Do backcrossed hybrids get marked as the hybrid or the main species in it's DNA?

Indeed, some plant species have been retrospectively recognized as having originated as hybrids between two other species (in some cases even intergeneric hybrids).

Yep, for sure. And fortunately, at species rank and below, the botanical Code makes it easy to switch between the hybrid and non-hybrid formats of a name without having to take formal (published) action. For example, according to one’s preference one can use Eriocoma × bloomeri or Eriocoma bloomeri interchangeably without change in authorship, even if one of the two versions has not previously appeared in publication.

You’ll find that the iNat default is for IDers to bump it back to genus and say “It’s a hybrid” for any organism that shows any morphological deviation from their species concept.

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