You mean add transparency to a picture? Note that there isn't such a thing as a "transparent color" in PNGs, they have an alpha layer that defines transparency, it's an additional layer next to the RGB color layers.
Anyway, add an alpha channel to the current layer by Layer > Transparency > Add alpha channel. You can then just use the eraser to add transparency, or you can use advanced tricks with masks and stuff - I redirect you to tutorials. The Color to Alpha filter can also be handy at times but remember it acts on the entire file. Don't forget to save as PNG if you want to keep the transparency.