Molecular marker

Last updated

A molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. For another example, some proteins can be molecular markers of Alzheimer's disease in a person from which they are taken. [1] Molecular markers may be non-biological. Non-biological markers are often used in environmental studies. [2]

Contents

Genetic markers

In genetics, a molecular marker (identified as genetic marker) is a fragment of DNA that is associated with a certain location within the genome. Molecular markers are used in molecular biology and biotechnology to identify a particular sequence of DNA in a pool of unknown DNA.

Types of genetic markers

There are many types of genetic markers, each with particular limitations and strengths. Within genetic markers there are three different categories: "First Generation Markers", "Second Generation Markers", and "New Generation Markers". [3] These types of markers may also identify dominance and co-dominance within the genome. [4] Identifying dominance and co-dominance with a marker may help identify heterozygotes from homozygotes within the organism. Co-dominant markers are more beneficial because they identify more than one allele thus enabling someone to follow a particular trait through mapping techniques. These markers allow for the amplification of particular sequence within the genome for comparison and analysis.

Molecular markers are effective because they identify an abundance of genetic linkage between identifiable locations within a chromosome and are able to be repeated for verification. They can identify small changes within the mapping population enabling distinction between a mapping species, allowing for segregation of traits and identity. They identify particular locations on a chromosome, allowing for physical maps to be created. Lastly they can identify how many alleles an organism has for a particular trait (bi allelic or poly allelic). [5]

List of MarkersAcronym
Restriction Fragment Length PolymorphismRFLP
Random Amplified Polymorphic DNARAPD
Amplified Fragment Length PolymorphismAFLP
Variable Number Tandem RepeatVNTR
Oligonucleotide PolymorphismOP
Single Nucleotide PolymorphismSNP
Allele Specific Associated PrimersASAP
Inverse Sequence-tagged RepeatsISTR
Inter-retrotransposon Amplified PolymorphismIRAP

Genomic markers as mentioned, have particular strengths and weakness, so, consideration and knowledge of the markers is necessary before use. For instance, a RAPD marker is dominant (identifying only one band of distinction) and it may be sensitive to reproducible results. This is typically due to the conditions in which it was produced. RAPD's are used also under the assumption that two samples share a same locus when a sample is produced. [4] Different markers may also require different amounts of DNA. RAPD's may only need 0.02 ug of DNA while an RFLP marker may require 10 ug of DNA extracted from it to produce identifiable results. [6] currently, SNP markers have turned out to be a potential tool in breeding programs in several crops. [7]

Mapping of genetic markers

Molecular mapping aids in identifying the location of particular markers within the genome. There are two types of maps that may be created for analysis of genetic material. First, is a physical map, that helps identify the location of where you are on a chromosome as well as which chromosome you are on. Secondly there is a linkage map that identifies how particular genes are linked to other genes on a chromosome. This linkage map may identify distances from other genes using (cM) centiMorgans as a unit of measurement. Co-dominant markers can be used in mapping, to identify particular locations within a genome and can represent differences in phenotype. [8] Linkage of markers can help identify particular polymorphisms within the genome. These polymorphisms indicate slight changes within the genome that may present nucleotide substitutions or rearrangement of sequence. [9] When developing a map it is beneficial to identify several polymorphic distinctions between two species as well as identify similar sequences between two species.

Application in plant sciences

When using molecular markers to study the genetics of a particular crop, it must be remembered that markers have restrictions. It should first be assessed what the genetic variability is within the organism being studied. Analyze how identifiable particular genomic sequence, near or in candidate genes. Maps can be created to determine distances between genes and differentiation between species. [10]

Genetic markers can aid in the development of new novel traits that can be put into mass production. These novel traits can be identified using molecular markers and maps. Particular traits such as color, may be controlled by just a few genes. Qualitative traits (requires less than 2 genes) such as color, can be identified using MAS (marker assisted selection). Once a desired marker is found, it is able to be followed within different filial generations. An identifiable marker may help follow particular traits of interest when crossing between different genus or species, with the hopes of transferring particular traits to offspring.

