'Hypocotyl' is a
botanical term for a part of a
germinating 'seedling' of a
seed plant. As the plant
embryo grows at germination, it sends out a shoot called a '''
radicle''' that becomes the primary root and penetrates down into the
soil. After emergence of the ''radicle'', the ''hypocotyl'' emerges and lifts the growing tip (usually including the seed coat) above the ground, bearing the embryonic leaves (called '''
cotyledons''') and the '''plumule''' that gives rise to the first true leaves. The ''hypocotyle'' is the primary organ of extension of the young plant and develops into the
stem.

seed of Scouler's willow (''Salix scouleriana'')
The early development of a
monocot seedling like
cereals and other
grasses is somewhat different. A structure called the
coleoptile, essentially a part of the ''cotyledon'', protects the young stem and plumule as growth pushes them up through the soil. A '''mesocotyl''' — that part of the young plant that lies between the seed (which remains buried) and the ''plumule'' — extends the shoot up to the soil surface, where secondary roots develop from just beneath the plumule. The primary root from the ''radicle'' may then fail to develop further. The ''mesocotyl'' is considered to be partly ''hypocotyl'' and partly ''cotyledon'' (see '''
scutellum''').
Not all monocots develop like the grasses. The
onion develops in a manner similar to the first sequence described above, the seed coat and '''endosperm''' (stored food reserve) pulled upwards as the cotyledon extends. Later, the first true leaf grows from the node between the radicle and the sheath-like cotyledon, breaking through the cotyledon to grow past it.
In some plants, the hypocotyl becomes enlarged as a
storage organ. Examples include
cyclamen and
gloxinia.
See also
★
Epicotyl