Embryonic Stage of Plant Ontogeny

A simplified diagram of the life cycle of a seed plant can be represented as the following sequence (Raven et al. 2005; Serebryakova et al. 2006):

Thus, the embryonic stage is a “bridge” between the haploid gametophyte and the diploid adult sporophyte. Without this stage, the formation of a new generation is impossible (Yakovlev et al. 2006).

Comparing the embryonic stage in plants occupying different systematic positions helps to understand the adaptive significance of this stage and its evolutionary complexity (Radoeva et al. 2019; Serebryakova et al. 2006). For clarity, the main differences are summarized in the table below.

Note to the table: In mosses, the embryo (sporophyte) remains attached to the gametophyte, receiving water and nutrients through specialized cells – haustoria. In ferns, the embryo (young sporophyte) also feeds on the gametophyte at first but quickly transitions to independent photosynthesis and water uptake through adventitious roots. In seed plants, the embryo from the very beginning is surrounded by storage tissue (endosperm) and protected by the seed coat, allowing the seed to withstand unfavourable periods (Raven et al. 2005; Evert 2006).

Comparative data show that the progressive evolution of the embryonic stage proceeded in the direction of:

For agriculture, understanding the embryonic stage as part of the life cycle has direct practical significance: seed quality, germination capacity, and stress resistance are determined precisely by how fully and correctly the embryonic stage has proceeded. Disturbances during this period (e.g., due to drought or high temperatures during embryo formation) lead to shrivelled grain, reduced germination, and crop loss (Kruglova 2023; Auroux et al. 2026).

In the following sections, we will examine in detail the successive stages of the embryonic stage using angiosperms, which have the greatest agronomic importance, and also briefly characterize the features of embryogenesis in gymnosperms (pine, spruce) to understand the diversity.

The angiosperm zygote typically has pronounced polarity: its apical (distal from the micropyle) part contains the nucleus and dense cytoplasm, while the basal (facing the micropyle) part is occupied by a large vacuole (Radoeva et al. 2019). In many species during the latent period, the zygote increases in size (e.g., in bean, wheat), or less often, it shrinks somewhat (in cotton, hibiscus) (Lersten 2004). The nature of these changes is related to osmotic processes and reorganization of the cytoskeleton: actin microfilaments and microtubules rearrange, ensuring polar transport of organelles (Radoeva et al. 2019).

It is important to note that during this period the zygote is often surrounded by callose (β-1,3-glucan), which probably isolates it from the surrounding ovule tissues, preventing premature signal reception and creating the microenvironment necessary for the initiation of embryogenesis (Lersten 2004). In some species (e.g., in citrus), the formation of a cuticle on the zygote surface has even been described, underscoring its isolated state (Bruck & Walker 1985, cited in Lersten 2004).

The factors triggering the first division of the zygote are not fully understood, but it has been established that both maternal and paternal signals play an important role. In Arabidopsis (Arabidopsis thaliana), the SHORT SUSPENSOR protein, encoded by a gene expressed in sperm cells, after fertilization activates the YODA MAP-kinase cascade, which is necessary for the correct asymmetry of the first division (Bayer et al. 2009, cited in Radoeva et al. 2019). Maternal factors, in turn, include transcription factors of the WRKY and HDG families, regulating the expression of the WOX8 gene, which determines the fate of the basal cell (Radoeva et al. 2019). Thus, the initiation of embryogenesis is a complex process integrating signals from both parents.

The first division of the zygote in angiosperms is almost always asymmetric and transverse (relative to the long axis of the cell) (Lersten 2004). As a result, two cells are formed that differ markedly in size and fate:

In most species, the apical cell is significantly smaller than the basal cell, but exceptions are known: in some plants (e.g., some legumes), the cell sizes may be nearly equal, or the apical cell may even be larger (Lersten 2004). It is important to emphasize that the orientation of the division (endoscopic – the apical cell faces the interior of the embryo sac) is critical for the proper establishment of the embryo axis. If the division plane shifts, embryo formation is disrupted (Lersten 2004).

