You have to use the Android SDK, specifically the command fastboot, to flash the stock system.img and stock recovery.img. Only flash the boot.img only if a custom kernel has been flashed, if not, this isn't required. With USB Debugging enabled in Settings - Developer Options, you'll need to boot into the bootloader. You'll also need the factory image for the current version of stock you are running.
You'll need to use the commmands:
fastboot flash system system.img
fastboot flash recovery recovery.img
fastboot flash boot boot.img
Rooting modifies /system, which OTA's will check and fail. Also, any other recovery except for stock recovery will also fail to flash the OTA.