I am not sure if your question makes much sense.
Usually what marks messages are read is the server that stores the messages. I don't think there is a way to control that if you retrieve messages using the POP3 protocol.
There is no standard to mark messages are read, but many mail systems use the Status: header to store a character that indicates whether the message is read, unread, deleted, etc.. Take a look at this RFC document.
ietf.org/rfc/rfc2076.txt