Yes. Yes they can. If they use crispr they have the proof its theirs and can patent their work. Thats how it works. Patent law is about taking a large enough step from what existed before. Its how monsanto got a patent for their soybeans that are round up resistant even though soybeans have been around longer than monsanto. The round up resistence was a novel step and allowed patent. They own the genetics of the plant they altered. Not talking about selective breeding. Which, even then, you can document your work and create new things with that, just takes longer.
You’re right they cannot patent anything preexisting. But they absolutely could patent something new they made. And if those genetics start getting into the larger pool outside that strain it gets messy. Legally speaking.
#notlegaladvice