The establishment of asymmetry is associated with the redistribution of vacuoles and the cytoskeleton. In the Arabidopsis zygote before division, the large vacuole shifts to the basal pole, and the nucleus migrates to the apical pole. Actin microfilaments facilitate nuclear movement, and microtubules facilitate elongation of the zygote (Kimata et al. 2016, cited in Radoeva et al. 2019). Disruption of vacuolar dynamics (e.g., in mutants of the SGR2 gene) leads to an incorrect position of the division plane and abnormalities in embryo development (Radoeva et al. 2019).

The suspensor is a temporary, morphologically diverse structure derived from the basal cell. In different angiosperm species, it can be a single large cell, a short filament of several cells, or a massive multicellular structure (e.g., in scarlet runner bean Phaseolus coccineus) (Lersten 2004). The suspensor is simplest in plants with a short embryogenesis period (e.g., in shepherd’s purse Capsella bursa-pastoris – a short filament of several cells). In legumes, the suspensor can reach considerable size and even invaginate into the nucellus tissues, functioning as a haustorium (Lersten 2004).

Functions of the suspensor (according to Raghavan 1986, summarized in Lersten 2004):

Interestingly, the suspensor has a high level of polyploidy (up to 8192_n_ in beans) and intensively synthesizes RNA and proteins, indicating its high metabolic activity (Lersten 2004). After embryogenesis is complete (usually by the torpedo or cotyledon stage), the suspensor undergoes programmed cell death and degenerates. In some species (e.g., in orchids and also in Arabidopsis), the suspensor retains the ability to undergo embryogenesis: when the embryo proper is damaged, suspensor cells can switch to an embryonic programme and give rise to additional embryos – a phenomenon of polyembryony (Lersten 2004; Radoeva et al. 2019). Normally, such “blocking” of the suspensor is controlled by signals from the proembryo.

In gymnosperms (pine, spruce), the process of embryogenesis initiation differs from that in angiosperms (Yakovlev et al. 2006; Raven et al. 2005). In gymnosperms:

In angiosperms, free nuclear mitosis is not characteristic of the zygote (it occurs only in the early stages of endosperm development). The zygote divides immediately with the formation of cell walls, and the suspensor is typically cellular from the very beginning. These differences reflect different degrees of reduction of the female gametophyte and different strategies for nourishing the embryo (Evert 2006).

After the first asymmetric division, the apical cell (and sometimes the basal cell, depending on the species) begins to divide actively, forming the proembryo – a group of cells not yet differentiated into tissues but already possessing polarity (Yakovlev et al. 2006). In typical dicots (e.g., shepherd’s purse Capsella bursa-pastoris), the apical cell divides sequentially, forming first a two-celled, then a four-celled, and then an eight-celled proembryo. Divisions occur in different planes, and soon the embryo becomes spherical – this is the globular stage (Lersten 2004). At this stage, three groups of cells can be distinguished:

In monocots, the protoderm, ground meristem, and procambium also form at the globular stage, but the number of cells and the pattern of divisions may be less orderly (Raven et al. 2005). The globular stage ends when the first signs of organ differentiation appear in the embryo. In many species, a transitional stage is observed during this period – from a spherical shape to one characteristic of the taxon (Lersten 2004).

In dicot plants, after the globular stage, the formation of two cotyledons begins. This stage is called the heart stage due to the external resemblance of the embryo to a heart (Raven et al. 2005). The mechanism of cotyledon formation is associated with the activation of cell divisions in two lateral zones of the future shoot apex. The cotyledons grow laterally, and the zone between them remains concave – here the shoot apical meristem will later form (Lersten 2004).

The next – torpedo stage – is characterized by the elongation of the embryo axis (hypocotyl) and the development of the radicle (embryonic root). During this time:

In many dicots (e.g., bean, pea, sunflower), the embryo may become curved during this period, lying in the seed in a bent position, which allows it to occupy a smaller volume (Lersten 2004). By the end of the torpedo stage, the embryo already possesses all the main organs but has not yet accumulated storage substances or acquired the ability to become dormant.

In monocot plants (e.g., wheat, maize, onion, palms), embryo morphogenesis has a number of differences related to the presence of only one cotyledon and a different position of the shoot apex (Raven et al. 2005; Evert 2006).

