Developmental and genomic architecture of plant embryogenesis: from model plant to crops

The pentatricopeptide repeat protein DG1 promotes the transition to bilateral symmetry during Arabidopsis embryogenesis through GUN1-mediated plastid signals

During Arabidopsis embryogenesis, the transition of the embryo's symmetry from radial to bilateral between the globular and heart stage is a crucial event, involving the formation of cotyledon primordia and concurrently the establishment of a shoot apical meristem (SAM). However, a coherent framework of how this transition is achieved remains to be elucidated. In this study, we investigated the function of DELAYED GREENING 1 (DG1) in Arabidopsis embryogenesis using a newly identified dg1-3 mutant. The absence of chloroplast-localized DG1 in the mutants led to embryos being arrested at the globular or heart stage, accompanied by an expansion of WUSCHEL (WUS) and SHOOT MERISTEMLESS (STM) expression. This finding pinpoints the essential role of DG1 in regulating the transition to bilateral symmetry. Furthermore, we showed that this regulation of DG1 may not depend on its role in plastid RNA editing. Nevertheless, we demonstrated that the DG1 function in establishing bilateral symmetry is genetically mediated by GENOMES UNCOUPLED 1 (GUN1), which represses the transition process in dg1-3 embryos. Collectively, our results reveal that DG1 functionally antagonizes GUN1 to promote the transition of the Arabidopsis embryo's symmetry from radial to bilateral and highlight the role of plastid signals in regulating pattern formation during plant embryogenesis.

Perspectives on embryo maturation and seed quality in a global climate change scenario

Global climate change has already brought noticeable alterations to multiple regions of our planet, including increased CO2 concentrations and changes in temperature. Several important steps of plant growth and development, such as embryogenesis, can be affected by such environmental changes; for instance, they affect how stored nutrients are used during early stages of seed germination during the transition from heterotrophic to autotrophic metabolism-a critical period for the seedling's survival. In this article, we briefly describe relevant processes that occur during embryo maturation and account for nutrient accumulation, which are sensitive to environmental change. Most of the nutrients stored in the seed during its development-including carbohydrates, lipids, and proteins, depending on the species-accumulate during the seed maturation stage. It is also known that iron, a key micronutrient for various electron transfer processes in plant cells, accumulates during embryo maturation. The existing literature indicates that climate change can not only affect the quality of the seed, in terms of total nutritional content, but also affect seed production. We discuss the potential effects of temperature and CO2 increases from an embryo-autonomous point of view, in an attempt to separate the effects on the parent plant from those on the embryo.

The contest between artificial management and natural environment determines the adaptive strategies of leaf morphogenesis in Sabina chinensis

Sabina chinensis is a typically heteromorphic leaf evergreen tree worldwide with both ornamental and ecological value. However, the shaping mechanism of heteromorphic leaves of S. chinensis and its adaptability to environment are important factors determining its morphology. The morphological change of S. chinensis under different habitats (tree around) and treatments (light, pruning and nutrients) was investigated. Our findings suggested that the prickle leaves proportion was associated with low light intensity and soil nutrient scarcity. Stems and leaves are pruned together to form clusters of large prickle leaves, while only pruning leaves often form alternately growing small prickle leaves and scale leaves, and the length of the prickle leaves is between 0.5 cm and 1 cm. The gene expression of prickle leaves is higher than that of scale leaves under adverse environmental conditions, and the gene expression correlations between small prickle leaf and scale leaf were the highest. Homologous and heterologous mutants of gene structure in prickle leaves were larger than those in scale leaves. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that phenylpropanone and flavonoid biosynthesis were common enrichment pathways, and that the enrichment genes were mainly related to metabolism, genetic information processing and organismal systems. Therefore, we concluded that the occurrence of the heteromorphic leaf phenomenon was related to the changes in photosynthesis, mechanical damage and nutrient supplementation. The organic matter in the S. chinensis prickle leaves was reduced under environmental stresses, and it will be allocated to the expression of prickle leaf or protective cuticles formation.

Widening Genetic Diversity Using Embryo Rescue in Cucurbit Crops: A Review

Embryo rescue is a vital technique in cucurbit breeding and propagation, addressing challenges such as embryo abortion, poor seed viability, and incompatibility barriers. This method involves the excision of immature embryos from seeds followed by their in vitro culture on a nutrient medium, providing an environment conducive to their growth and development. In cucurbits, embryo rescue has been extensively utilized to overcome barriers to hybridization, enabling the production of interspecific and intergeneric hybrids with desired traits. Various factors, including genotype, developmental stage of embryos, and culture conditions, influence the success of embryo rescue in cucurbits. Optimal nutrient formulations, growth regulators, and culture techniques are critical for promoting embryo germination, shoot elongation, and subsequent plantlet establishment. Additionally, embryo rescue facilitates the recovery of valuable genetic material from wild and exotic cucurbit species, expanding genetic diversity and developing novel cultivars with improved traits such as disease resistance, yield, and quality. This review highlights the principles, applications, and advancements in embryo rescue technology in cucurbits, emphasizing its significance in cucurbit breeding programs and crop improvement efforts.

