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Cocoa seed is recalcitrant and there are no effective methods of prolonging seed viability in storage beyond 4-5 weeks without the seed starting to germinate. Seeds in unopened pods may remain viable for 3-4 weeks after harvesting and an inhibitor in the mucilage prevents early germination. Fresh seed placed flat about 1 cm deep in nursery pots will germinate almost immediately, with the closed cotyledons emerging above the ground within a week. A few weeks later the cotyledons open, exposing the plumule, and the first growth phase ends with the hardening-off of the first four leaves that stand out horizontally at the same level. Subsequently, leaves appear at about 6-week intervals, well spaced in a spiral arrangement. Seedlings are ready for planting in the field 4-6 months after sowing, when 40-50 cm tall. Orthotropic growth of the single stem continues until the seedling is 1-1.5 m tall, usually one year after field planting, when the first jorquette is formed. This is the product of five axial subterminal buds that grow out sideways simultaneously, whilst the apical bud ceases to function. The internodes between the side shoots are reduced so much that they grow out at the same level. These plagiotropic shoots are called "fan" branches. Some years later an orthotropic shoot or "chupon" may grow out from below the jorquette joint and, after growing a certain length, form another tier of fan branches. This process may be repeated several times. The dimorphic branching in ''Theobroma cacao'' is not absolute, as is the case in ''Coffea'' spp., and orthotropic shoots can be induced on mature plagiotropic stems.
First flowering starts 1.5-5 years after field planting, depending on cultivar and ecological conditions. Cocoa is allogamous, with a unique system of gameto-sporophytic self- and cross-incompatibility controlled by a single gene with several dominant and co-dominant alleles. This self-incompatibility gene is operative in all Forastero cocoa germplasm collected from the main centres of genetic diversity (upper Amazon basin), but not always in other types, such as the self-compatible Criollo, Trinitario and Amelonado cocoa. However, even self-incompatible genotypes can be induced to self-fertilize when the pollen mix also contains pollen (called mentor pollen) from a cross-compatible genotype. This phenomenon has important consequences for seed production from biclonal seed gardens. Pollination is effected by insects, the most important being very small midges of the genus ''Forcipomyia'' , which results in 25-50% cross pollination. Pollination efficiency is low, usually less than 10%, but that is compensated for by the large number of flowers produced. Only one in every 500 flowers may develop into a mature pod, or even fewer in the presence of cross-incompatibility. Initial growth of the young fruits, called "cherelles", is slow. Cherelle wilt, in which fruits stop growing, blacken and shrivel but remain attached to the stem, is considered to be a physiological mechanism to regulate the crop load on the tree in accordance with available assimilates. It occurs mostly during the first 2-3 months. Full pod size is attained 4-5 months after successful fertilization and another month is required for ripening.
== Other botanical information ==
