How Ponies Reproduce

In order for a mare to become pregnant, the stallion must first turn into a tree.  This is a difficult, and often fatal, process.

Once the stallion has been transfigured, the mare must do the same, though her form takes something like a bird or wasp or bee or ice-cube or hat or anything that can fly and get things caught in their wings.

The birdbeewaspicecubehatmare flies up to the stalliontree and eats one of their fruit.  Seed included.  The seed goes into the stomach of the mare, who turns back into a pony, and then the seed turns into a little pony who is soon born through the mouth or anus of the mare (depending on their body angle).

Mares (and stallions) can eat apples without being birds or trees.  The reason ponies like the taste of apples so much is because of the sexual factor.  And yes, that inherently means stallions are kind of gay.

The Apple Family has an high rate of stallion attrition.  Hence why they have so many apple trees.

Oh, and ponies can have sex too, like all the damn clopfics on this site show us.  But you can't get pregnant from it.  Because that's not how sex works.