A genetic marker is a

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

DNA sequence A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nu ...

with a known location on a

chromosome A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most import ...

that can be used to identify individuals or

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

. 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 In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...

, SNP), or a long one, like

minisatellite In genetics, a minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated two to several hundred times. Minisatellites occur at more than 1,000 locations in the huma ...

Background

For many years,

gene mapping Gene mapping or genome mapping describes the methods used to identify the location of a gene on a chromosome and the distances between genes. Gene mapping can also describe the distances between different sites within a gene. The essence of all ...

was limited to identifying organisms by traditional phenotypes markers. This included genes that encoded easily observable characteristics, such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the possible mapping efforts. This prompted the development of gene markers, which could identify genetic characteristics that are not readily observable in organisms (such as protein variation).

Types

Some commonly used types of genetic markers are: * RFLP (or

Restriction fragment length polymorphism In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms, populations, or species or to pinpoint the locations of genes within a sequence. T ...

) * SSLP (or Simple sequence length polymorphism) * AFLP (or

Amplified fragment length polymorphism Amplified fragment length polymorphism (AFLP-PCR or AFLP) is a PCR-based tool used in genetics research, DNA fingerprinting, and in the practice of genetic engineering. Developed in the early 1990s by Pieter Vos, AFLP uses restriction enzymes t ...

) * RAPD (or

Random amplification of polymorphic DNA Random amplified polymorphic DNA (RAPD), pronounced "rapid", is a type of polymerase chain reaction (PCR), but the segments of DNA that are amplified are random. The scientist performing RAPD creates several arbitrary, short primers (10–12 nuc ...

) * VNTR (or

Variable number tandem repeat A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length (number of repeats) among indivi ...

) * SSCP (or Single-strand conformation polymorphism) *

Microsatellite A microsatellite is a tract of repetitive DNA in which certain Sequence motif, DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organ ...

polymorphism, (or Simple sequence repeat) . * SNP (or

Single nucleotide polymorphism In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...

) * STR (or Short tandem repeat) * SFP (or Single feature polymorphism) * DArT (or Diversity Arrays Technology) * RAD markers (or

Restriction site associated DNA markers Restriction site associated DNA (RAD) markers are a type of genetic marker which are useful for association mapping, QTL-mapping, population genetics, ecological genetics and evolutionary genetics. The use of RAD markers for genetic mapping is of ...

) * (using

Sequence-tagged site A sequence-tagged site (or STS) is a short (200 to 500 base pair) DNA sequence that has a single occurrence in the genome and whose location and base sequence are known. Usage STSs can be easily detected by the polymerase chain reaction (PCR) using ...

s) Molecular genetic markers can be divided into two classes: a) biochemical markers which detect variation at the gene product level such as changes in proteins and amino acids and b) molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or insertion. Markers can exhibit two modes of inheritance, i.e. dominant/recessive or co-dominant. If the genetic pattern of homo-zygotes can be distinguished from that of hetero-zygotes, then a marker is said to be co-dominant. Generally co-dominant markers are more informative than the dominant markers.

Uses

Genetic markers can be used to study the relationship between an

inherited disease A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosome abnormality. Although polygenic disorders are ...

and its genetic cause (for example, a particular

mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, ...

of a

that results in a defective

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

). 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 are employed in

genealogical DNA test A genealogical DNA test is a DNA-based Genetic testing, genetic test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to ...

ing for

genetic genealogy Genetic genealogy is the use of genealogical DNA tests, i.e., DNA profiling and DNA testing, in combination with traditional genealogical methods, to infer genetic relationships between individuals. This application of genetics came to be use ...

to determine

genetic distance Genetic distance is a measure of the genetics, genetic divergence between species or between population#Genetics, populations within a species, whether the distance measures time from common ancestor or degree of differentiation. Populations with ...

between individuals or populations. Uniparental markers (on

mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...

or Y chromosomal DNA) are studied for assessing maternal or paternal lineages.

Autosomal An autosome is any chromosome that is not a sex chromosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosomal (sex chromosome) pairs, which may have different structures. The DNA in autosome ...

markers are used for all ancestry. Genetic markers have to be easily identifiable, associated with a specific locus, and highly polymorphic, because

homozygotes Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. Mos ...

do not provide any information. Detection of the marker can be direct by RNA sequencing, or indirect using

allozyme Alloenzymes (or also called allozymes) are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus. These are opposed to isozymes, which are enzymes that p ...

s. Some of the methods used to study the

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

are RFLP, AFLP, RAPD, SSR. They can be used to create genetic maps of whatever organism is being studied. There was a debate over what the transmissible agent of CTVT (

canine transmissible venereal tumor A canine transmissible venereal tumor (CTVT), also known as a transmissible venereal tumor (TVT), canine transmissible venereal sarcoma (CTVS), sticker tumor and infectious sarcoma, is a histiocytic tumor of the external genitalia of the dog and ...

) was. Many researchers hypothesized that virus like particles were responsible for transforming the cell, while others thought that the cell itself was able to infect other canines as an

allograft Allotransplant (''allo-'' meaning "other" in Ancient Greek, Greek) is the Organ transplant, transplantation of cell (biology), cells, Biological tissue, tissues, or Organ (anatomy), organs to a recipient from a genetically non-identical donor of ...

. With the aid of genetic markers, researchers were able to provide conclusive evidence that the cancerous tumor cell evolved into a transmissible parasite. Furthermore, molecular genetic markers were used to resolve the issue of natural transmission, the breed of origin (

), and the age of the canine tumor.Murgia C, Pritchard JK, Kim SY, Fassati A, Weiss RA. Clonal origin and evolution of a transmissible cancer. Cell. 2006 Aug 11;126(3):477-87. Genetic markers have also been used to measure the genomic response to selection in livestock. Natural and artificial selection leads to a change in the genetic makeup of the cell. The presence of different alleles due to a distorted segregation at the genetic markers is indicative of the difference between selected and non-selected livestock.

References

External links

{{Authority control Genetics techniques Genomics techniques DNA Molecular biology

Background

Types

Uses

See also

References

Further reading

External links