RSA keys can be used to generate signatures with a choice of secure hash function. Typically, any version of OpenSSH new enough to support certificates at all will also be new enough to avoid using SHA-1, so the default settings of accepting the more modern SHA-256 and SHA-512 should be suitable for nearly all cases. For completeness, however, you can configure which types of RSA signature PuTTY will accept in a certificate from a CA using an RSA key.