On versions of macOS before Sierra, all you had to do to add an SSH key to the Keychain was to run this command:
ssh-add -K keyname
macOS Sierra implements OpenSSH version 7.3p1, which makes this command behave differently. Using ssh-add -K results in the key being added only temporarily: after a reboot, you need to run the command again.
However, if you want to permanently add an SSH to the macOS Keychain, the fix is quick and simple. Create a file ./ssh/config in your user folder and paste the following content inside:
# Add this SSH key to the Keychain
If you already have a .ssh/config file, simply paste this content at the bottom of the existing file.
Now, even after you reboot your system, your SSH key will keep being recognized without the need to run ssh-add -K every time.