Tropical peanut maturation scale for harvesting seeds with superior quality

Determining the moment for harvesting the tropical peanut with a focus on superior seed quality is not an easy task. Particularities such as indeterminate flowering, underground fruiting and uneven maturation further increase this technical challenge. It is in this context that we aim to investigate harvest indicators based on the maturation and late maturation phases of tropical peanuts to obtain seeds with superior physiological and health quality. The plants were grown in field conditions and their development stages were carefully monitored until seed production. The water content, dry weight, germination capacity, desiccation tolerance, vigor, longevity, and seed pathogens were evaluated throughout these stages. We showed that seeds from early stages (R5 and R6) did not fully tolerate desiccation and were highly sensitive to pathogen contamination after storage (Aspergillus, Penicillium, and Bacteria). At late stages (R7, R8, and R9), the seeds had optimized vigor, longevity and bioprotection against fungi and thermal stress. The peanut maturation scale for tropical agriculture provides unique harvesting guidelines that make it possible to monitor the plants' development stages with a focus on producing superior quality seeds.

Multifaceted roles of transcription factors during plant embryogenesis

Transcription factors (TFs) are diverse groups of regulatory proteins. Through their specific binding domains, TFs bind to their target genes and regulate their expression, therefore TFs play important roles in various growth and developmental processes. Plant embryogenesis is a highly regulated and intricate process during which embryos arise from various sources and undergo development; it can be further divided into zygotic embryogenesis (ZE) and somatic embryogenesis (SE). TFs play a crucial role in the process of plant embryogenesis with a number of them acting as master regulators in both ZE and SE. In this review, we focus on the master TFs involved in embryogenesis such as BABY BOOM (BBM) from the APETALA2/Ethylene-Responsive Factor (AP2/ERF) family, WUSCHEL and WUSCHEL-related homeobox (WOX) from the homeobox family, LEAFY COTYLEDON 2 (LEC2) from the B3 family, AGAMOUS-Like 15 (AGL15) from the MADS family and LEAFY COTYLEDON 1 (LEC1) from the Nuclear Factor Y (NF-Y) family. We aim to present the recent progress pertaining to the diverse roles these master TFs play in both ZE and SE in Arabidopsis, as well as other plant species including crops. We also discuss future perspectives in this context.

Functional Modules in the Meristems: "Tinkering" in Action

BACKGROUND

A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem).

CONCLUSIONS

The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.

Embryo Rescue in Plant Breeding

Embryo rescue (ER) techniques are among the oldest and most successful in vitro tissue culture protocols used with plant species. ER refers to a series of methods that promote the development of an immature or lethal embryo into a viable plant. Intraspecific, interspecific, or intergeneric crosses allow the introgression of important alleles of agricultural interest from wild species, such as resistance or tolerance to abiotic and biotic stresses or morphological traits in crops. However, pre-zygotic and post-zygotic reproductive barriers often present challenges in achieving successful hybridization. Pre-zygotic barriers manifest as incompatibility reactions that hinder pollen germination, pollen tube growth, or penetration into the ovule occurring in various tissues, such as the stigma, style, or ovary. To overcome these barriers, several strategies are employed, including cut-style or graft-on-style techniques, the utilization of mixed pollen from distinct species, placenta pollination, and in vitro ovule pollination. On the other hand, post-zygotic barriers act at different tissues and stages ranging from early embryo development to the subsequent growth and reproduction of the offspring. Many crosses among different genera result in embryo abortion due to the failure of endosperm development. In such cases, ER techniques are needed to rescue these hybrids. ER holds great promise for not only facilitating successful crosses but also for obtaining haploids, doubled haploids, and manipulating the ploidy levels for chromosome engineering by monosomic and disomic addition as well substitution lines. Furthermore, ER can be used to shorten the reproductive cycle and for the propagation of rare plants. Additionally, it has been repeatedly used to study the stages of embryonic development, especially in embryo-lethal mutants. The most widely used ER procedure is the culture of immature embryos taken and placed directly on culture media. In certain cases, the in vitro culture of ovule, ovaries or placentas enables the successful development of young embryos from the zygote stage to maturity.

