Epigram Germination. Hypogeal germination is the process in which the seed leaves or the cotyledons remain below the … The hypocotyl is the part of the stem of an embryo plant beneath the stalks of the cotyledons. After emerging out of the soil, these cotyledons are called seed leaves, which become photosynthetic as well. Germination, in a seed, process by which the plant embryo within the seed resumes growth after a period of dormancy and the seedling emerges.