(Credit to Mavriniac for bringing this up)

It is possible to upgrade your gems for a much lower mana cost by following these steps:

1. Create any Grade 1 Gem and plant it into a tower.
2. Create another Grade 1 Gem (this one will be upgraded) and keep it in your inventory.
3. Hover your mouse over the tower with the Grade 1 Gem.
4. While keeping "Shift" pressed, press "B", then press "U". Repeat this step a couple of times and you will notice that while the gem's grade increases, only little mana is spent (the update cost from Grade 1 to 2)

The gem planted in the tower determines the mana cost of upgrading the gem in your inventory.

With this bug, you are able to create immensely powerful gems pretty much at the start of the game.