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I think the most likely scenario would be the plant expressing a new (or modified) allergenic protein, and it seems like there are some decent methods to look for those things already in use.

https://www.researchgate.net/publication/251449018_Mitigatin...

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Also likely is that part of the genome that produces toxins in one part of the plant that isn't normally eaten gets turned on in edible part.

For example: asparagus berries are toxic, but the toxin doesn't appear in the stalk. The mechanism to produce the toxic chemical is there, just turned off in those cells. Enabling it is the sort of thing that small mutations might do.

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