One example of using molecular markers in identifying a particular trait within a plant is, Fusarium head blight in wheat. Fusarium head blight can be a devastating disease in cereal crops but certain varieties or offspring or varieties may be resistant to the disease. This resistance is inferred by a particular gene that can be followed using MAS (Marker Assisted Selection) and QTL (Quantitative Trait Loci). [11] QTLs identify particular variants within phenotypes or traits and typically identify where the GOI (Gene of Interest) is located. Once the cross has been made, sampling of offspring may be taken and evaluated to determine which offspring inherited the traits and which offspring did not. This type of selection is becoming more beneficial to breeders and farmers because it is reducing the amount of herbicides, fungicides and insecticides needed to be used on crops. [11] Another way to insert a GOI is through mechanical or bacterial transmission. This is more difficult but may save time and money.

Applications of markers in cereal breeding

  1. Assessing variability of genetic differences and characteristics within a species.
  2. Identification and fingerprinting of genotypes.
  3. Estimating genetic distances between species and offspring.
  4. Identifying location of QTLs.
  5. Identification of DNA sequence from useful candidate genes. [11]

Applications of markers in aquaculture

  1. Species identification.
  2. Genetic variation and population structure study in natural populations.
  3. Comparison between wild and hatchery populations.
  4. Assessment of demographic bottlenecks in natural populations.
  5. Marker assisted breeding.

Biochemical markers

Biochemical markers are generally the protein marker. These are based on the change in the sequence of amino acids in a protein molecule. The most important protein marker is alloenzyme. Alloenzymes are variant forms of an enzyme that are coded by different alleles at the same locus and this alloenzymes differs from species to species. So for detecting the variation alloenzymes are used. These markers are type-i markers.

Advantages:

Disadvantages:

Applications:

See also

Related Research Articles

<span class="mw-page-title-main">Genetics</span> Science of genes, heredity, and variation in living organisms

Genetics is the study of genes, genetic variation, and heredity in organisms. It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.

Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly unlinked, although the penetrance of potentially deleterious alleles may be influenced by the presence of other alleles, and these other alleles may be located on other chromosomes than that on which a particular potentially deleterious allele is located.

A quantitative trait locus (QTL) is a locus that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers correlate with an observed trait. This is often an early step in identifying the actual genes that cause the trait variation.

Forward genetics is a molecular genetics approach of determining the genetic basis responsible for a phenotype. Forward genetics provides an unbiased approach because it relies heavily on identifying the genes or genetic factors that cause a particular phenotype or trait of interest.

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 that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change, or a long one, like minisatellites.

<span class="mw-page-title-main">Gene mapping</span> Process of locating specific genes

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.

Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence.

<span class="mw-page-title-main">Locus (genetics)</span> Location of a gene or region on a chromosome

In genetics, a locus is a specific, fixed position on a chromosome where a particular gene or genetic marker is located. Each chromosome carries many genes, with each gene occupying a different position or locus; in humans, the total number of protein-coding genes in a complete haploid set of 23 chromosomes is estimated at 19,000–20,000.

<span class="mw-page-title-main">Genetic analysis</span>

Genetic analysis is the overall process of studying and researching in fields of science that involve genetics and molecular biology. There are a number of applications that are developed from this research, and these are also considered parts of the process. The base system of analysis revolves around general genetics. Basic studies include identification of genes and inherited disorders. This research has been conducted for centuries on both a large-scale physical observation basis and on a more microscopic scale. Genetic analysis can be used generally to describe methods both used in and resulting from the sciences of genetics and molecular biology, or to applications resulting from this research.

Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker linked to a trait of interest, rather than on the trait itself. This process has been extensively researched and proposed for plant- and animal- breeding.

A doubled haploid (DH) is a genotype formed when haploid cells undergo chromosome doubling. Artificial production of doubled haploids is important in plant breeding.

<span class="mw-page-title-main">Neurogenetics</span>

Neurogenetics studies the role of genetics in the development and function of the nervous system. It considers neural characteristics as phenotypes, and is mainly based on the observation that the nervous systems of individuals, even of those belonging to the same species, may not be identical. As the name implies, it draws aspects from both the studies of neuroscience and genetics, focusing in particular how the genetic code an organism carries affects its expressed traits. Mutations in this genetic sequence can have a wide range of effects on the quality of life of the individual. Neurological diseases, behavior and personality are all studied in the context of neurogenetics. The field of neurogenetics emerged in the mid to late 20th century with advances closely following advancements made in available technology. Currently, neurogenetics is the center of much research utilizing cutting edge techniques.

In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes to genotypes, uncovering genetic associations.

