OpenSSH and X509 Authentication
OpenSSH itself supports SSH Certificates that are not X.509 Certificates.
The following resources provide some guidance for using SSH with X.509 certificates, or more commonly with smart cards and USB tokens:
https://github.com/OpenSC/OpenSC/wiki/OpenSSH-and-smart-cards-PKCS%2311
https://developers.yubico.com/PIV/Guides/SSH_with_PIV_and_PKCS11.html
For information on using SSH with X.509 certificates from EJBCA, refer to the OpenSSH and X509 authentication guide contributed by Bruno Bonfils.