Gene transfer is the movement of genetic material from the genome of one organism into the genome of another organism. The frequency of gene transfer in the wild is hard to predict or measure, though gene transfer is known to occur among bacteria. One criticism of GMOs is that the genes inserted into transgenic plants may be transferred to other plants, bacteria, or even to humans. The primary transgenes of concern are ones that confer antibiotic resistance (used a selectable marker to identify transformed plants), herbicide resistance, or insect resistance. Potentially these could spread to other organisms providing weeds with herbicide resistance or insect resistance. Bacteria may also take up such genes. Some worry that bacteria in the human gut may take up and express these genes creating adverse health effects for those that eat GMOs. Alternatively, GM crops could cross with wild relatives and pass transgenic material. It has been proposed that the transfer of transgenes to wild relatives could create 'super weeds' that would be resistant to herbicides or insects (depending on the transgene). GM crops lacking 'real' transgenes would pose little risk in this respect (for example markerless RNAi lines).
Unexpected and harmful consequences to host metabolism
Some claim that the process of transforming a plant with foreign DNA can disrupt the native DNA in unpredictable ways that could be harmful for the health of those that consume them. Alternatively, the gene regulation and metabolism of the plant could be affected by the expression of the transgenes in unpredicable ways that could make the plant unsafe to consume. Methods to address these issues are becoming increasingly available, such as deep-sequencing to look for changes in the genome, RNA-Seq to look are the plant transcriptome, and metabolomics to investigate any possible changes in the metabolism of the plant.
Poor safety testing and approval process
The safety testing and approval process for GMOs has been criticized as being inadequate, and heavily influenced by commercial interests.
Allergic reactions to GM crops
The expression of transgenes in plants can produce proteins that are not in the non-GM form of the plants. There is potential that humans could have allergic reactions to these proteins. The likelihood of proteins to cause allergic reactions can be evaluated based on the features of other proteins known to cause allergies, though this approach is not guaranteed. GM crops can be tested to see if they induce an allergic response in trial groups. Some GMOs do not involve the production of a novel protein, meaning that allergic reactions are not a concern.
Promotion of monoculture / loss of diversity
Monoculture is a serious concern for large scale agricultural systems. Monocultures are particularly vulnerable to disease and changing environmental conditions. This is also a concern for crops produced by tradition breeding methods. Many fruit trees are propagated extensively through cuttings and are consequently heavily monocultured (bananas are an example). The major reasons driving the creation of monocultures are a lack of genetic backgrounds for a particular crop that contain the desired characteristics. Some critics of GM crops feel that the creation of GM super-crops will lead to a particular strain being grown exclusively. However, genetic engineering need not promote monoculture and can actually be used to reduce it. Desirable traits can be taken from crops that are currently monocultured and transformed into other genetic backgrounds to create more lines of a particular crop that are commercially viable.