I want to start only one application without any desktop after booting the system, it is like only application should be there not anything in RHEL 6.
OP clarified in a comment that the idea is to launch the application on login, not on boot.
~/.xinitrc (this file normally doesn't exist, X starts
/etc/X11/xinitrc as a fallback here on Fedora, it might do differently on other distributions). That file determines what applications to start by default. Depending on the desktop environment configured for the account, other startup files could come into play.
Be careful, playing with this could lock the account out for good.
If your application has a proper init-script:
chkconfig application on
The default-runlevel can be set to 3 (multiuser without GUI).