument) and oi1 layers of the integument and showed polar localization. AUX1 was expressed in both layers of the outer integument and the endosperm and displayed a uniform localization. Further research demonstrated that the accumulation of auxin in the seed coat regulates seed size. Transgenic plants that specifically express the YUC8 gene in the oi2 or ii1 seed coat produced larger seeds. These results provide useful tools for cultivating high-yielding crops.

Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest

The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signaling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA-induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.

Meiocyte size is a determining factor for unreduced gamete formation in Arabidopsis thaliana

Polyploidy, the presence of more than two sets of chromosomes within a cell, is a widespread phenomenon in plants. The main route to polyploidy is considered through the production of unreduced gametes that are formed as a consequence of meiotic defects. Nevertheless, for reasons poorly understood, the frequency of unreduced gamete formation differs substantially among different plant species. The previously identified meiotic mutant jason (jas) in Arabidopsis thaliana forms about 60% diploid (2n) pollen. JAS is required to maintain an organelle band as a physical barrier between the two meiotic spindles, preventing previously separated chromosome groups from uniting into a single cell. In this study, we characterized the jas suppressor mutant telamon (tel) that restored the production of haploid pollen in the jas background. The tel mutant did not restore the organelle band, but enlarged the size of male jas tel meiocytes, suggesting that enlarged meiocytes can bypass the requirement of the organelle band. Consistently, enlarged meiocytes generated by a tetraploid jas mutant formed reduced gametes. The results reveal that meiocyte size impacts chromosome segregation in meiosis II, suggesting an alternative way to maintain the ploidy stability in meiosis during evolution.

High temporal-resolution transcriptome landscapes of maize embryo sac and ovule during early seed development

Here we provided a high temporal-resolution transcriptome atlas of maize embryo sac and ovule to reveal the gene activity dynamic during early seed development. The early maize (Zea mays) seed development is initiated from double fertilization in the embryo sac and needs to undergo a highly dynamic and complex development process to form the differentiated embryo and endosperm. Despite the importance of maize seed for food, feed, and biofuel, many regulators responsible for controlling its early development are not known yet. Here, we reported a high temporal-resolution transcriptome atlas of embryo sac and ovule based on 44 time point samples collected within the first four days of seed development. A total of 25,187 genes including 1598 transcription factors (TFs) involved in early seed development were detected. Global comparisons of the expressions of these genes revealed five distinct development stages of early seed, which are mainly related to double fertilization, asymmetric cell division of the zygote, as well as coenocyte formation, cellularization and differentiation in endosperm. We identified 3327 seed-specific genes, which more than one thousand seed-specific genes with main expressions during early seed development were newly identified here, including 859 and 186 genes predominantly expressed in the embryo sac and ovule, respectively. Combined with the published transcriptome data of seed, we uncovered the dominant auxin biosynthesis, transport and signaling related genes at different development stages and subregions of seed. These results are helpful for understanding the genetic control of early seed development.

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Many eukaryotes form multinucleated cells during their development. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellularization and how is it achieved across the eukaryotic tree of life? Are there common pathways among all species supporting a shared ancestry, or are there key differences, suggesting independent evolutionary paths? In this review, we discuss common strategies and key mechanistic differences in how cellularization is executed across vastly divergent eukaryotic species. We present a number of novel methods and non-model organisms that may provide important insight into the evolutionary origins of cellularization.

Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.

Transcriptome characteristics during cell wall formation of endosperm cellularization and embryo differentiation in Arabidopsis

Embryonic and endosperm development are important biological events during Arabidopsis seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the naa15 mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of Arabidopsis, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted naa15 seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from naa15-1/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and naa15. The heatmap and qPCR analyses showed that auxin response genes (ARFs), auxin transport genes (PINs) cytokinin synthesis genes (LOGs), cytokinin dehydrogenase genes (CKXs), cytokinin receptor, transcription factors (MYB, bHLH, MADS-box, and ERF) were significantly downregulated in naa15 compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of naa15 were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of naa15. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.

Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development

The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants.

