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From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

Antibiotic resistance genes have been introduced to GM plants either as part of the bacterial cloning vectors used for the initial gene constructions or under the control of plant promoters to select for successfully modified cells. The concern is that the presence of antibiotic resistance genes in GM plants could provide a reservoir for the appearance of new drug resistant bacteria through HGT from plants to pathogenic bacteria.

I'm afraid I don't understand the "either ... or" contrast here. As I understand, antibiotic resistance genes are routinely introduced into GM plants with the sole goal: to check what cells have underwent transformation (got the neccessary foreign genes in their genome) and what have not.

I would be grateful to learn what are "initial gene constructions" here, and how does the method using "the control of plant promoters" differ from the first method. Is the purpose of introducing antibiotic resistance genes similar in both cases - to check what cells have underwent transformation? Sorry if the questions are too stupid. Please direct me to relevant Wikipedia pages or articles.

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    $\begingroup$ I think the distinction here is: When you want to introduce a new gene, then you either design a plasmid de novo and transfer it into the cell, or you insert the gene into the genome. But in the latter case you have to put it into a region that is controlled by a promoter (hence under the control of a plant promoter). I am not sure on the initial gene constructions part, though. $\endgroup$ – cel Oct 3 '15 at 17:45
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    $\begingroup$ I think initial gene constructions is referring to the construction of the actual vectors i.e. you build the antibiotic resistance marker into the vector. In the latter case they simply edited a resistance marker into a region controlled by a promoter. Pretty straightforward in my opinion. $\endgroup$ – CKM Oct 3 '15 at 18:54
  • $\begingroup$ @Kendall - Did they simply edit the marker into a plant? Before shooting with bio guns? But why use bio guns and vectors at all, if you can simply edit a gene precisely "under the control of a plant promoter" by some other means? $\endgroup$ – CopperKettle Oct 4 '15 at 1:56
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So basically, most plasmids that you buy have an antibiotic resistance marker, I think it's relatively standard, because you want to know which bacteria were transformed, right? Ergo, the initial cloning vectors being used. These markers are under control of a plasmid promoter like T7, for example, not a plant promoter (unless you contsructed it de novo to do this). But your plasmid is going to have a cloning site where you can make a cut, insert more DNA, and ligate it back together.

At least pursuant to the patent by Monsanto here, my assumption is that if you're looking to modify plants, your insert for the cloning site is probably a plant promoter, followed by a structural gene, and then a UTR sequence. I think what the authors are saying is that some groups put an antibiotic resistance gene into the insert as the structural part, and when you use something like an A. tumefaciens system to integrate that vector into the plant genome, you end up with an antibiotic structural gene under the control of a plant promoter. You should keep in mind that the whole plasmid gets integrated, but not all of it is transcribed by the plant, only that within the transcribed region controlled by a promoter the plant can utilize!!*

*I'll add, what they're worrying about in the linked OP article, is that whether or not the plant is actively producing antibiotic proteins, that the sequence for the antibiotic resistance has been introduced at any point in the plant's genome carries the risk that some bacteria will randomly obtain it through horizontal gene transfer.

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