Systems-level proteomics and metabolomics reveals the diel molecular landscape of diverse kale cultivars

Kale is a group of diverse Brassicaceae species that are nutritious leafy greens consumed for their abundance of vitamins and micronutrients. Typified by their curly, serrated and/or wavy leaves, kale varieties have been primarily defined based on their leaf morphology and geographic origin, despite having complex genetic backgrounds. Kale is a very promising crop for vertical farming due to its high nutritional content; however, being a non-model organism, foundational, systems-level analyses of kale are lacking. Previous studies in kale have shown that time-of-day harvesting can affect its nutritional composition. Therefore, to gain a systems-level diel understanding of kale across its wide-ranging and diverse genetic landscape, we selected nine publicly available and commercially grown kale cultivars for growth under near-sunlight LED light conditions ideal for vertical farming. We then analyzed changes in morphology, growth and nutrition using a combination of plant phenotyping, proteomics and metabolomics. As the diel molecular activities of plants drive their daily growth and development, ultimately determining their productivity as a crop, we harvested kale leaf tissue at both end-of-day (ED) and end-of-night (EN) time-points for all molecular analyses. Our results reveal that diel proteome and metabolome signatures divide the selected kale cultivars into two groups defined by their amino acid and sugar content, along with significant proteome differences involving carbon and nitrogen metabolism, mRNA splicing, protein translation and light harvesting. Together, our multi-cultivar, multi-omic analysis provides new insights into the molecular underpinnings of the diel growth and development landscape of kale, advancing our fundamental understanding of this nutritious leafy green super-food for horticulture/vertical farming applications.

ORIGIN OF RECOGNITION COMPLEX 3 controls the development of maternal excess endosperm in the Paspalum simplex agamic complex (Poaceae)

Pseudogamous apomixis in Paspalum simplex generates seeds with embryos genetically identical to the mother plant and endosperms deviating from the canonical 2(maternal):1(paternal) parental genome contribution into a maternal excess 4m:1p genome ratio. In P. simplex, the gene homologous to that coding for subunit 3 of the ORIGIN OF RECOGNITION COMPLEX (PsORC3) exists in three isogenic forms: PsORC3a is apomixis specific and constitutively expressed in developing endosperm whereas PsORCb and PsORCc are up-regulated in sexual endosperms and silenced in apomictic ones. This raises the question of how the different arrangement and expression profiles of these three ORC3 isogenes are linked to seed development in interploidy crosses generating maternal excess endosperms. We demonstrate that down-regulation of PsORC3b in sexual tetraploid plants is sufficient to restore seed fertility in interploidy 4n×2n crosses and, in turn, its expression level at the transition from proliferating to endoreduplication endosperm developmental stages dictates the fate of these seeds. Furthermore, we show that only when being maternally inherited can PsORC3c up-regulate PsORC3b. Our findings lay the basis for an innovative route-based on ORC3 manipulation-to introgress the apomictic trait into sexual crops and overcome the fertilization barriers in interploidy crosses.

Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development

Lentil (Lens culinaris Medik.) is a nutritious legume with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature seed and thus its end-use quality. Understanding the molecular and cellular events and metabolic processes of seed development is essential for improving lentil yield and seed nutritional value. However, such information remains largely unknown, especially at the seed compartment level. In this study, we generated high-resolution spatiotemporal gene expression profiles in lentil embryo, seed coat and whole seeds from fertilization through maturation. Apart from anatomic differences between the embryo and seed coat, comparative transcriptomics and weighted gene co-expression network analysis revealed embryo- and seed coat-specific genes and gene modules predominant in specific tissues and stages, which highlights distinct genetic programming. Furthermore, we investigated the dynamic profiles of flavonoid, isoflavone, phytic acid and saponin in seed compartments across seed development. Coupled with transcriptome data, we identified sets of candidate genes involved in the biosynthesis of these metabolites. The global view of the transcriptional and metabolic changes of lentil seed tissues throughout development provides a valuable resource for dissecting the genetic control of secondary metabolism and development of molecular tools for improving seed nutritional quality.

Morphogenesis of leaves: from initiation to the production of diverse shapes

The manner by which plant organs gain their shape is a longstanding question in developmental biology. Leaves, as typical lateral organs, are initiated from the shoot apical meristem that harbors stem cells. Leaf morphogenesis is accompanied by cell proliferation and specification to form the specific 3D shapes, with flattened lamina being the most common. Here, we briefly review the mechanisms controlling leaf initiation and morphogenesis, from periodic initiation in the shoot apex to the formation of conserved thin-blade and divergent leaf shapes. We introduce both regulatory gene patterning and biomechanical regulation involved in leaf morphogenesis. How phenotype is determined by genotype remains largely unanswered. Together, these new insights into leaf morphogenesis resolve molecular chains of events to better aid our understanding.

Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat

BACKGROUND

Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.

RESULTS

Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal-distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.

CONCLUSIONS

Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.

Developing Genetic Engineering Techniques for Control of Seed Size and Yield

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

The role of APC/C in cell cycle dynamics, growth and development in cereal crops

Cereal crops can be considered the basis of human civilization. Thus, it is not surprising that these crops are grown in larger quantities worldwide than any other food supply and provide more energy to humankind than any other provision. Additionally, attempts to harness biomass consumption continue to increase to meet human energy needs. The high pressures for energy will determine the demand for crop plants as resources for biofuel, heat, and electricity. Thus, the search for plant traits associated with genetic increases in yield is mandatory. In multicellular organisms, including plants, growth and development are driven by cell division. These processes require a sequence of intricated events that are carried out by various protein complexes and molecules that act punctually throughout the cycle. Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. Considering the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. Studies on plant APC/C subunits and activators, mainly in the model plant Arabidopsis, revealed that they play a pivotal role in several developmental processes during growth. However, little is known about the role of APC/C in cereal crops. Here, we discuss the current understanding of the APC/C controlling cereal crop development.

Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation

Many over-wintering plants grown in temperate climate acquire competence to flower upon prolonged cold exposure in winter, through vernalization. In Arabidopsis thaliana, prolonged cold exposure induces the silencing of the potent floral repressor FLOWERING LOCUS C (FLC) through repressive chromatin modifications by Polycomb proteins. This repression is maintained to enable flowering after return to warmth, but is reset during seed development. Here, we show that embryonic FLC reactivation occurs in two phases: resetting of cold-induced FLC silencing during embryogenesis and further FLC activation during embryo maturation. We found that the B3 transcription factor (TF) ABSCISIC ACID-INSENSITIVE 3 (ABI3) mediates both FLC resetting in embryogenesis and further activation of FLC expression in embryo maturation. ABI3 binds to the cis-acting cold memory element at FLC and recruits a scaffold protein with active chromatin modifiers to reset FLC chromatin into an active state in late embryogenesis. Moreover, in response to abscisic acid (ABA) accumulation during embryo maturation, ABI3, together with the basic leucine zipper TF ABI5, binds to an ABA-responsive cis-element to further activate FLC expression to high level. Therefore, we have uncovered the molecular circuitries underlying embryonic FLC reactivation following parental vernalization, which ensures that each generation must experience winter cold prior to flowering.

Understanding the root xylem plasticity for designing resilient crops

Xylem is the main route for transporting water, minerals and a myriad of signalling molecules within the plant. With its onset during early embryogenesis, the development of the xylem relies on hormone gradients, the activity of unique transcription factors, the distribution of mobile microRNAs, and receptor-ligand pathways. These regulatory mechanisms are often interconnected and together contribute to the plasticity of this water-conducting tissue. Environmental stresses, such as drought and salinity, have a great impact on xylem patterning. A better understanding of how the structural properties of the xylem are regulated in normal and stress conditions will be instrumental in developing crops of the future. In addition, vascular wilt pathogens that attack the xylem are becoming increasingly problematic. Further knowledge of xylem development in response to these pathogens will bring new solutions against these diseases. In this review, we summarize recent findings on the molecular mechanisms of xylem formation that largely come from Arabidopsis research with additional insights from tomato and monocot species. We emphasize the impact of abiotic factors and pathogens on xylem plasticity and the urgent need to uncover the underlying mechanisms. Finally, we discuss the multidisciplinary approach to model xylem capacities in crops.

Chrysanthemum embryo development is negatively affected by a novel ERF transcription factor, CmERF12

Embryo abortion often occurs during distant hybridization events. Apetala 2/ethylene-responsive factor (AP2/ERF) proteins are key transcription factor (TF) regulators of plant development and stress resistance, but their roles in hybrid embryo development are poorly understood. In this study, we isolated a novel AP2/ERF TF, CmERF12, from chrysanthemum and show that it adversely affects embryo development during distant hybridization. Transcriptome and real-time quantitative PCR demonstrate that CmERF12 is expressed at significantly higher levels in aborted ovaries compared with normal ones. CmERF12 localizes to the cell nucleus and contains a conserved EAR motif that mediates its transcription repressor function in yeast and plant cells. We generated artificial microRNA (amiR) CmERF12 transgenic lines of Chrysanthemum morifolium var. 'Yuhualuoying' and conducted distant hybridization with the wild-type tetraploid, Chrysanthemum nankingense, and found that CmERF12-knock down significantly promoted embryo development and increased the seed-setting rates during hybridization. The expression of various genes related to embryo development was up-regulated in developing ovaries from the cross between female amiR-CmERF12 C. morifolium var. 'Yuhualuoying'× male C. nankingense. Furthermore, CmERF12 directly interacted with CmSUF4, which is known to affect flower development and embryogenesis, and significantly reduced its ability to activate its target gene CmEC1 (EGG CELL1). Our study provides a novel method to overcome barriers to distant hybridization in plants and reveals the mechanism by which CmERF12 negatively affects chrysanthemum embryo development.