In flowering plants, fertilization triggers auxin synthesis in the endosperm to promote seed and fruit development. Here the authors show that an MADS-box transcription factor AGL62 is required to activate auxin synthesis in the endosperms of Fragaria vesca, a diploid strawberry, and Arabidopsis.

BABY BOOM regulates early embryo and endosperm development

The zygote is a totipotent structure that develops into an embryo with all of the cells needed to produce an entire plant. The BABY BOOM (BBM) transcription factor induces spontaneous asexual embryo development on plant organs when ectopically expressed. Although BBM is at the top of a transcriptional network that promotes asexual embryo development, little is known about its expression and role during zygotic embryogenesis. Here we show in Arabidopsis that BBM regulates the progression of zygotic embryo development and embryo patterning, and division and cellularization of the filial endosperm. In line with its role as a totipotency factor, ectopic BBM expression in the egg cell is also sufficient to induce haploid embryo development in Arabidopsis and dicot crops.

The BABY BOOM (BBM) AINTEGUMENTA-LIKE (AIL) AP2/ERF domain transcription factor is a major regulator of plant cell totipotency, as it induces asexual embryo formation when ectopically expressed. Surprisingly, only limited information is available on the role of BBM during zygotic embryogenesis. Here we reexamined BBM expression and function in the model plant Arabidopsis thaliana (Arabidopsis) using reporter analysis and newly developed CRISPR mutants. BBM was expressed in the embryo from the zygote stage and also in the maternal (nucellus) and filial (endosperm) seed tissues. Analysis of CRISPR mutant alleles for BBM (bbm-cr) and the redundantly acting AIL gene PLETHORA2 (PLT2) (plt2-cr) uncovered individual roles for these genes in the timing of embryo progression. We also identified redundant roles for BBM and PLT2 in endosperm proliferation and cellularization and the maintenance of zygotic embryo development. Finally, we show that ectopic BBM expression in the egg cell of Arabidopsis and the dicot crops Brassica napus and Solanum lycopersicon is sufficient to bypass the fertilization requirement for embryo development. Together these results highlight roles for BBM and PLT2 in seed development and demonstrate the utility of BBM genes for engineering asexual embryo development in dicot species.

Embryo-Endosperm Interactions

In angiosperms, double fertilization triggers the concomitant development of two closely juxtaposed tissues, the embryo and the endosperm. Successful seed development and germination require constant interactions between these tissues, which occur across their common interface. The embryo-endosperm interface is a complex and poorly understood compound apoplast comprising components derived from both tissues, across which nutrients transit to fuel embryo development. Interface properties, which affect molecular diffusion and thus communication, are themselves dynamically regulated by molecular and physical dialogues between the embryo and endosperm. We review the current understanding of embryo-endosperm interactions, with a focus on the structure, properties, and function of their shared interface. Concentrating on Arabidopsis, but with reference to other species, we aim to situate recent findings within the broader context of seed physiology, developmental biology, and genetic factors such as parental conflicts over resource allocation.

Molecular mechanisms of maize endosperm transfer cell development

Endosperm transfer cells function as the nutrient transporter, antimicrobic barrier, and signal mediator between filial and maternal tissues. Sugar supply of maternal tissues, sugar demand of filial tissues, and requirement for defence against pathogens are three elemental factors inducing differentiation of endosperm transfer cells. Epigenetic factors, especially MEG1, moderate the key genetic factor ZmMRP-1 to activate endosperm transfer cell-specific genes that control the flange wall ingrowth formation and defensin-like protein secretion in maize. Auxin and cytokinin are primary hormones involved in development of maize endosperm transfer cells. Crosstalk between glucose and hormone signaling regulates endosperm transfer cell development via modifying ZmMRP-1 expression. This review summarizes the current knowledge on maize endosperm transfer cell development, and discusses its potential molecular mechanisms. It is expected to strengthen the theoretical basis for structural and functional optimization of endosperm transfer cells, and yield improvement of kernels in maize.

