Strain (biology)

Prokaryotes (bacteria and archaea) have a vertical pattern of inheritance, with the exception of horizontal gene transfer events. The concept of a strain is traditionally based on cell culture lineage: the Prokaryotic Code defines a strain as the group "of the descendants of a single isolation in pure culture". Accordingly, prokaryotes in the same strain are expected to have minimal phenotypic and genetic differences. (There has been some complication in the case of lost records about culture lineages.)^[2] A strain can be identified by a name assigned by some author (e.g. "B6", "natto"), or by the abbreviation of a culture collection followed by a number (e.g. ATCC 23308).

The above fits well for artificial strains, often constructed in labs via mutagenesis followed by selection, or through more direct genetic modification. In biotechnology, microbial strains have been constructed to establish metabolic pathways suitable for treating a variety of applications.^[3] Historically, a major effort of metabolic research has been devoted to the field of biofuel production.^[4] Escherichia coli is most common species for prokaryotic strain engineering. Scientists have succeeded in establishing viable minimal genomes from which new strains can be developed.^[5] These minimal strains provide a near guarantee that experiments on genes outside the minimal framework will not be effected by non-essential pathways. Optimized strains of E. coli are typically used for this application. E. coli are also often used as a chassis for the expression of simple proteins. These strains, such as BL21, are genetically modified to minimize protease activity, hence enabling potential for high efficiency industrial scale protein production.^[6]

Fungi and plants are both governed by the Botanical Code. As a result, the term "strain" has no official taxonomic meaning. In common usage, the concept of a "strain" is similar to the prokaryotic one (descendants of a single isolation in pure culture). The practice of naming is also similar to the prokaryotic case (e.g. "PC-3-7" = "NRRL 15500").

Strains of yeasts are the most common subjects of eukaryotic genetic modification, especially with respect to industrial fermentation.^[8]

With the exception of recombination events, viruses have a vertical pattern of inheritance, making for an obvious borrowing of the strain concept from microbiology. However, significant divergence has since happened: it has been said that "there is no universally accepted definition for the terms 'strain', 'variant', and 'isolate' in the virology community, and most virologists simply copy the usage of terms from others".^[9]

The term has no official ranking status in botany; the term refers to the collective descendants produced from a common ancestor that share a uniform morphological or physiological character.^[15] A strain is a designated group of offspring that are either descended from a modified plant (produced by conventional breeding or by biotechnological means), or which result from genetic mutation. ^{[citation needed]}

As an example, some rice strains are made by inserting new genetic material into a rice plant,^[16] all the descendants of the genetically modified rice plant are a strain with unique genetic information that is passed on to later generations; the strain designation, which is normally a number or a formal name, covers all the plants that descend from the originally modified plant. The rice plants in the strain can be bred to other rice strains or cultivars, and if desirable plants are produced, these are further bred to stabilize the desirable traits; the stabilized plants that can be propagated and "come true" (remain identical to the parent plant) are given a cultivar name and released into production to be used by farmers. ^{[citation needed]}

A laboratory mouse or rat strain is a group of animals that is genetically uniform. Strains are used in laboratory experiments. Mouse strains can be inbred, mutated, or genetically modified, while rat strains are usually inbred. A given inbred rodent population is considered genetically identical after 20 generations of sibling-mating. Many rodent strains have been developed for a variety of disease models, and they are also often used to test drug toxicity.^[17][18][19]

The common fruit fly (Drosophila melanogaster) was among the first organisms used for genetic analysis, has a simple genome, and is very well understood. It has remained a popular model organism for many other reasons, like the ease of its breeding and maintenance, and the speed and volume of its reproduction. Various specific strains have been developed, including a flightless version with stunted wings (also used in the pet trade as live food for small reptiles and amphibians).^{[citation needed]}

• Genetic isolate
• Clone (cell biology)
• Race (taxonomy)
• Variant (biology)
• Fish stocks