Embryogenesis and Seed Formation

Embryogenesis and seed formation provide two key processes necessary for the existence of a species: first, the creation of a new, genetically unique multicellular organism (the sporophyte), and second, its effective dispersal and survival of unfavorable conditions.

The biological significance of embryogenesis lies in:

The biological significance of seed formation as an integrated structure includes:

The emergence of the seed is one of the major evolutionary advances in land plants, allowing them to escape strict dependence on water for fertilization and to conquer diverse climatic zones.

The transition from spores to seeds. Unlike spore plants (ferns, horsetails), which disperse via single-celled spores lacking nutrient reserves and quickly dying upon desiccation, the seed is a multicellular, well-protected, and nourished "capsule" containing a preformed sporophyte primordium (Serebryakova et al., 2006; Heidemann et al., 2025). Thanks to seeds, gymnosperms and angiosperms were able to spread into arid and cold regions.

Double fertilization and the evolutionary success of angiosperms. A unique evolutionary acquisition of angiosperms is double fertilization, leading to the formation of triploid endosperm (Raven et al., 2013; Khouider & Gehring, 2024). Unlike the haploid female gametophyte of gymnosperms, which develops in advance and requires significant maternal investment even in unfertilized ovules, the endosperm of angiosperms begins development only after fertilization. This allows the mother plant to allocate resources more efficiently, investing only in those ovules that have been successfully fertilized.

Moreover, the triploid (3_n_) genome of the endosperm creates a special arena for parental conflict: maternal and paternal genes "compete" for control over nutrient distribution (Haig & Westoby, 1989). Maternal genes generally limit embryo growth, striving to conserve resources for all offspring, while paternal genes instead stimulate nutrient uptake, favoring that particular seed (Khouider & Gehring, 2024; Pankaj et al., 2025). This conflict is thought to have accelerated the evolution of epigenetic mechanisms (particularly imprinting) and contributed to rapid speciation and dominance of angiosperms in the world’s flora.

Evolution of seed diversity. During evolution, different seed types have emerged: those with endosperm persisting to maturity (cereals, castor bean) and non-endospermic seeds, where reserves accumulate in the cotyledons (legumes, cucurbits) (Lersten, 2004; Ajayo et al., 2026). This diversity reflects different resource allocation strategies: in the first case, the embryo is "backed up" by a long-lasting nutrient depot; in the second, the embryo actively absorbs the endosperm during its development but loses some protective potential. Understanding these evolutionary strategies has direct practical implications for breeding for grain productivity and stress tolerance (Ajayo et al., 2026).

Thus, embryogenesis and seed formation are not merely stages of the life cycle but key evolutionary and ecological adaptations that enabled the dominance of flowering plants and form the foundation of modern agriculture.

Several main types of early embryo development are distinguished in angiosperms, differing in the orientation of the first zygote divisions, the involvement of suspensor cells in embryo body formation, and the final seedling structural plan. Classical schemes (Onagrad type, Asterad type, Solanad type, Caryophyllad type) are based on the number and order of cell specification in the proembryo (Lersten, 2004; Serebryakova et al., 2006). For agricultural practice, the most significant difference is between dicot and monocot embryo development.

Dicot embryogenesis. After the first unequal division of the zygote, a small apical cell (which gives rise to the embryo proper) and a large basal cell (which develops into the suspensor – a temporary structure for nutrient transport) are formed. Subsequent divisions follow a strict spatial organization, passing through globular, heart-shaped, torpedo-shaped, and mature embryo stages with two cotyledons (Beck, 2010; Huang & Sun, 2025). In legumes, cucurbits, and many other dicots, by seed maturity the endosperm is completely or partially consumed, and most storage reserves are concentrated in the cotyledons (Lersten, 2004).

Monocot embryogenesis. The early stages are similar to dicots, but soon only one cotyledon (scutellum in cereals) forms, the embryo becomes elongated and does not pass through a "heart" stage. In cereals (wheat, maize, rice), additional specialized structures differentiate: the coleoptile (protective sheath covering the stem) and the coleorhiza (root sheath) (Beck, 2010; Ajayo et al., 2026). In most monocots, the endosperm persists to seed maturity and serves as the main site for starch and protein deposition (Raven et al., 2013).