Maternal-filial transfer structures in endosperm: A nexus of nutritional dynamics and seed development

Although the ultimate purpose of a seed is the successful establishment of the next generation, seed development involves more than embryo growth. In angiosperms, seed development requires the intimate coordination of three distinct entities - maternal tissue and two offspring, embryo and embryo-nourishing endosperm. Although seeds are cornerstones of many terrestrial ecosystems and human diets, we are only beginning to understand the interactions among seed tissues and the molecular processes and genes that determine them. Recent studies of gene expression and function in distantly related angiosperms, combined with over 100 years of embryological research, have repeatedly highlighted the endosperm associated with maternal-filial boundaries as a central point in seed developmental dynamics. In this review, we highlight evidence that links this zone with nutritional dynamics, developmental signaling, and imprinted gene expression. We suggest that the underappreciated diversity of this specialized endosperm across angiosperms deserves further study from developmental, molecular, and genetic perspectives.

Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas

The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.

RH17 restricts reproductive fate and represses autonomous seed coat development in sexual Arabidopsis

Plant sexual and asexual reproduction through seeds (apomixis) is tightly controlled by complex gene regulatory programs, which are not yet fully understood. Recent findings suggest that RNA helicases are required for plant germline development. This resembles their crucial roles in animals, where they are involved in controlling gene activity and the maintenance of genome integrity. Here, we identified previously unknown roles of Arabidopsis RH17 during reproductive development. Interestingly, RH17 is involved in repression of reproductive fate and of elements of seed development in the absence of fertilization. In lines carrying a mutant rh17 allele, development of supernumerary reproductive cell lineages in the female flower tissues (ovules) was observed, occasionally leading to formation of two embryos per seed. Furthermore, seed coat, and putatively also endosperm development, frequently initiated autonomously. Such induction of several features phenocopying distinct elements of apomixis by a single mutation is unusual and suggests that RH17 acts in regulatory control of plant reproductive development. Furthermore, an in-depth understanding of its action might be of use for agricultural applications.

Endosperm-based incompatibilities in hybrid monkeyflowers

Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.

Localised expression of OsIAA29 suggests a key role for auxin in regulating development of the dorsal aleurone of early rice grains

Non-canonical AUX/IAA protein, OsIAA29, and ZmMPR-1 homologues, OsMRPLs, are part of an auxin-related signalling cascade operating in the dorsal aleurone during early rice grain development. Endosperm of rice and other cereals accumulates high concentrations of the predominant in planta auxin, indole-3-acetic acid (IAA) during early grain development. However, IAA signalling and function during endosperm development are poorly understood. Here, we report that OsYUC12 (an auxin biosynthesis gene) and OsIAA29 (encoding a non-canonical AUX/IAA) are both expressed exclusively in grains, reaching a maximum 5-6 days after pollination. OsYUC12 expression is localised in the aleurone, sub-aleurone and embryo, whereas OsIAA29 expression is restricted to a narrow strip in the dorsal aleurone, directly under the vascular bundle. Although rice has been reported to lack endosperm transfer cells (ETCs), this region of the aleurone is enriched with sugar transporters and is likely to play a key role in apoplastic nutrient transfer, analogous to ETCs in other cereals. OsIAA29 has orthologues only in grass species; expression of which is also specific to early grain development. OsYUC12 and OsIAA29 are temporally co-expressed with two genes (AL1 and OsPR602) previously linked to the development of dorsal aleurone or ETCs. Also up-regulated at the same time is a cluster of MYB-related genes (designated OsMRPLs) homologous to ZmMRP-1, which regulates maize ETC development. Wheat homologues of ZmMRP-1 are similarly expressed in ETCs. Although previous work has suggested that other cereals do not have orthologues of ZmMRP-1, our work suggests OsIAA29 and OsMRPLs and their homologues in other grasses are part of an auxin-regulated, conserved signalling network involved in the differentiation of cells with ETC-like function in developing cereal grains.

