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Coming into the Genome Age Part IV: Detecting Transgenes in Genetically Modified Food

David Micklos
DNA Learning Center (DNALC), Cold Spring Harbor Laboratory

Updated March 2017

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In “Coming into the Genome Age Part III,” I introduce some experiments that allow students to use their own DNA variations as entrees into modern molecular genetics and bioinformatics. In this article, I discuss a similar approach to studying plants.

Molecular genetic techniques have been used to add transgenes into the genomes of a number of important food plants, and these foreign genes can be readily detected using polymerase chain reaction (PCR). The experiment capitalizes on student interest in forensic science. Finding the fingerprint of transgenes in supermarket foods is analogous to finding DNA evidence at a crime scene. It also provides a platform for discussing the technology of gene transfer, and the pros and cons of GM crops.


Most students would be surprised to learn that the majority of fresh and processed foods in the US have at least one GM component. First, consider the major GM food crops: soybeans, corn, canola, tomatoes, potatoes, and papaya. Next, consider how many processed foods contain components made from corn or soy. These include cornstarch, cornmeal, high-fructose corn syrup, corn oil, soy protein, soy sauce, tofu, and soy oil. Finally, consider that 91% of soybeans and 64% of corn planted in the US in 2009 were genetically modified for herbicide resistance. The most common GM crops are resistant to the herbicide glyphosate (Roundup®), which inhibits 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS), an enzyme involved in the synthesis of aromatic amino acids. GM plants are transformed with a copy of a bacterial version of the EPSPS gene that is resistant to glyphosate and is expressed at high levels under the direction of the 35S promoter of the cauliflower mosaic virus. Once the crop is established, treatment with Roundup® kills off all weeds but spares the resistant corn or soy plants.

The experiment

For this experiment, students bring in food products that likely contain a corn or soy component. Dry products, such as cereals, cornmeal, and corn chips, work best—and it is always fun to include some organic foods. A small sample of the food product is pulverized with a mini mortar and pestle to break down the cell walls, and sodium dodecyl sulfate (SDS) detergent is used to dissolve fats from cell membranes. DNA is precipitated from the crude extract with alcohol, dried, and resuspended in buffer.

PCR is then performed with primers to amplify a portion of the 35S promoter. Herbicide resistance correlates with an insertion allele containing part of the 35S promoter, which is readily identified as a length polymorphism by agarose gel electrophoresis. Amplification of tubulin, a protein found in all plants, provides evidence of amplifiable DNA in the preparation, while tissue samples from wild-type and Roundup Ready® soy plants are negative and positive controls for the 35S promoter.

GM crops—pros and cons

Proponents see many advantages to glyphosate-resistant crops. They increase yield, and save time and fuel by enabling farmers to practice reduced- or no-till farming, which also conserves soil fertility and lessens erosion. Glyphosate is safe, especially in comparison to the previous generation of herbicides, and quickly degrades in the environment. Opponents worry that herbicide resistance could "escape" if GM crops pollinate organic crops or wild relatives. Although not directly caused by this sort of "lateral" gene transfer between close relatives, a number of glyphosate-resistant weeds have nonetheless emerged over the last decade. Insect resistance, which can dramatically decrease insecticide applications to crops, is another important GM trait. In the most common system, plants are transformed with a gene from the soil bacterium Bacillus thuringiensis (Bt). This produces a crystalline protein that kills caterpillars, such as corn rootworm and cotton bollworm. In 2009, plantings of Bt transgenics composed 63% of the US corn crop, and 65% of cotton, the most important non-food GM crop. Because the Bt protein is a potential allergen, Bt corn is only used for livestock feed. There has been at least one major Bt contamination of corn for human consumption. Critics also worry that Bt toxin kills non-target species, such as the monarch butterfly.


Classical breeding over centuries has slowly bent plants to human needs—turning humble weeds, such as corn's wild relative teosinte, into modern agricultural wonders. Direct breeding of semi-dwarf varieties of wheat and rice over the last several decades shifted energy from stem to grain production—dramatically increasing yields and making many underdeveloped countries self-sufficient in grain production. Now, direct gene transfer promises to shorten the time needed to make new plant varieties. Genes are actively being sought that can improve nutritional value, increase yield, or bring more acreage into production—notably by improving salt, drought, and frost tolerance. Increasingly, multiple genes are transformed, or "stacked," in a single plant, endowing it at once with several discrete traits. In this way, the art of plant breeding is being converted into a precise science.

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