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In plant physiology, the epicotyl is the embryonic shoot above the cotyledons. In most plants the epicotyl will eventually develop into the leaves of the plant. In dicots, the hypocotyl is what appears to be the base stem under the spent withered cotyledons, and the shoot just above that is the epicotyl. In monocot plants, the first shoot that emerges from the ground or from the seed is the epicotyl, from which the first shoots and leaves emerge.

In sunflower seedlings, the difference between epicotyl and hypocotyl can be seen from the parts of the stem divided by the first pair of leaves. Here the stem above the cotyledons is covered in tiny hairs whereas the region of stem below (hypocotyl) is smooth.

Lengthening of the epicotyl is thought to be controlled by the phytochrome photoreceptors.

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