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The scar, visible on the seed coat, is called the hilum (colors include black, brown, buff, gray and yellow) and at one end of the hilum is the micropyle, or small opening in the seed coat which can allow the absorption of water for sprouting.

Remarkably, seeds such as soybeans containing very high levels of protein can undergo desiccation, yet survive and revive after water absorption. Carl Leopold, son of Aldo Leopold, began studying this capability at the Boyce Thompson Institute for Plant Research at Cornell University in the mid-1980s.

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Nodulation typically continues for 8 weeks before the symbiotic infection process stabilizes.

The final characteristics of a soybean plant are variable, with factors such as genetics, soil quality, and climate affecting its form; however, fully mature soybean plants are generally between 51–127 cm (20–50 in) in height Soybeans form inconspicuous, self-fertile flowers which are borne in the axil of the leaf and are white, pink or purple.

For human consumption, soybeans must be cooked with "wet" heat to destroy the trypsin inhibitors (serine protease inhibitors).

Raw soybeans, including the immature green form, are toxic to all monogastric animals.

Soybeans comprise approximately 8% seed coat or hull, 90% cotyledons and 2% hypocotyl axis or germ.