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Genetic modification of plants is achieved by adding a specific gene or genes to a plant, or by knocking down a gene with RNAi, to produce a desirable phenotype. The plants resulting from adding a gene are often referred to as transgenic plants. If for genetic modification genes of the species or of a crossable plant are used under control of their native promoter, then they are called cisgenic plants. Sometimes genetic modification can produce a plant with the desired trait or traits faster than classical breeding because the majority of the plant's genome is not altered.

To genetically modify a plant, a genetic construct must be designed so that the gene to be added or removed will be expressed by the plant. To do this, a promoter to drive transcription and a termination sequence to stop transcription of the new gene, and the gene or genes of interest must be introduced to the plant. A marker for the selection of transformed plants is also included. In the laboratory, antibiotic resistance is a commonly used marker: Plants that have been successfully transformed will grow on media containing antibiotics; plants that have not been transformed will die. In some instances markers for selection are removed by backcrossing with the parent plant prior to commercial release.

The construct can be inserted in the plant genome by genetic recombination using the bacteria Agrobacterium tumefaciens or A. rhizogenes, or by direct methods like the gene gun or microinjection. Using plant viruses to insert genetic constructs into plants is also a possibility, but the technique is limited by the host range of the virus. For example, Cauliflower mosaic virus (CaMV) only infects cauliflower and related species. Another limitation of viral vectors is that the virus is not usually passed on the progeny, so every plant has to be inoculated.

The majority of commercially released transgenic plants are currently limited to plants that have introduced resistance to insect pests and herbicides. Insect resistance is achieved through incorporation of a gene from Bacillus thuringiensis (Bt) that encodes a protein that is toxic to some insects. For example, the cotton bollworm, a common cotton pest, feeds on Bt cotton it will ingest the toxin and die. Herbicides usually work by binding to certain plant enzymes and inhibiting their action. The enzymes that the herbicide inhibits are known as the herbicides target site. Herbicide resistance can be engineered into crops by expressing a version of target site protein that is not inhibited by the herbicide. This is the method used to produce glyphosate resistant crop plants (See Glyphosate)

Genetic modification can further increase yields by increasing stress tolerance to a given environment. Stresses such as temperature variation, are signalled to the plant via a cascade of signalling molecules which will activate a Transcription factor to regulate Gene expression. Overexpression of particular genes involved in cold acclimation has been shown to become more resistant to freezing, which is one common cause of yield loss

Genetic modification of plants that can produce pharmaceuticals (and industrial chemicals), sometimes called pharming, is a rather radical new area of plant breeding.[1]