Despite differences in detail, in all cases embryogenesis ensures the establishment of apical meristems and the primary axis (hypocotyl–radicle), allowing the seedling to quickly transition to independent growth after germination.

The most important classification for agronomy is based on which tissue serves as the main storage depot in the mature seed (Lersten, 2004; Serebryakova et al., 2006).

Although in the mature seed the endosperm is always cellular tissue, its early developmental pathways differ (Lersten, 2004). Understanding these types is important for interpreting seed development disruptions under stress:

Thus, knowledge of embryogenesis types and seed classification by storage tissue allows the agronomist and breeder to purposefully select varieties, optimize plant nutrition regimes, and minimize losses during storage and seed preparation for sowing.

After fertilization, the zygote — the first cell of the new sporophyte — enters a period previously erroneously called "dormancy". In fact, intensive preparatory processes occur during this time. The duration of this stage varies widely: in lettuce (Lactuca), the zygote divides within 3–6 hours after fertilization; in wheat and barley, within 10–12 hours; while in some tree species (walnut, coffee), the delay can reach several weeks (Lersten, 2004; Ajayo et al., 2026).

Key processes at this stage:

Importantly, in most species, zygote division is preceded by several cycles of primary endosperm nucleus division (Pankaj et al., 2025). The endosperm is thought to create the necessary hormonal environment (particularly through auxin and brassinosteroid production) to prepare the zygote for mitosis (Figueiredo et al., 2015; Pankaj et al., 2025).

The first division of the zygote is typically unequal and transverse (more rarely oblique). This results in two cells:

Subsequent divisions of the apical cell initially follow a strict program, forming a spherical cluster of small, isodiametric, cytoplasm-rich cells — the proembryo. This structure is called the globular embryo. At this stage:

In dicots, the globular stage ends with a transition to bilateral symmetry when the embryo begins to flatten in one plane. In monocots, conversely, it remains elongated and columnar, bypassing the heart stage (Lersten, 2004).

This stage is characteristic of most dicots and is a key phase of organogenesis. The embryo acquires a characteristic outline resembling a heart (Beck, 2010; Serebryakova et al., 2006). The main events of this stage:

Thus, the heart stage is the moment when the main structural elements of the embryo — cotyledons, hypocotyl, root primordium, and apical meristems — are established. Further development (torpedo stage and maturation) mainly involves growth, storage reserve accumulation, and acquisition of desiccation tolerance.

After organogenesis completes at the heart stage, a period of intensive linear growth and histological differentiation ensues. In dicots, this stage is called the torpedo stage (or elongated stage) due to the characteristic elongated shape of the embryo with streamlined cotyledons (Beck, 2010; Lersten, 2004). In monocots, the analogous stage is called the cylindrical stage, as the embryo takes the form of a short cylinder (a "cob") with a single cotyledon (Serebryakova et al., 2006; Ajayo et al., 2026).

Main events at this stage:

In most species, it is at the torpedo stage that the embryo reaches its maximum length; further shape change mainly involves thickening and curvature (in dicots) or completion of protective sheath formation (in monocots).

This is the final stage of embryogenesis, during which the embryo reaches functional maturity and prepares for a long period of dormancy (Bewley & Black, 1978; Serebryakova et al., 2006). Main processes:

At the maturation stage, hormones play a key role: abscisic acid (ABA) induces the synthesis of late embryogenesis abundant (LEA) proteins, which promote desiccation tolerance, and suppresses metabolism, while gibberellins (GA) and auxins promote growth and differentiation (Pankaj et al., 2025; Ajayo et al., 2026). An optimal balance of these hormones is necessary for the formation of high-quality, viable seeds with good germination capacity.

Endospermogenesis is the development of the triploid nutritive tissue from the fertilized central cell (primary endosperm nucleus). It begins earlier than the zygote and proceeds parallel to embryogenesis. As mentioned, three main pathways are distinguished (Lersten, 2004; Pankaj et al., 2025):

The functions of the endosperm are not limited to nourishing the embryo. It also:

For the agronomist, knowledge of the endospermogenesis type is important for predicting crop sensitivity to stress during grain filling (critical coenocyte phases in cereals) and for optimizing seed drying and storage regimes.

The embryo develops inside the maternal sporophyte but is still sensitive to external conditions, especially during phases of active division and filling.