Endosperm-Embryo Communications: Recent Advances and Perspectives

Seed maturation depends on well-coordinated communications between the processes of endosperm and embryo development. The endosperm is considered to be destined to support embryo development and the timing of endosperm cellularization is critical for embryo growth. Recent findings suggest that the endosperm development and the onset of embryo maturation are two independent processes during seed development. Meanwhile, it is lately reported that several mobile regulators originating from the endosperm are needed to ensure proper embryo growth and seed maturation. In this opinion article, we highlight processes on how endosperm communicates with embryo during seed development and discuss some intriguing questions in light of the latest advancements.

Auxin and Target of Rapamycin Spatiotemporally Regulate Root Organogenesis

The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and stress tolerance. Hormones and signaling pathways play regulatory roles during root development. Among these, auxin is the most important hormone regulating root development. The target of rapamycin (TOR) signaling pathway has also been shown to play a key role in root developmental programs. In this article, the milestones and influential progress of studying crosstalk between auxin and TOR during the development of ERs, PRs, LRs and ARs, as well as their functional implications in root morphogenesis, development, and architecture, are systematically summarized and discussed.

Transcriptomic Time-Series Analyses of Gene Expression Profile During Zygotic Embryo Development in Picea mongolica

Zygotic embryogenesis is a critical process during seed development in gymnosperms. However, knowledge on the genome-wide transcriptional activation that guides this process in conifers is limited, especially in Picea mongolica. This tree species is endemic to semiarid habitats of Inner Mongolia in China. To extend what is known about the molecular events underpinning its zygotic embryogenesis, comparative transcriptomic analyses of gene expression in zygotic embryos were performed by RNA sequencing in P. mongolica. Our results showed that most changes in transcript levels occurred in the early embryonic pattering determination and formation of mature embryos. Transcripts related to embryogenic competence, cell division pattern, hormones, and stress response genes were identified during embryogenesis. Auxin is essential for early embryo patterning and pre-cotyledon embryonic formation. However, ABA is a major regulator of embryo maturation. Moreover, we found that methylation-related gene expression is associated with activation of early-stage embryos, late embryogenesis abundant proteins, and storage/energy-related genes with late and mature embryos. Furthermore, network analysis revealed stage-specific and multistage gene expression clusters during embryogenesis. WOX, MYB, AP2, and HLH transcription factors seem more relevant to embryogenesis in different stages. Our results provide large-scale and comprehensive transcriptome data for embryo development in P. mongolica. These data will lay a foundation for the protection and utilization of P. mongolica resources.

Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development

KEY MESSAGE

Developmental and transcriptomic analysis of Brachypodium embryogenesis and comparison with Arabidopsis identifies conserved and divergent phases of embryogenesis and reveals widespread heterochrony of developmental gene expression. Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana. However, the major crops are monocots and the transcriptional programs associated with the differentiation processes during embryogenesis in this clade were largely unknown. Here, we combined analysis of cell division patterns with development of a temporal transcriptomic resource during embryogenesis of the monocot model plant Brachypodium distachyon. We found that early divisions of the Brachypodium embryo were highly regular, while later stages were marked by less stereotypic patterns. Comparative transcriptomic analysis between Brachypodium and Arabidopsis revealed that early and late embryogenesis shared a common transcriptional program, whereas mid-embryogenesis was divergent between species. Analysis of orthology groups revealed widespread heterochronic expression of potential developmental regulators between the species. Interestingly, Brachypodium genes tend to be expressed at earlier stages than Arabidopsis counterparts, which suggests that embryo patterning may occur early during Brachypodium embryogenesis. Detailed investigation of auxin-related genes shows that the capacity to synthesize, transport and respond to auxin is established early in the embryo. However, while early PIN1 polarity could be confirmed, it is unclear if an active response is mounted. This study presents a resource for studying Brachypodium and grass embryogenesis and shows that divergent angiosperms share a conserved genetic program that is marked by heterochronic gene expression.