If your root pass is SMAW, then no PQR is needed for that.
For other processes, it comes down to how different your root pass is from the rest of the weld. If you can get both root and fill passes within the range qualified by the PQR, then you only need one. If your root pass is radically different, you might need a separate PQR for that, welded entirely at the parameters you normally use for root pass (or close enough to be within the limits of 5.12 or 5.13). 5.12 gives you a lot of leeway; 5.13 not so much.
You could put both types of pass (root & fill) on one WPS (at least I've approved them that way), but you still might need multiple PQRs to qualify them both. However, this should probably be thought of more as combining multiple procedures onto a single document. 5.7.9 says you can combine WPSs within a single joint; it makes sense to put them on the same piece of paper with the picture of the different passes. But each pass is welded to a fully qualified procedure, tied back to a specific test within the allowable range of essential variables.
Your PQR is not a mockup of your production weld. Putting a root pass with your preferred parameters into your PQR doesn't mean anything. The PQR is basically a metallurgical test of how your weld metal and fusion area will behave. Your all-weld-metal test and Charpies include only the very middle of that test weld; the root pass isn't even taking part in those tests. The PQR says that you can weld this base metal with this consumable with this range of current, this range of volts, this range of travel speed. If you want to do anything outside of that range, you need another PQR (unless it's SMAW). Every pass has to be welded to a qualified procedure, which means it needs to be within the range qualified by a test reported on a PQR. There are no exceptions for fillet welds, root passes, or anything else--except SMAW.
But, again, if your root and fill pass parameters are close enough together to be qualified by a single PQR, great, you're done. In most cases, this is what happens. It's just that once in a while, especially with qualification under 5.13, the fabricator wants the root pass to be so different from the fill passes that the fill pass PQR can't be used to qualify the root pass too. If you haven't run into this, it may be because you haven't been in that situation.
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