The Rab Geranylgeranyl Transferase Beta Subunit Is Essential for Embryo and Seed Development in Arabidopsis thaliana

Auxin is a key regulator of plant development affecting the formation and maturation of reproductive structures. The apoplastic route of auxin transport engages influx and efflux facilitators from the PIN, AUX and ABCB families. The polar localization of these proteins and constant recycling from the plasma membrane to endosomes is dependent on Rab-mediated vesicular traffic. Rab proteins are anchored to membranes via posttranslational addition of two geranylgeranyl moieties by the Rab Geranylgeranyl Transferase enzyme (RGT), which consists of RGTA, RGTB and REP subunits. Here, we present data showing that seed development in the rgtb1 mutant, with decreased vesicular transport capacity, is disturbed. Both pre- and post-fertilization events are affected, leading to a decrease in seed yield. Pollen tube recognition at the stigma and its guidance to the micropyle is compromised and the seed coat forms incorrectly. Excess auxin in the sporophytic tissues of the ovule in the rgtb1 plants leads to an increased tendency of autonomous endosperm formation in unfertilized ovules and influences embryo development in a maternal sporophytic manner. The results show the importance of vesicular traffic for sexual reproduction in flowering plants, and highlight RGTB1 as a key component of sporophytic-filial signaling.

The Role of Trehalose 6-Phosphate (Tre6P) in Plant Metabolism and Development

Trehalose 6-phosphate (Tre6P) has a dual function as a signal and homeostatic regulator of sucrose levels in plants. In source leaves, Tre6P regulates the production of sucrose to balance supply with demand for sucrose from growing sink organs. As a signal of sucrose availability, Tre6P influences developmental decisions that will affect future demand for sucrose, such as flowering, embryogenesis, and shoot branching, and links the growth of sink organs to sucrose supply. This involves complex interactions with SUCROSE-NON-FERMENTING1-RELATED KINASE1 that are not yet fully understood. Tre6P synthase, the enzyme that makes Tre6P, plays a key role in the nexus between sucrose and Tre6P, operating in the phloem-loading zone of leaves and potentially generating systemic signals for source-sink coordination. Many plants have large and diverse families of Tre6P phosphatase enzymes that dephosphorylate Tre6P, some of which have noncatalytic functions in plant development.

Endosperm development is an autonomously programmed process independent of embryogenesis

The seeds of flowering plants contain three genetically distinct structures: the embryo, endosperm, and seed coat. The embryo and endosperm need to interact and exchange signals to ensure coordinated growth. Accumulating evidence has confirmed that embryo growth is supported by the nourishing endosperm and regulated by signals originating from the endosperm. Available data also support that endosperm development requires communication with the embryo. Here, using single-fertilization mutants, Arabidopsis thaliana dmp8 dmp9 and gex2, we demonstrate that in the absence of a zygote and embryo, endosperm initiation, syncytium formation, free nuclear cellularization, and endosperm degeneration occur as in the wild type in terms of the cytological process and time course. Although rapid embryo expansion accelerates endosperm breakdown, our findings strongly suggest that endosperm development is an autonomously organized process, independent of egg cell fertilization and embryo-endosperm communication. This work confirms both the altruistic and self-directed nature of the endosperm during coordinated embryo-endosperm development. Our findings provide insights into the intricate interaction between the two fertilization products and will help to distinguish the physiological roles of the signaling between endosperm and embryo. These findings also open new avenues in agro-biotechnology for crop improvement.

Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis

BACKGROUND

Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1, encoding the largest subunit of the plant-specific RNA polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guide de novo methylation in the RNA-directed DNA methylation (RdDM) pathway. Recent work suggests that suppression of the triploid block by mutants in RdDM components differs, depending on whether the diploid pollen is derived from tetraploid plants or from the omission in second division 1 (osd1) mutant. This study aims to understand this difference.

RESULTS

In this study, we find that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. While first homozygous generation mutants in RdDM components NRPD1, RDR2, NRPE1, and DRM2 have weak or no ability to rescue the triploid block, they are able to suppress the triploid block with successive generations of inbreeding. Inbreeding of nrpd1 was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3.

CONCLUSIONS

Our data reveal that loss of RdDM function differs in its effect in early and late generations, which has important implications when interpreting the effect of RdDM mutants.

Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance

The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

OsYUC11-mediated auxin biosynthesis is essential for endosperm development of rice

Auxin is a phytohormone essential for plant development. However, our understanding of auxin-regulated endosperm development remains limited. Here, we described rice YUCCA (YUC) flavin-containing monooxygenase encoding gene OsYUC11 as a key contributor to auxin biosynthesis in rice (Oryza sativa) endosperm. Grain filling or storage product accumulation was halted by mutation of OsYUC11, but the deficiencies could be recovered by the exogenous application of auxin. A rice transcription factor (TF) yeast library was screened, and 41 TFs that potentially bind to the OsYUC11 promoter were identified, of which OsNF-YB1, a member of the nuclear factor Y family, is predominantly expressed in the endosperm. Both osyuc11 and osnf-yb1 mutants exhibited reduced seed size and increased chalkiness, accompanied by a reduction in indole-3-acetic acid biosynthesis. OsNF-YB1 can bind the OsYUC11 promoter to induce gene expression in vivo. We also found that OsYUC11 was a dynamically imprinted gene that predominantly expressed the paternal allele in the endosperm up to 10 d after fertilization (DAF) but then became a non-imprinted gene at 15 DAF. A functional maternal allele of OsYUC11 was able to recover the paternal defects of this gene. Overall, the findings indicate that OsYUC11-mediated auxin biosynthesis is essential for endosperm development in rice.

Mutation of the imprinted gene OsEMF2a induces autonomous endosperm development and delayed cellularization in rice

In angiosperms, endosperm development comprises a series of developmental transitions controlled by genetic and epigenetic mechanisms that are initiated after double fertilization. Polycomb repressive complex 2 (PRC2) is a key component of these mechanisms that mediate histone H3 lysine 27 trimethylation (H3K27me3); the action of PRC2 is well described in Arabidopsis thaliana but remains uncertain in cereals. In this study, we demonstrate that mutation of the rice (Oryza sativa) gene EMBRYONIC FLOWER2a (OsEMF2a), encoding a zinc-finger containing component of PRC2, causes an autonomous endosperm phenotype involving proliferation of the central cell nuclei with separate cytoplasmic domains, even in the absence of fertilization. Detailed cytological and transcriptomic analyses revealed that the autonomous endosperm can produce storage compounds, starch granules, and protein bodies specific to the endosperm. These events have not been reported in Arabidopsis. After fertilization, we observed an abnormally delayed developmental transition in the endosperm. Transcriptome and H3K27me3 ChIP-seq analyses using endosperm from the emf2a mutant identified downstream targets of PRC2. These included >100 transcription factor genes such as type-I MADS-box genes, which are likely required for endosperm development. Our results demonstrate that OsEMF2a-containing PRC2 controls endosperm developmental programs before and after fertilization.

The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (♀)/9311 (♂) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.

The maternally expressed polycomb group gene OsEMF2a is essential for endosperm cellularization and imprinting in rice

Cellularization is a key event in endosperm development. Polycomb group (PcG) genes, such as Fertilization-Independent Seed 2 (FIS2), are vital for the syncytium-to-cellularization transition in Arabidopsis plants. In this study, we found that OsEMF2a, a rice homolog of the Arabidopsis PcG gene Embryonic Flower2 (EMF2), plays a role similar to that of FIS2 in regard to seed development, although there is limited sequence similarity between the genes. Delayed cellularization was observed in osemf2a, associated with an unusual activation of type I MADS-box genes. The cell cycle was persistently activated in osemf2a caryopses, which was likely caused by cytokinin overproduction. However, the overaccumulation of auxin was not found to be associated with the delayed cellularization. As OsEMF2a is a maternally expressed gene in the endosperm, a paternally inherited functional allele was unable to recover the maternal defects of OsEMF2a. Many imprinted rice genes were deregulated in the defective hybrid seeds of osemf2a (♀)/9311 (♂) (m9). The paternal expression bias of some paternally expressed genes was disrupted in m9 due to either the activation of maternal alleles or the repression of paternal alleles. These findings suggest that OsEMF2a-PRC2-mediated H3K27me3 is necessary for endosperm cellularization and genomic imprinting in rice.