Temperature. The optimum for embryogenesis in most crops is 15–25 °C. Elevated temperature (heat stress) accelerates early divisions but disrupts differentiation and reduces storage reserve accumulation. Low temperatures (frost during flowering–milk ripeness) cause embryo abortion and shriveled grain (Bewley & Black, 1978; Pankaj et al., 2025).

Humidity and water stress. Drought or waterlogging during seed formation reduces turgor in maternal tissues, disrupts assimilate transport, and impairs starch synthesis. Under water deficit, ABA synthesis increases, which can prematurely induce dormancy and arrest embryo growth (Ober & Setter, 1990; Ajayo et al., 2026).

Light regime. Although the embryo develops inside the seed coat, in many species (including maize, wheat, legumes) embryos at the torpedo and maturation stages contain chlorophyll and are capable of photosynthesis (Whatley & Price, 1983). Light penetrates the seed coat and stimulates chlorophyll synthesis, which may improve filling energetics (so-called "green embryos"). In rice and barley, irradiation of mature ears increases 1000-grain weight and protein content (Beck, 2010).

Mineral nutrition. Deficiency of nitrogen, phosphorus, and potassium during the growing season sharply reduces the number of set ovules and disrupts grain filling (phases from flowering to milk ripeness are particularly critical). Sulfur and micronutrients (zinc, boron, copper) are necessary for the synthesis of amino acids, phytohormones, and storage protein enzymes (Ajayo et al., 2026).

Under stress factors (drought, extreme temperatures, nutrient deficiency), characteristic disturbances occur in embryogenesis:

Grain shriveling (shrunken grain) – underdevelopment or degeneration of the embryo and endosperm. Often arises from heat or water stress during the coenocyte phase (in cereals) or during the endosperm cellularization phase (in legumes) (Lersten, 2004).

Aborted seed – complete seed death at an early stage. Observed under severe desiccation, herbicide stress, or genome incompatibility (triploid block, interspecific crosses) (Khouider & Gehring, 2024).

Morphological embryo abnormalities (absence or fusion of cotyledons, lack of apical meristem, curved axis). Often caused by disruption of polar auxin transport due to boron deficiency or action of herbicides that inhibit auxin transport (Pankaj et al., 2025).

Precocious germination (vivipary) – seed germination while still on the mother plant, without entering dormancy. Observed with ABA deficiency (mutations in ABA biosynthesis genes) or prolonged rains after ripening (in maize, tomatoes, mangoes). Vivipary sharply reduces seed storage ability and germination (Bewley & Black, 1978).

Thus, embryogenesis is a dynamic, multifactorially regulated process in which genetic programming, hormonal signaling, epigenetic mechanisms, and environmental influences intertwine. Understanding these regulatory circuits is the basis for creating stress-tolerant varieties and for developing agronomic practices that ensure high-quality, viable seeds.

Seed abortion is the premature cessation of ovule development or formation of a seed with a non-viable embryo (Bewley & Black, 1978; Serebryakova et al., 2006). In agronomy, this phenomenon is called "empty grain", "shrunken grain", or "lentil-shaped grain". Causes can be genetic (unbalanced ploidy, lethal mutations) or environmental (stresses).

Ploidy disturbance (triploid block). As mentioned, in most angiosperms normal endosperm development requires a ratio of 2 maternal genomes : 1 paternal genome (2m:1p). Crossing a diploid (2n) mother with a tetraploid (4n) father results in a 2m:2p ratio in the endosperm – excess paternal genome. This leads to delayed cellularization, uncontrolled endosperm proliferation, and subsequent seed abortion (Scott et al., 1998; Khouider & Gehring, 2024). The opposite case – excess maternal genome (4n×2n) – causes premature cellularization and endosperm growth arrest. The triploid block is an important postzygotic barrier preventing crossing of individuals of different ploidy (Lersten, 2004).

Environmental stresses. Water deficit, high temperature, nitrogen, boron, or zinc deficiency during the period from flowering to milk ripeness cause massive ovule abortion. Water stress, for example, increases ABA synthesis in maternal tissues, which can block assimilate transport into the seed (Ober & Setter, 1990). Abortion can affect up to 30–50% of potential seeds, sharply reducing yield (Ajayo et al., 2026).

Genetic defects. Mutations in genes controlling zygote division (e.g., wrky2, yda) or in auxin biosynthesis and signaling genes lead to early embryogenesis arrest and empty seeds (Huang & Sun, 2025; Pankaj et al., 2025).

