That is an interesting idea. Corn has 10 pairs of chromosomes. I wonder if you can tell for each pair, which one came from which parent? But then again, it shouldn't matter. As long as a set of 10, and its complement, both produce viable individuals, their offspring should be identical to the desired hybrid.
Now we just must not tell this to the Chinese...
For humans the chromosomes are marked in this way. I don't know about corn.
I'd like to read about this. Can you give a link (or just relevant words for googling), please?
https://en.wikipedia.org/wiki/DNA_methylation
That's about as much as I know. Genomic imprinting is specifically to do with DNA that behaves differently depending on whether it's paternal or maternal. The most famous example of this "in real life" is Prader-Willi syndrome (mentioned in the imprinting article), in which the same genetic defect causes one of two radically different pathologies, depending on whether it came from the mother or father.
I think it's worth noting here that plant genetics is vastly more complex in basically every way than animal genetics.
> So how do agricultural companies do this? By building special inbred varieties that have [t]he same genotype as phenotype.
Are you sure you have "the background"? What do you mean by this? Genotypes and phenotypes can't be said to be "the same" in any dimension; they cover completely different ideas. Possible genotypes are things like "A allele" or "G allele", where phenotypes are things like "tall" or "slimy".
If you mean that the company strains are all homozygous at certain locations of interest, and the seed they sell is heterozygous, that just means that you'll lose a certain amount of seed to quality issues when you breed your seeds directly. It also means you can trivially recreate the company strains by lifting chromosomes out of non-gamete cells. (Granted, I have no idea where the technology is for this -- it's cloning in the conventional "I have a biology lab" sense.)
If you mean that the company strains actually have just the one chromosome N times over for each chromosome, that's hard to believe. An animal would almost definitely immediately die with genetic makeup like that. But, again, genetic engineering could still do this. Also, there's no way the genetic information of these company strains could be considered "trade secrets", since it's all freely released to the public in the hybrid strains.