I have multiple ssh keys. Each time I reboot I have to do ssh-add for each of them and type passphrases to unlock each one. Is it possible to store all the in one container file which is added and decrypted with single command?
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No, it is not possible to do that. Each file contains a single key for OpenSSH. If you could put multiple keys in the same file, it would be impossible to tell OpenSSH which one to use simply by specifying the file name.
Depending on your environment, you may wish to store each key's passphrase in your keychain and unlock it with your login passphrase or with a separate keychain and passphrase. That would allow you to keep your files encrypted but enter only one passphrase. How you do that depends on your operating system and, on Linux, desktop environment.
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