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response of Fie1 in grains developing under HNT stress. We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

Seed coat development in explosively dispersed seeds of Cardamine hirsuta

BACKGROUND AND AIMS

Seeds are dispersed by explosive coiling of the fruit valves in Cardamine hirsuta. This rapid coiling launches the small seeds on ballistic trajectories to spread over a 2 m radius around the parent plant. The seed surface interacts with both the coiling fruit valve during launch and subsequently with the air during flight. We aim to identify features of the seed surface that may contribute to these interactions by characterizing seed coat differentiation.

METHODS

Differentiation of the outermost seed coat layers from the outer integuments of the ovule involves dramatic cellular changes that we characterize in detail at the light and electron microscopical level including immunofluorescence and immunogold labelling.

KEY RESULTS

We found that the two outer integument (oi) layers of the seed coat contributed differently to the topography of the seed surface in the explosively dispersed seeds of C. hirsuta vs. the related species Arabidopsis thaliana where seed dispersal is non-explosive. The surface of A. thaliana seeds is shaped by the columella and the anticlinal cell walls of the epidermal oi2 layer. In contrast, the surface of C. hirsuta seeds is shaped by a network of prominent ridges formed by the anticlinal walls of asymmetrically thickened cells of the sub-epidermal oi1 layer, especially at the seed margin. Both the oi2 and oi1 cell layers in C. hirsuta seeds are characterized by specialized, pectin-rich cell walls that are deposited asymmetrically in the cell.

CONCLUSIONS

The two outermost seed coat layers in C. hirsuta have distinct properties: the sub-epidermal oi1 layer determines the topography of the seed surface, while the epidermal oi2 layer accumulates mucilage. These properties are influenced by polar deposition of distinct pectin polysaccharides in the cell wall. Although the ridged seed surface formed by oi1 cell walls is associated with ballistic dispersal in C. hirsuta, it is not restricted to explosively dispersed seeds in the Brassicaceae.

PHERES1 Controls Endosperm Gene Imprinting and Seed Development

In contrast to mammals, genomic imprinting primarily occurs in the endosperm in flowering plants. Nevertheless, the imprinting drivers and functions of imprinted genes remain poorly understood. Batista et al. identified the type I MADS-box transcription factor (TF) PHERES1 (PHE1) as a key regulator of some imprinted and nonimprinted genes required for endosperm development.

Auxin: Hormonal Signal Required for Seed Development and Dormancy

The production of viable seeds is a key event in the life cycle of higher plants. Historically, abscisic acid (ABA) and gibberellin (GAs) were considered the main hormones that regulate seed formation. However, auxin has recently emerged as an essential player that modulates, in conjunction with ABA, different cellular processes involved in seed development as well as the induction, regulation and maintenance of primary dormancy (PD). This review examines and discusses the key role of auxin as a signaling molecule that coordinates seed life. The cellular machinery involved in the synthesis and transport of auxin, as well as their cellular and tissue compartmentalization, is crucial for the development of the endosperm and seed-coat. Thus, auxin is an essential compound involved in integuments development, and its transport from endosperm is regulated by AGAMOUS-LIKE62 (AGL62) whose transcript is specifically expressed in the endosperm. In addition, recent biochemical and genetic evidence supports the involvement of auxins in PD. In this process, the participation of the transcriptional regulator ABA INSENSITIVE3 (ABI3) is critical, revealing a cross-talk between auxin and ABA signaling. Future experimental aimed at advancing knowledge of the role of auxins in seed development and PD are also discussed.

Spatiotemporal Restriction of FUSCA3 Expression by Class I BPCs Promotes Ovule Development and Coordinates Embryo and Endosperm Growth

