It refers to the version of PCI-e x16 it has. It's the transfer speed and systems involved in the slot.
1.0 has a transfer rate of 2.5GT/s, 250mbps data rate.
2.0 has a transfer rate of 5.0GT/S, 500mbps data rate
2.1 has the same speed as 2.0, with technologies being incorporated into 3.0
3.0 has a transfer rate of 8.0GT/S, and one of the technologies is removing the 20% overhead that was on 2.0, so it effectively doubles the transfer rate of 2.0.
which motherboard do you have?