Re: [DIYbio] Re: I want to test my own food - where do I start

> I think the question was "For any given gene how would you detect
> modification of that gene". More of an informatics exercise than a molecular
> one: I imagine hidden markov modelling of the surrounding genome would help
> identify areas that are "too simple" because of our present difficulty and
> disinclination towards matching deep genomic patterns.
>
> That's assuming you don't just glance at it and say "that's awfully
> prokaryotic for a plant!". :)


Oooh, I see. Yeah, I misinterpreted that question.

The good thing is that today, at least, all of the traits on the
market are large transgene insertions that look very different from
the plants' innate sequences. Prokaryotic and viral sequences spliced
to eukaryotic sequences surrounded by restriction sites. Plus, the
variety of sequences used in practice is quite limited: a handful of
promoters, herbicide tolerance genes and pest resistance genes. So
the number of things to look for is quite small.

In theory, though, someone could make single nucleotide changes that
would be completely indistinguishable from naturally occurring or
random X-ray or EMS induced mutations. In that case, like Cathal
says, there's not much you could do except build a statistical model
of what "natural" sequences look like and compare your observed
mutations against the model.

Ultimately, though, I think it will be more useful (but more
difficult) to judge plants on the functionality of their mutations
rather than how those mutations arrived. IMO, good traits are good
traits regardless of whether it came from a lab or cross-breeding or
HGT. Same for bad traits.

-cory

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