Spatiotemporal regulation of gene expression is critical for proper developmental timing in plants and animals. The transcription factor FUSCA3 (FUS3) regulates developmental phase transitions by acting as a link between hormonal pathways in Arabidopsis (Arabidopsis thaliana). However, the mechanisms governing its spatiotemporal expression pattern are poorly understood. Here, we show that FUS3 is repressed in the ovule integuments and seed endosperm. FUS3 repression requires class I BASIC PENTACYSTEINE (BPC) proteins, which directly bind GA/CT cis-elements in FUS3 and restrict its expression pattern. During vegetative and reproductive development, FUS3 derepression in bpc1-1 bpc2 (bpc1/2) double mutant or misexpression in ProML1:FUS3 lines causes dwarf plants carrying defective flowers and aborted ovules. After fertilization, ectopic FUS3 expression in bpc1/2 endosperm or ProML1:FUS3 endosperm and endothelium increases endosperm nuclei proliferation and seed size, causing delayed or arrested embryo development. These phenotypes are rescued in bpc1/2 fus3-3 Finally, class I BPCs interact with FIS-PRC2 (FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex2), which represses FUS3 in the endosperm during early seed development. We propose that BPC1 and 2 promote the transition from reproductive to seed development by repressing FUS3 in ovule integuments. After fertilization, BPC1 and 2 and FIS-PRC2 repress FUS3 in the endosperm to coordinate early endosperm and embryo growth.

Functional Features of TREHALOSE-6-PHOSPHATE SYNTHASE1, an Essential Enzyme in Arabidopsis

In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.

Into the Seed: Auxin Controls Seed Development and Grain Yield

Seed development, which involves mainly the embryo, endosperm and integuments, is regulated by different signaling pathways, leading to various changes in seed size or seed weight. Therefore, uncovering the genetic and molecular mechanisms of seed development has great potential for improving crop yields. The phytohormone auxin is a key regulator required for modulating different cellular processes involved in seed development. Here, we provide a comprehensive review of the role of auxin biosynthesis, transport, signaling, conjugation, and catabolism during seed development. More importantly, we not only summarize the research progress on the genetic and molecular regulation of seed development mediated by auxin but also discuss the potential of manipulating auxin metabolism and its signaling pathway for improving crop seed weight.

MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice

MADS box transcription factors (TFs) are subdivided into type I and II based on phylogenetic analysis. The type II TFs regulate floral organ identity and flowering time, but type I TFs are relatively less characterized. Here, we report the functional characterization of two type I MADS box TFs in rice (Oryza sativa), MADS78 and MADS79 Transcript abundance of both these genes in developing seed peaked at 48 h after fertilization and was suppressed by 96 h after fertilization, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing MADS78 and MADS 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9-mediated single knockout mutants showed precocious endosperm cellularization. MADS78 and MADS 79 were indispensable for seed development, as a double knockout mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type I MADS box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED-POLYCOMB REPRESSOR COMPLEX2 component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting that Fie1 could be involved in negative regulation of MADS78 and MADS 79 Misregulation of MADS78 and MADS 79 perturbed auxin homeostasis and carbon metabolism, as evident by misregulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show that MADS78 and MADS 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice.

Clonal Reproduction through Seeds in Sight for Crops

Apomixis or asexual reproduction through seeds, enables the preservation of hybrid vigor. Hybrids are heterozygous and segregate for genotype and phenotype upon sexual reproduction. While apomixis, that is, clonal reproduction, is intuitively antithetical to diversity, it is rarely obligate and actually provides a mechanism to recover and maintain superior hybrid gene combinations for which sexual reproduction would reveal deleterious alleles in less fit genotypes. Apomixis, widespread across flowering plant orders, does not occur in major crop species, yet its introduction could add a valuable tool to the breeder's toolbox. In the past decade, discovery of genetic mechanisms regulating meiosis, embryo and endosperm development have facilitated proof-of-concept for the synthesis of apomixis, bringing apomictic crops closer to reality.

Family plot: the impact of the endosperm and other extra-embryonic seed tissues on angiosperm zygotic embryogenesis

The zygotic embryos of angiosperms develop buried deep within seeds and surrounded by two main extra-embryonic tissues: the maternally derived seed coat tissues and the zygotic endosperm. Generally, these tissues are considered to play an important role in nurturing the developing embryo by acting as conduits for maternally derived nutrients. They are also critical for key seed traits (dormancy establishment and control, longevity, and physical resistance) and thus for seed and seedling survival. However, recent studies have highlighted the fact that extra-embryonic tissues in the seed also physically and metabolically limit embryonic development and that unique mechanisms may have evolved to overcome specific developmental and genetic constraints associated with the seed habit in angiosperms. The aim of this review is to illustrate how these studies have begun to reveal the highly complex physical and physiological relationship between extra-embryonic tissues and the developing embryo. Where possible I focus on Arabidopsis because of space constraints, but other systems will be cited where relevant.