Externally, aborted seeds may appear completely empty ("white empty grain" in sunflower) or have an underdeveloped, often deformed embryo and shriveled endosperm (Lersten, 2004; Bewley & Black, 1978).

Apomixis (from Greek apo – without and mixis – mixing) is the ability of a plant to form viable seeds without fertilization of the egg cell, i.e., asexually, but via seed (Nogler, 1984; Heidemann et al., 2025). Unlike vegetative propagation (cuttings, tubers), apomixis uses the seed structure, but the offspring is genetically a clone of the mother plant. Apomixis occurs in about 0.1% of flowering plants (including some genera of Asteraceae, Poaceae, Rosaceae), but is absent in major agricultural crops (wheat, maize, rice, soybean) (Ozias-Akins & van Dijk, 2007).

Two main forms of gametophytic apomixis are distinguished (Koltunow & Grossniklaus, 2003; Heidemann et al., 2025):

In either type of gametophytic apomixis, the diploid egg cell must develop into an embryo without fertilization – a process called parthenogenesis. Genes controlling parthenogenesis have been identified in pearl millet (PsASGR-BBML) and dandelion (ToPAR) (Conner et al., 2015; Underwood et al., 2022). These genes encode transcription factors (AP2/ERF and K2-2 zinc finger) which, when introduced into the genome of a sexual species, can induce parthenogenesis (Heidemann et al., 2025).

Significance of apomixis for agronomy and breeding:

Polyembryony is the formation of multiple embryos within a single seed (Cao et al., 2018; Serebryakova et al., 2006). Two main types are distinguished:

For breeding and seed production, polyembryony has dual significance:

The molecular mechanisms of polyembryony are associated with the failure to repress embryogenic programs in somatic cells. In citrus, this is inherited as a dominant trait controlled by the CitRWP locus (RWP-RK domain gene), in whose promoter a mobile element insertion was found (Wang et al., 2017; Heidemann et al., 2025).

To assess seed quality and identify genetic anomalies, the following are used:

Thus, deviations from normal embryogenesis are not only a cause of yield loss but also a source of unique reproductive strategies (apomixis, polyembryony) that can be utilized in breeding and biotechnology to fix heterosis, propagate elite genotypes, and accelerate the breeding process.

In addition to the main macronutrients (N, P, K), micronutrients involved in the synthesis of phytohormones, enzymes, and structural components of the embryo and endosperm are critically important for embryogenesis.

Practical conclusion: Soil agrochemical analysis and leaf diagnostics allow identification of micronutrient deficiencies. Corrective applications during the critical phase (from flowering onset to milk ripeness) are among the most effective ways to increase seed fill and weight (Ajayo et al., 2026).

Modern crop production widely uses synthetic analogues of phytohormones and their inhibitors to manage seed filling and ripening.

Controlled water deficit (so-called "managed hardening") in late filling stages can accelerate ripening, increase shatter resistance, and improve seed storage ability. Conversely, drought during active endosperm division (milk ripeness) is a major cause of empty grain (Ober & Setter, 1990; Ajayo et al., 2026). Drip irrigation allows precise water dosing during this period.

Nitrogen nutrition: split nitrogen (N) application with emphasis on the period from stem elongation to the start of grain filling increases both seed weight and protein content (especially in wheat and soybean). However, excess nitrogen in early stages can lead to vegetative overgrowth and reduced seed set. Sulfur (S) is necessary for methionine and cysteine synthesis – amino acids of storage proteins. Combined N and S application at heading significantly improves wheat baking properties (Ajayo et al., 2026).

Seed maturity is not achieved immediately after harvest: in many crops, the embryo completes differentiation and storage reserve accumulation after threshing, during so-called "post-harvest ripening" (Bewley & Black, 1978; Serebryakova et al., 2006).

The most radical way to manage seed quality is breeding and genetic modification.

Thus, modern agronomy has a wide arsenal of tools for managing seed formation – from precise agrochemical provision to genetic modification. The key principle is that interventions should be timely and directed at specific phases of embryogenesis (endosperm cellularization, cotyledon formation, reserve accumulation, desiccation). Integration of these methods allows production of seeds with desired properties: high germination, germination energy, stress tolerance, and nutritional value.