Plant patents are out of my usual practice, but generally the patent applicant is supposed to compare the allegedly novel variety with the "closest art" variety, which may be a parent plant, and to provide data that illustrates the differences between the allegedly novel variety and the "prior art" variety.
This does not need to be based on genetic data, and applicants can satisfy this requirement by providing, e.g., field data demonstrating improved yield, or improved disease resistance, or different floral color/structure, etc., etc. But I feel that nowadays there is no reason that one shouldn't provide some genetic data (e.g., sequencing, or at least markers). Sequencing is so inexpensive and fast nowadays--you can get a complete genome sequenced for about $1000 and in less than a week. At least the scientists I work with do so all the time. And that is pretty definitive proof.
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