A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species. 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, SNP), or a long one, like minisatellites.
Background
For many years, gene mapping 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)
- SSLP (or Simple sequence length polymorphism)
- AFLP (or Amplified fragment length polymorphism)
- RAPD (or Random amplification of polymorphic DNA)
- VNTR (or Variable number tandem repeat)
- SSCP (or Single-strand conformation polymorphism)
- SSR Microsatellite polymorphism, (or Simple sequence repeat)
- SNP (or Single nucleotide polymorphism)
- STR (or Short tandem repeat)
- SFP (or )
- DArT (or Diversity Arrays Technology)
- RAD markers (or Restriction site associated DNA markers)
- STS (using Sequence-tagged sites)
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 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 are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations. Uniparental markers (on mitochondrial or Y chromosomal DNA) are studied for assessing maternal or paternal lineages. Autosomal markers are used for all ancestry.
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 RNA sequencing, or indirect using allozymes.
Some of the methods used to study the genome or phylogenetics 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) 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. 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 (phylogenetics), and the age of the canine tumor.
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.
See also
- Marker gene
- Molecular marker
- DNA marking
- Eukaryotic chromosome fine structure
- Repeated sequence (DNA)
References
- Benjamin A. Pierce (2013-12-27). Genetics: A Conceptual Approach. Macmillan Learning. ISBN 978-1-4641-0946-1.
- Mehta, Sahil; Singh, Baljinder; Dhakate, Priyanka; Rahman, Mehzabin; Islam, Muhammad Aminul (2019). "5 Rice, Marker-Assisted Breeding, and Disease Resistance". In Wani, Shabir Hussain (ed.). Disease Resistance in Crop Plants : Molecular, Genetic and Genomic Perspectives. Cham, Switzerland: Springer. pp. 83–112/xii+307. ISBN 978-3-030-20727-4. OCLC 1110184027. ISBN 978-3-030-20728-1.
- N Manikanda Boopathi (2012-12-12). Genetic Mapping and Marker Assisted Selection: Basics, Practice and Benefits. Springer Science & Business Media. pp. 60–. ISBN 978-81-322-0958-4.
- 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.
- Gomez-Raya L, Olsen HG, Lingaas F, Klungland H, Våge DI, Olsaker I, Talle SB, Aasland M, Lien S (November 2002). "The use of genetic markers to measure genomic response to selection in livestock". Genetics. 162 (3): 1381–8. doi:10.1093/genetics/162.3.1381. PMC 1462338. PMID 12454081.
Further reading
- de Vicente C, Fulton T (2003). Molecular Marker Learning Modules – Vol. 1. IPGRI, Rome, Italy and Institute for Genetic Diversity, Ithaca, New York, USA.[permanent dead link]
- de Vicente C, Fulton T (2004). Molecular Marker Learning Modules – Vol. 2. IPGRI, Rome, Italy and Institute for Genetic Diversity, Ithaca, New York, USA.
- de Vicente C, Glaszmann JC (2006). Molecular Markers for Allele Mining. AMS (Bioversity's Regional Office for the Americas), CIRAD, GCP, IPGRI, M.S. Swaminathan Research Foundation. p. 85. Archived from the original on 2007-12-04. Retrieved 2007-12-12.
- Spooner D, van Treuren R, de Vicente MC (2005). Molecular markers for genebank management. CGN, IPGRI, USDA. p. 126. Archived from the original on 2008-05-03. Retrieved 2007-12-12.
External links
Media related to Genetic markers at Wikimedia Commons
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species 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 SNP or a long one like minisatellites BackgroundFor many years gene mapping 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 TypesSFP discovery principle for gene probing Some commonly used types of genetic markers are RFLP or Restriction fragment length polymorphism SSLP or Simple sequence length polymorphism AFLP or Amplified fragment length polymorphism RAPD or Random amplification of polymorphic DNA VNTR or Variable number tandem repeat SSCP or Single strand conformation polymorphism SSR Microsatellite polymorphism or Simple sequence repeat SNP or Single nucleotide polymorphism STR or Short tandem repeat SFP or DArT or Diversity Arrays Technology RAD markers or Restriction site associated DNA markers STS using Sequence tagged sites 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 UsesGenetic 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 are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations Uniparental markers on mitochondrial or Y chromosomal DNA are studied for assessing maternal or paternal lineages Autosomal markers are used for all ancestry 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 RNA sequencing or indirect using allozymes Some of the methods used to study the genome or phylogenetics 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 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 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 phylogenetics and the age of the canine tumor 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 See alsoMarker gene Molecular marker DNA marking Eukaryotic chromosome fine structure Repeated sequence DNA ReferencesBenjamin A Pierce 2013 12 27 Genetics A Conceptual Approach Macmillan Learning ISBN 978 1 4641 0946 1 Mehta Sahil Singh Baljinder Dhakate Priyanka Rahman Mehzabin Islam Muhammad Aminul 2019 5 Rice Marker Assisted Breeding and Disease Resistance In Wani Shabir Hussain ed Disease Resistance in Crop Plants Molecular Genetic and Genomic Perspectives Cham Switzerland Springer pp 83 112 xii 307 ISBN 978 3 030 20727 4 OCLC 1110184027 ISBN 978 3 030 20728 1 N Manikanda Boopathi 2012 12 12 Genetic Mapping and Marker Assisted Selection Basics Practice and Benefits Springer Science amp Business Media pp 60 ISBN 978 81 322 0958 4 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 Gomez Raya L Olsen HG Lingaas F Klungland H Vage DI Olsaker I Talle SB Aasland M Lien S November 2002 The use of genetic markers to measure genomic response to selection in livestock Genetics 162 3 1381 8 doi 10 1093 genetics 162 3 1381 PMC 1462338 PMID 12454081 Further readingde Vicente C Fulton T 2003 Molecular Marker Learning Modules Vol 1 IPGRI Rome Italy and Institute for Genetic Diversity Ithaca New York USA permanent dead link de Vicente C Fulton T 2004 Molecular Marker Learning Modules Vol 2 IPGRI Rome Italy and Institute for Genetic Diversity Ithaca New York USA de Vicente C Glaszmann JC 2006 Molecular Markers for Allele Mining AMS Bioversity s Regional Office for the Americas CIRAD GCP IPGRI M S Swaminathan Research Foundation p 85 Archived from the original on 2007 12 04 Retrieved 2007 12 12 Spooner D van Treuren R de Vicente MC 2005 Molecular markers for genebank management CGN IPGRI USDA p 126 Archived from the original on 2008 05 03 Retrieved 2007 12 12 External linksMedia related to Genetic markers at Wikimedia Commons