A role for auxin signaling in the acquisition of longevity during seed maturation

Seed longevity, the maintenance of viability during dry storage, is a crucial factor to preserve plant genetic resources and seed vigor. Inference of a temporal gene-regulatory network of seed maturation identified auxin signaling as a putative mechanism to induce longevity-related genes. Using auxin-response sensors and tryptophan-dependent auxin biosynthesis mutants of Arabidopsis thaliana L., the role of auxin signaling in longevity was studied during seed maturation. DII and DR5 sensors demonstrated that, concomitant with the acquisition of longevity, auxin signaling input and output increased and underwent a spatiotemporal redistribution, spreading throughout the embryo. Longevity of seeds of single auxin biosynthesis mutants with altered auxin signaling activity was affected in a dose-response manner depending on the level of auxin activity. Longevity-associated genes with promoters enriched in auxin response elements and the master regulator ABSCISIC ACID INSENSITIVE3 were induced by auxin in developing embryos and deregulated in auxin biosynthesis mutants. The beneficial effect of exogenous auxin during seed maturation on seed longevity was abolished in abi3-1 mutants. These data suggest a role for auxin signaling activity in the acquisition of longevity during seed maturation.

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

Natural Variation in Ovule Morphology Is Influenced by Multiple Tissues and Impacts Downstream Grain Development in Barley (Hordeum vulgare L.)

The ovule plays a critical role in cereal yield as it is the site of fertilization and the progenitor of the grain. The ovule primordium is generally comprised of three domains, the funiculus, chalaza, and nucellus, which give rise to distinct tissues including the integuments, nucellar projection, and embryo sac. The size and arrangement of these domains varies significantly between model eudicots, such as Arabidopsis thaliana, and agriculturally important monocotyledonous cereal species, such as Hordeum vulgare (barley). However, the amount of variation in ovule development among genotypes of a single species, and its functional significance, remains unclear. To address this, wholemount clearing was used to examine the details of ovule development in barley. Nine sporophytic and gametophytic features were examined at ovule maturity in a panel of 150 European two-row spring barley genotypes, and compared with grain traits from the preceding and same generation. Correlations were identified between ovule traits and features of grain they produced, which in general highlighted a negative correlation between nucellus area, ovule area, and grain weight. We speculate that the amount of ovule tissue, particularly the size of the nucellus, may affect the timing of maternal resource allocation to the fertilized embryo sac, thereby influencing subsequent grain development.

Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation

Seed development is a complex regulatory process that includes a transition from gametophytic to sporophytic program. The synchronized development of different seed compartments (seed coat, endosperm and embryo) depends on a balance in parental genome contributions. In the most severe cases, the disruption of the balance leads to seed abortion. This represents one of the main obstacles for the engineering of asexual reproduction through seeds (apomixis), and for generating new interspecies hybrids. The repression of auxin synthesis by the Polycomb Repressive Complex 2 (PRC2) is a major mechanism contributing to sensing genome balance. However, current efforts focusing on decreasing PRC2 or elevating auxin levels have not yet resulted in the production of apomictic seed. Here, we show that EMSY-Like Tudor/Agenet H3K36me3 histone readers EML1 and EML3 are necessary for early stages of seed development to proceed at a normal rate in Arabidopsis. We further demonstrate that both EML1 and EML3 are required to prevent the initiation of seed development in the absence of fertilization. Based on the whole genome expression analysis, we identify auxin transport and signaling genes as the most enriched downstream targets of EML1 and EML3. We hypothesize that EML1 and EML3 function to repress and soften paternal gene expression by fine-tuning auxin responses. Discovery of this pathway may contribute to the engineering of apomixis and interspecies hybrids.