A seed certainly looks dead. It does not seem to move, to grow, nor do anything. In fact, even with biochemical tests for the metabolic processes we associate with life (respiration, etc.) the rate of these processes is so slow that it would be difficult to determine whether there really was anything alive in a seed.
Indeed if a seed is not allowed to germinate (sprout) within some certain length of time, the embryo inside will die. Each species of seed has a certain length of viability. Some maple species have seeds that need to sprout within two weeks of being dispersed, or they die. Some seeds of Lotus plants are known to be up to 2000 years old and still can be germinated.
Assuming the seed is still viable, the embryo inside the seed coat needs something to get its metabolism actived to start the embryo growing. The process of getting a seed to germinate can be simple or complicated, and this our present subject.
Common vegetable garden seeds generally lack any kind of dormancy. The seeds are ready to sprout. All they need is some moisture to get their biochemistry activated, and temperature warm enough to allow the chemistry of life to proceed. Seeds taken from the wild, however, are frequently endowed with deeper forms of dormancy.
There are several mechanisms that permit seeds to be truly dormant.
Many kinds of seeds have very thick seed coats. These obviously keep water out of the seed, so the embryo cannot get the water needed to activate its metabolism and start growing. The lotus seeds are an example of this. An outstanding example from the northern temperate zone is the Kentucky coffee tree (Gymnocladus dioica). The seed coat is perhaps two millimeters thick! You can throw them as hard as you can against a concrete sidewalk and they just bounce! How could such a seed actually sprout?
The Kentucky coffee tree holds its seed pods in the the top of the tree all winter. The inside of the pod is fleshy (lots of water). The pods are very dark in color. If you put the fickle winter and sunshine and darkness into this picture, I think you can come up with the answer. Here is a hint: you might want to recall what happens if you fill the ice cube trays in your freezer too full with water, or you might recall what happens to a container filled with soda that is then frozen.
Other species might use some pounding along a river or drop seeds into seacoast surf to abrade the thick seed coat. Some of the sea beans do this. Other seeds might need an vertebrate or other animal to attack the seed coat (but give up trying to eat the seed) and thereby weaken the coat. The process of nicking the thick seed coat to initiate germination is called scarification.
A final, and very common, example of a way to scarify a seed coat is observed in strawberry and raspberry. The thick seed coat is designed to be swallowed by the frugivore. The animal digests the fruit pulp, but the seed coat passes through the digestive system still protecting the viable embryo inside, but weakened enough to allow sprouting! The seed is deposited with a little organic fertilizer in the environment and can now sprout!
A thin seed coat is so thin that it is no barrier to water. Some other kind of dormancy mechanism is needed. Knowing that light can penetrate thin layers of plant tissue (leaves for example) should give you the idea that light might be a signal. That plants can absorb light and respond biochemically is a fact you know from your study of photosynthesis. All we need is a pigment molecule that can absorb light and cause a change in the behavior of the embryo.
The pigment is phytochrome. Like chlorophyll, it is made of a chromophore with tetrapyrole structure and is associated with proteins. This pigment is different from chlorophyll, however, in one critical way. It exists in two inter-convertible forms.
One form of phytochrome, named Pfr, is the form of the phytochome found in plant cells that are exposed to red (660 nm) or common white light. This form of phytochrome is biologically very active and plays a role in all systems when a plant needs to know if the lights are "on" or "off." In lettuce (Lactuca sativa) seeds, Pfr causes the seeds to begin to germinate as we will soon see. Thus lettuce seeds germinate only when placed in white or red light. Buried in deep soil, they will not germinate. Given that lettuce has a small seed, I think you can figure out why evolution arrived at this solution.
The other form of phytochrome, named Pr, is formed when phytochrome is exposed to far-red (730 nm) light. This form is biologically inactive or inhibits responses. Thus if lettuce seeds are placed in far-red light they do not germinate.
Large seeds have lots of storage material. If their seed coat is very thin, their evolution may have arrived at a completely different response. Think about pea seeds. They are large and have very thin seed coats. How would they respond to light?
If a seed's embryo is not completely developed, some additional maturation may be needed before the seed can sprout. This happens in seeds with little-to-no storage material invested in the seed. Examples include orchid seeds. They are the size of dust and have almost nothing but a very immature embryo on-board. Such a seed needs an association with fungi in the soil or other environments to feed the developing embryo until the embryo is mature enough to actually penetrate the seed coat. These seeds are also likely to have a very brief viability. The fungal association must be established rapidly or the embryo dies.
Many plant species invest chemicals in the developing seeds, and these chemicals inhibit the development of the embryos. They keep the embryos dormant. Obviously the seed must have some way to eliminate these chemicals before they can sprout.
Many temperate zone species that use inhibitors use abscisic acid. This chemical induces dormancy in the embryo. The chemical is produced in abundance in the late summer and early fall. The seeds in the fruits become dormant so, even if they are dispersed in autumn, they cannot sprout. During the winter enzymes in the seeds degrade the abscisic acid. By spring the abscisic acid is gone and the seed can sprout.
We can collect seeds of these species and get them to sprout early. The seeds are put in moist soil and refrigerated for about four weeks (a process often called stratification). This is sufficient time to degrade the abscisic acid. Then the planted seeds are placed in a warm greenhouse. The seeds assume winter is over, spring has come, and they begin to sprout. This process is called vernalization. If you think of "vernal" as meaning "spring" then you understand how we got this name!
Plants that live in deserts have a different problem. There is no cold, moist, winter to allow vernalization of abscisic acid. These plants instead use more potent toxins, phenolic compounds, to keep their seeds dormant until the proper season for germination. Phenolic compounds are freely water-soluble, the plant is living in a desert. Deserts typically have very long dry seasons and a short wet season accompanied by flash floods and so on. How do you think the phenolic compounds are lost? How would the mechanism ensure that seeds do not sprout in the dry season, but only after the seed could be sure it is in the wet season? The word leaching might give you a hint?
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