Nested association mapping (NAM) is a technique designed by the labs of Edward Buckler, James Holland, and Michael McMullen for identifying and dissecting the genetic architecture of complex traits in corn. It is important to note that nested association mapping is a specific technique that cannot be performed outside of a specifically designed population such as the Maize NAM population, the details of which are described below.

Quantitative trait loci mapping or QTL mapping is the process of identifying genomic regions that potentially contain genes responsible for important economic, health or environmental characters. Mapping QTLs is an important activity that plant breeders and geneticists routinely use to associate potential causal genes with phenotypes of interest. Family-based QTL mapping is a variant of QTL mapping where multiple-families are used.

Molecular breeding is the application of molecular biology tools, often in plant breeding and animal breeding. In the broad sense, molecular breeding can be defined as the use of genetic manipulation performed at the level of DNA to improve traits of interest in plants and animals, and it may also include genetic engineering or gene manipulation, molecular marker-assisted selection, and genomic selection. More often, however, molecular breeding implies molecular marker-assisted breeding (MAB) and is defined as the application of molecular biotechnologies, specifically molecular markers, in combination with linkage maps and genomics, to alter and improve plant or animal traits on the basis of genotypic assays.

A sequence related amplified polymorphism (SRAP) is a molecular technique, developed by G. Li and C. F. Quiros in 2001, for detecting genetic variation in the open reading frames (ORFs) of genomes of plants and related organisms.

This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.

SoyBase is a database created by the United States Department of Agriculture. It contains genetic information about soybeans. It includes genetic maps, information about Mendelian genetics and molecular data regarding genes and sequences. It was started in 1990 and is freely available to individuals and organizations worldwide.

Physical map is a technique used in molecular biology to find the order and physical distance between DNA base pairs by DNA markers. It is one of the gene mapping techniques which can determine the sequence of DNA base pairs with high accuracy. Genetic mapping, another approach of gene mapping, can provide markers needed for the physical mapping. However, as the former deduces the relative gene position by recombination frequencies, it is less accurate than the latter.

References

  1. ↑ Choe, Leila H.; Dutt, Michael J.; Relkin, Norman; Lee, Kelvin H. (July 23, 2002). "Studies of potential cerebrospinal fluid molecular markers for Alzheimer's disease". Electrophoresis. 23 (14): 2247–2251. doi:10.1002/1522-2683(200207)23:14<2247::aid-elps2247>3.0.co;2-m. PMID   12210229. S2CID   29462550.
  2. ↑ Fraser, M.P.; Yue, Z.W.; Buzcu, B. (May 2003). "Source apportionment of fine particulate matter in Houston, TX, using organic molecular markers". Atmospheric Environment. 37 (15): 2117–2123. Bibcode:2003AtmEn..37.2117F. doi:10.1016/S1352-2310(03)00075-X.
  3. ↑ Maheswaran, M. (2004). "Molecular Markers: History, Features and Applications". Department of Plant Molecular Biology and Biotechnology.
  4. 1 2 "Traditional Molecular Markers - eXtension". articles.extension.org. Retrieved 2015-12-13.
  5. ↑ Maheswaran, M. (August 2014). "Molecular Markers: History, Features and Applications". Advanced Biotech.
  6. ↑ "Molecular Breeding and Marker-Assisted Selection". International Service For The Acquisition of Agri-Biotech Applications. ISAAA. Retrieved 2015-12-12.
  7. ↑ Contreras-Soto RI, Mora F, de Oliveira MAR, Higashi W, Scapim CA, Schuster I ( (2017). "A Genome-Wide Association Study for Agronomic Traits in Soybean Using SNP Markers and SNP-Based Haplotype Analysis". PLOS ONE. 12 (2): 1–22. Bibcode:2017PLoSO..1271105C. doi: 10.1371/journal.pone.0171105 . PMC   5289539 . PMID   28152092 – via Web of Sciences.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  8. ↑ Griffiths, Anthony JF; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. (2000-01-01). "Mapping with molecular markers".{{cite journal}}: Cite journal requires |journal= (help)
  9. ↑ "Molecular Linkage Maps". forages.oregonstate.edu. Retrieved 2015-12-13.
  10. ↑ "Molecular breeding and marker-assisted selection". International Service For The Acquisition of Agri-Biotech Applications. ISAAA. Retrieved 2015-12-12.
  11. 1 2 3 Korzun, Viktor. "Molecular markers and their applications in cereals breeding" (PDF). Session I: MAS in Plants. Retrieved 2015-12-12.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.