There are a total of 7 Great Runes, 6 of them are dropped by the Shardbearer Bosses while the other is dropped by Rennala. After getting any of the Shardbearer's Great Runes you will need to go to a divine tower to activate it while the one you get for defeating Rennala is already activated and the trophy will pop along with the one for defeating her if you have not activated another Great Rune before then.