Early stages (proembryo and globular) are similar to those in dicots. However, instead of two cotyledons, only one is initiated, and it often occupies a terminal (apical) position, while the shoot apex is displaced laterally. For example, in grasses (wheat, maize), the early embryo has a symmetrical shape, but then one of the potential cotyledons is suppressed, and a single cotyledon – the scutellum – is formed (Raven et al. 2005; Serebryakova et al. 2006).

Main structures of the monocot embryo (using grasses as an example):

In other monocots (onion, lily, palms), the embryo structure may differ somewhat: the cotyledon often takes the form of a cylindrical outgrowth (a so-called haustorial cotyledon) that penetrates the endosperm and absorbs nutrients (Lersten 2004).

Throughout embryo morphogenesis, histogenesis – the formation of primary permanent tissues from primary meristems – occurs simultaneously with organogenesis (Raven et al. 2005; Evert 2006).

It is important to emphasize that in angiosperm embryos (especially in species with a short maturation period), some tissues may remain undifferentiated until germination. For example, the procambium may persist until emergence from the seed, and only upon germination do full-fledged vessels form (Evert 2006).

For a clear comparison of the main stages of morphogenesis, they are presented in a table.

For a better understanding of embryo morphogenesis, it is useful to consider specific examples from the most important agricultural crops.

Grain legumes (bean, pea, soybean) – typical dicots with large cotyledons. In them, embryogenesis proceeds quickly (10–20 days after pollination), and already at the torpedo stage, the cotyledons begin to accumulate proteins and starch, becoming the main site of storage substance deposition (Lersten 2004). The mature embryo occupies almost the entire seed; the endosperm is absent (absorbed).

Cereals (wheat, rice, maize) – classic monocots. In them, the embryo develops longer (up to 40–50 days in maize). In the early stages, embryogenesis is similar to that of dicots, but then the scutellum (cotyledon) expands, and the shoot apex becomes embedded in a depression of the scutellum. The coleoptile and coleorhiza form quite early and reach considerable size already in the mature seed (Raven et al. 2005).

Palms (coconut palm, date palm) – monocots with very large seeds. In them, the embryo in the mature seed is small and poorly differentiated (e.g., in coconut, it appears as a cylindrical body with a small scutellum). A significant part of embryogenesis occurs after germination begins (the so-called “latent” stage), which is related to the peculiarities of nutrition and protection of the embryo in the hard endosperm (Lersten 2004).

Disturbances in embryo morphogenesis (e.g., due to stress temperatures, drought, nutrient deficiency) lead to the formation of deformed, underdeveloped, or non-viable seeds. The following processes are most commonly affected (Kruglova 2023; Auroux et al. 2026):

Therefore, knowledge of the normal course of embryo morphogenesis is necessary for breeders and seed producers: it allows the diagnosis of disturbances and the development of techniques to improve seed quality (e.g., optimization of irrigation regimes and temperature conditions during grain filling).

In the next section (4), we will consider the final phase of the embryonic stage – the transition from an actively developing embryo to a dormant state and preparation for germination.

One of the main tasks of the final phase of the embryonic stage is the creation of a reserve of nutrients that will be used during germination until the seedling transitions to independent photosynthesis and soil nutrition (Lersten 2004). Storage substances can be deposited in different tissues depending on the systematic group of plants:

Main types of storage substances:

Accumulation of storage substances occurs acropetally (from base to apex) and is strictly coordinated with tissue differentiation processes. For example, in wheat, starch synthesis begins in the central part of the endosperm and then spreads to the periphery, while proteins accumulate somewhat later (Auroux et al. 2026). The regulation of these processes is carried out by a complex of phytohormones (abscisic acid, gibberellins, cytokinins) as well as transcription factors (e.g., proteins of the LEC, FUS3, ABI3 families in Arabidopsis) (Auroux et al. 2026). In our article, focused primarily on morphology and ontogenetic stages, we do not delve into molecular mechanisms – they will be covered in articles on plant physiology and genetics.

