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A genetic marker is a known DNA sequence. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci, that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism), or a long one, like microsatellites.

Some commonly used types of genetic markers are

• RFLP (or Restriction Fragment Length Polymorphism)
• AFLP (or Amplified Fragment Length Polymorphism)
• RAPD (or Random Amplification of Polymorfic DNA)
• VNTR (or Variable Number of Tandem Repeat)
• Microsatellite Polymorphism
• SNP (or Single Nucleotide Polymorphism)
• STR (or Short Tandem Repeat)

Genetic markers can be used to study the relationship between an inherited disease and its genetic cause (for example, a particular mutation of a gene that results in a defective protein). It is known that pieces of DNA that lie near each other on a chromosome tend to be inherited together. This property enables the use of a marker, which can then be used to determine the precise inheritance pattern of the gene that has not yet been exactly localized.

Genetic markers have to be easily identifiable, associated with a specific locus, and highly polymorphic, because homozygotes do not provide any information. Detection of the marker can be direct by DNA sequencing, or indirect using allozymes.

Some of the methods used to study the genome or phylogenetics are RFLP, Amplified fragment length polymorphism AFLP, RAPD, SSR.

Genetic markers also play a role in genetic engineering, as they can be used to produce normal, functioning proteins to replace defective ones. The damaged or faulty section of DNA is removed and replaced with the identical, but functioning, gene sequence from another source.

This is done by removal of the faulty section of DNA and its replacement with the functioning gene from another source, usually a human donor. These gene sections are placed in solution with bacterial cells, a small number of which take up the genetic material and reproduce the new DNA sequence. Engineers need to know which bacteria have been successful in duplicating these genes so another gene is added, altering the bacteria's resistance to antibiotics. Replica plating or a fermenter is used to grow enough bacteria to test resistance to antibiotics. It is important that the cultures are not mixed.

This process can be used as a treatment for diabetes mellitus. Bacterial DNA often has two resistency genes: one for tetracycline and one for ampicillin. The insulin gene can be inserted in the middle of the ampicillin gene after it has been removed using restriction endonucleases. If the gene has been taken up, the bacteria both produces insulin and is also no longer ampicillin resistant. The bacteria are then allowed to grow on an agar plate containing a culture medium. The bacteria grow and produce colonies on the agar jelly. A piece of filter paper can be placed onto the top of this agar plate so that the exact positions of the colonies are remembered. This produces a copy which can then be transferred onto a second agar plate containing ampicillin. All of the bacteria that are not resistant to ampicillin will die. These locations on the second plate show the places on the first plate where bacteria are not resistant and therefore produce insulin. Another similar method is followed, in which an epitope sequence is added to insert. When the insert is expressed so is the epitope. Then this epitope can be effectively bound using an antibody on a filter paper. And the expressing colonies can be easily selected.

• AFLP
• STR
• SNP

• de Vicente, C., T. Fulton (2003). Molecular Marker Learning Modules – Vol. 1.. IPGRI, Rome, Italy and Institute for Genetic Diversity, Ithaca, New York, USA.. 
• de Vicente, C., T. Fulton (2004). Molecular Marker Learning Modules – Vol. 2.. IPGRI, Rome, Italy and Institute for Genetic Diversity, Ithaca, New York, USA.. 
• de Vicente, C., J-C. Glaszmann, editors (2006). Molecular Markers for Allele Mining. AMS (Bioversity's Regional Office for the Americas), CIRAD, GCP, IPGRI, M.S. Swaminathan Research Foundation.  85 p.
• de Vicente, C., T. Metz and A. Alercia (2004). Descriptors for genetic markers technologies. IPGRI.  30 p.
• Spooner, S., R van Treuren and M.C. de Vicente (2005). Molecular markers for genebank management. CGN, IPGRI, USDA.  126 p.

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