We are planning to use Spring Roo to generate GWT artifacts, would it be possible to use our RDBMS database or should the application rely on the app engine datastore if we eventually deploy the application on google app engine.
you will use jpa over your database and when moving to app engine you just need to change the persistence setup to google_app_engine. with roo it's a one liner.
It may be possible to swap out your datastore with a single line, but I'm not sure it's the best idea to do so. The App Engine datastore is not a relational database, and in fact is very different from one.
When you design your schema, you should either do it thinking in a relational mindset, or in a non-relational one, and even if it's a one-liner to change your datastore provider, it definitely won't be a one-liner to redesign your schema.
Trying to shoehorn your relational schema onto a non-relational datastore will be hugely inefficient, at best. And vice versa.
So my advice is to either design your schema based on the knowledge that it will be in a non-relational datastore like App Engine's, or relationally, on some other datastore system.