In parallel with the maturation of the embryo and endosperm, the final formation of the seed coat (testa) occurs, which develops from the integuments of the ovule. In different plants, the seed coat can be:

The seed coat not only performs a protective function (against mechanical damage, microbial penetration, excessive desiccation) but can also regulate gas exchange and water entry, and may contain germination inhibitors (e.g., phenolic compounds, abscisic acid) (Raven et al. 2005). In some species (e.g., apple, cherry), the stone (the hard inner layer of the pericarp) also serves as additional protection, although it is not part of the seed.

In cereals, the seed coat often fuses with the pericarp, forming the caryopsis – a fruit with thin, poorly separable coverings (Raven et al. 2005). In such cases, the “seed coat” in common parlance refers to the fruit coat.

One of the most important physiological characteristics of the completion of the embryonic stage is desiccation, i.e., water loss. Mature seeds of most angiosperms contain only 5–15% water (Raven et al. 2005). This drastic dehydration leads to:

Dormancy (long-term metabolic inactivity) should not be confused with long-term dormancy (dormancy proper), which may be due to properties of the seed coat or the need for stratification. Quiescence is a temporary growth pause due to lack of water or other factors; it is easily reversed upon imbibition. Dormancy is a deeper form of dormancy, requiring specific conditions for awakening (cold, light, coat rupture) (Auroux et al. 2026). In many cultivated plants (wheat, barley, sunflower), seeds have short-term dormancy or lack it entirely, which is important for uniform emergence, but can lead to pre-harvest sprouting in wet weather.

Functionally, the embryonic stage ends when the embryo reaches physiological maturity. Depending on the biological characteristics of the species, the further fate of the embryo can follow one of two scenarios (Raven et al. 2005; Serebryakova et al. 2006):

In both cases, germination begins with imbibition – water uptake, which activates enzymes, initiates respiration, and resumes growth. However, the details of the processes occurring during germination are beyond the scope of the embryonic stage and will be discussed in a separate article on vegetative ontogeny.

Understanding the physiological completion of the embryonic stage has direct applied significance:

In the next section (5), we will summarize the embryonic stage as a whole and present a comparative table for different plant groups, along with self-assessment questions.

For an objective analysis, the following criteria, reflecting the most significant differences in embryonic development, have been selected:

The comparison convincingly demonstrates that the key evolutionary innovation of seed plants is the formation of the seed – a complex structure containing a protected embryo supplied with a store of nutrients (Evert 2006; Raven et al. 2005). The seed solved three main problems faced by plants during the colonization of land:

Furthermore, the seed provides effective temporal and spatial dispersal. Fern spores are dispersed by wind, but their embryos cannot wait long for favourable conditions. Seeds, on the other hand, can remain in the soil for many years and then germinate when conditions become suitable (e.g., after a fire or forest clearing) (Raven et al. 2005).

Seed quality refers to the set of traits determining their suitability for sowing: germination capacity, germination energy, 1000-seed weight, absence of pathogens and mechanical damage. All these indicators directly depend on how fully and correctly the embryonic stage has proceeded (Raven et al. 2005).

In agricultural practice, seed quality control is carried out by determining germination capacity (percentage of seeds that produce normal seedlings within a set period) and germination energy (uniformity of seedling emergence) (Raven et al. 2005). Low values often indicate disturbances that occurred during the embryonic stage (unfavourable weather during grain filling, disease infestation, nutrient deficiency).

The embryo is particularly sensitive to the action of stress factors during so-called critical periods – times of active organ and tissue differentiation. In angiosperms, these periods are (Kruglova 2023; Kruglova et al. 2022):

The most common stressors in field conditions:

The outcomes of disturbances in the embryonic stage can be:

Knowledge of the physiology of the completion of the embryonic stage allows the agronomist and seed producer to purposefully treat seeds to synchronize and enhance germination. The main practices (Raven et al. 2005; Stern & Jansky 2021):

On the other hand, in some cases it is necessary to prolong seed dormancy to prevent pre-harvest sprouting (especially important for cereals in wet harvest weather). Breeding for the so-called “dormant” form is conducted in many breeding centres. Temporary maintenance of dormancy is possible by drying seeds to 12–14% moisture and storing them at low positive temperatures (Raven et al. 2005).

Characteristics of the embryonic stage are targets for breeding in several directions:

Thus, the embryonic stage is not merely a theoretical construct but a real object of breeding work and agronomic practices.