The use of antibiotic markers is an older technology. It is more common now to use a fluorescent protein marker. Further, the technology has gotten reliable enough that generally a marker is not needed. In the end, doing a simple PCR confirms or denies the presence of the transgene

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> The techniques used for transferring a new gene into a plant are rather inefficient. Very few cells actually take up the gene of interest; when conditions are favourable, only some five cells in a thousand are genetically modified. Most often this ratio is lower. In order to find the cells that have been successfully transformed, some kind of marker is needed.

> To do this, the gene that will give the plant its new trait (gene of interest) is coupled with a marker gene. Plant cells are then transformed with both genes simultaneously. The vast majority of these marker genes work by giving  genetically modified cells the ability to break down a poisonous substance.

> Plant cells expressing an antibiotic resistance marker gene (ABR gene) are thus not harmed by that antibiotic. Treating the cells after the gene transfer with an antibiotic allows only the successfully transformed cells to survive. These cells also possess the gene of interest. Genetically modified plants containing the gene of interest are then regenerated from these individual, successfully transformed cells.

> Visible markers: These marker genes make transgenic plants visually recognisable. The gene for the green fluorescent protein (GFP) makes genetically modified plant cells appear green when exposed to UV light. A major disadvantage to this technique is that modified and unmodified cells must later be visually separated, which can be very tedious.

http://www.gmo-compass.org/eng/safety/human_health/45.antibiotic_resistance_genes_transgenic_plants.html

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> During the efficient genetic transformation of plants with the gene of interest, some selectable marker genes are also used in order to identify the transgenic plant cells or tissues. Usually, antibiotic- or herbicide-selective agents and their corresponding resistance genes are used to introduce economically valuable genes into crop plants. 

> From the biosafety authority and consumer viewpoints, the presence of selectable marker genes in released transgenic crops may be transferred to weeds or pathogenic microorganisms in the gastrointestinal tract or soil, making them resistant to treatment with herbicides or antibiotics, respectively. 

> The production of marker-free transgenic plants is now a critical requisite for their commercial deployment and also for engineering multiple and complex trait.

Recent advances in development of marker-free transgenic plants: regulation and biosafety concern. J Biosci. 2012 Mar; 37(1):167-97.
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