I accidentally dug out an almond seedling to realize that all the 3 shoots come from the same seed.
Is this a common occurrence? What is the branch in the middle with a brownish tip that I broke please?
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Likely the germinating seed initially had one main shoot (the brown tip), but this was damaged for some reason and could not fulfill its role. The response of the plant will be to try to replace the broken main shoot by sending out one or more side shoots in an attempt to replace the "leader". In this case there are two shoots. Quite possibly one will naturally become larger than the other and will eventually be the strong leader.
Once the strong leader establishes itself, if you want you can remove the lesser side shoot. Things happen from time to time, not a problem in this case, pot it up and watch it grow into a magnificent plant.