There seems to be a biut of an argument going on at the moment between MSI and Gigabyte regarding this exact question. Personally I feel that Gigabyte boards just support cards that support PCIE3.0 but not actually use it. In other words you can fit a PCIE3.0 card into a Gigabyte motherboard and it will work fine but not at PCIE3.0 standards.
I am sure somebody will jump on me if I am wrong!