Hypocotyl

As the plant embryo grows at germination, it sends out a shoot called a radicle that becomes the primary root, and then penetrates down into the soil.

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 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.

One of the widely used assays in the field of photobiology is the investigation of the effect of changes in light quantity and quality on hypocotyl elongation.