Lesson-2 Seed Germination and Dormancy 18OCT2026
From Seed to Seedling: How Seeds Survive, Wait and Germinate
Notes from AGR3301 Crop Physiology, Lesson 2, Universiti Putra Malaysia (UPM)
Every crop we grow begins as a seed, a small package that must survive storage, wait for the right moment and then turn into a living seedling. In this lesson we follow that journey in four steps: how seeds survive, how they leave dormancy, how germination is completed, and how the young seedling establishes itself. Telling these four apart is the key to understanding many everyday problems on the farm.
How a seed is made
Most seeds arise through sexual reproduction. After pollination, flowering plants carry out double fertilisation. One sperm fuses with the egg to form the zygote (2n), which becomes the embryo. A second sperm fuses with the two polar nuclei in the central cell to form a triploid (3n) cell that develops into the endosperm, the seed’s food store. The integuments around the ovule harden into the seed coat (testa). In short, the ovule becomes the seed and the ovary becomes the fruit.
Seeds bring new gene combinations, which is why breeders rely on them. Vegetative propagation, by contrast, usually produces genetically identical offspring.
Diversity among seeds
Seeds range enormously in size. Orchids produce “dust seeds” with no endosperm. Some are as small as 0.05 mm, a single gram of Aerides odorata seed holds about 3.4 million seeds, and most orchids need a mycorrhizal fungus to germinate. At the other extreme, the coco-de-mer (Lodoicea maldivica) produces the largest seed in the world, weighing up to 25 kg and reaching 50 cm long.
Seeds survive in different ways: a hard seed coat (as in saga, Adenanthera pavonina), physiological dormancy, a seed-size strategy (few large seeds or many small ones), and persistence in the soil seed bank. Dispersal by wind, animals, water or explosive pods helps offspring reach new sites.
Inside the seed
A seed has three parts: the embryo, the food reserves and the protective testa. The embryo includes the radicle (future root), plumule (future shoot), hypocotyl, epicotyl and the cotyledons. In monocots such as maize, the single cotyledon is the scutellum. In dicots such as the bean, there are two cotyledons.
Seeds also differ in where they store food. Endospermic seeds such as maize, rice and castor keep their endosperm as the main store. Non-endospermic seeds such as bean and pea absorb the endosperm into their cotyledons during development. In cereals, the outer living layer of the endosperm, called the aleurone, plays a key role during germination.
Survival: drying and storage
As many seeds mature, they dry out, their metabolism almost stops and their cytoplasm enters a glassy state. This maturation drying is how a seed survives storage, but it is not the same as dormancy. A dry seed may be non-dormant and ready to germinate as soon as it gets water.
Seeds differ in how well they tolerate drying. Orthodox seeds such as rice and maize can be dried and stored cold for years. Recalcitrant seeds, such as cocoa and rubber, are damaged by drying and cannot be frozen. Intermediate seeds such as coffee and papaya fall in between. A useful classroom question is this: why can dried rice seed be stored for years, while drying kills cocoa seed? The answer lies in storage behaviour, not geography, since temperate oaks also produce recalcitrant seeds. A rough rule (Harrington’s rule) is that seed lifespan doubles for every 1% drop in moisture.
Dormancy: when a living seed waits
A dormant seed is viable but does not germinate even when conditions are favourable. This differs from a quiescent seed, which simply lacks water, oxygen or warmth, and from a dead seed. Failure to germinate alone cannot tell the three apart. A viability test, such as the tetrazolium test, is needed as well.
Seed scientists recognise five classes of dormancy: physical (a water-impermeable coat), physiological (a block involving the embryo and covering tissues), morphological (an underdeveloped embryo), morphophysiological (both) and combinational (physical plus physiological). Each needs its own treatment. Physical dormancy is broken by scarification. Physiological dormancy is broken by moist stratification, dry after-ripening or gibberellin (GA) in some species.
Two Malaysian crops show why this matters. Oil palm seed is dormant, and controlled dry heat is used to promote germination for nurseries. In rice, some dormancy protects against pre-harvest sprouting, but too much delays germination at sowing.
Germination: from water uptake to radicle emergence
A seed needs water, oxygen and a suitable temperature to germinate, and some species also need light or darkness. Each species has cardinal temperatures: a minimum, an optimum and a maximum.
Germination begins with imbibition and is complete when the radicle protrudes through the surrounding tissues. Water uptake follows three phases: rapid uptake (phase I), a plateau (phase II) when metabolism restarts and repairs occur, and renewed uptake as the radicle emerges and grows (phase III). Mitochondrial respiration, DNA repair and protein synthesis all restart early and overlap. Early radicle emergence relies mainly on cell expansion.
Mobilising the food store
Stored reserves are broken down into small molecules that the growing seedling can use. Amylases turn starch into maltose and glucose, proteases turn proteins into amino acids, and lipases turn oils into fatty acids and glycerol. Gibberellin (GA) promotes this breakdown, abscisic acid (ABA) inhibits it, and accumulating sugars slow it down through negative feedback.
Barley shows the process clearly. After imbibition, the embryo releases GA, which signals the aleurone layer to make α-amylase. The enzyme breaks down starch in the endosperm, and the scutellum absorbs the sugars to feed the growing seedling. Remove the embryo, and starch breakdown largely stops. Add GA, and it resumes.
Light as a switch
Lettuce seeds of the Grand Rapids variety germinate in response to light through the pigment phytochrome. Red light (about 660 nm) converts phytochrome to its active form (Pfr), raising GA and lowering ABA. Far-red light (about 730 nm) reverses this. In the classic experiments of Borthwick and colleagues (1952), alternating red and far-red flashes showed that the final flash largely decides the outcome. Seeds given red last germinated at 98 to 100%, and those given far-red last at only 43 to 54%.\
Seedling establishment
There are two patterns of emergence. In epigeal germination (bean), the hypocotyl forms a hook and lifts the cotyledons above ground. In hypogeal germination (pea), the epicotyl forms the hook and the cotyledons stay below ground. Cereals use a protective coleoptile instead.
The total dry mass of the seed plus seedling first falls as respiration uses up reserves, then rises once photosynthesis takes over. If reserves run out before the shoot reaches light, the seedling dies, which is why deep planting is risky.
Why it matters on the farm
Each stage links to a practical problem: seed survival to storage losses, dormancy release to pre-harvest sprouting, germination to uneven emergence, and establishment to planting depth. Understanding seed physiology helps us manage water, oxygen, temperature and light, so that every seed planted has the best chance of becoming a healthy crop.
Note for the lesson:
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