How does one identify a seed's species & variety?
Yes, their name are "molecular marker". Every gene carrying a phenotype, quantitative or qualitative, is identified as an allele of every gene encoding for proteins. 
In order to identify a phenotype using just infos gained from DNA, you'll need a previous library made by these gene regions, were every polymorphism between them is associated with a phenotype. For example, a kind of marker used for this kind of work is SSR , or "Simple sequence repeats" : it is made by a simple sequence of DNA interspaced between two other region. The number of repeats of the internal sequence could be associated with a phenotype.

So, by a simple PCR you could amplify this regions:



And by a electrophoresis you could see how much repetitions are in your band, using just the molecular weight.
Here is an example of SSR used for phenotype/genotype screening