A molecular marker is a molecule contained within a sample taken from
an organism (biological markers) or other matter. It can be used to
reveal certain characteristics about the respective source. DNA, for
example, is a molecular marker containing information about genetic
disorders, genealogy and the evolutionary history of life. Specific
regions of the
DNA (genetic markers) is are used to diagnose the
autosomal recessive genetic disorder cystic fibrosis, taxonomic
affinity (phylogenetics) and identity (
DNA Barcoding). Further, life
forms are known to shed unique chemicals, including DNA, into the
environment as evidence of their presence in a particular location.
Other biological markers, like proteins, are used in diagnostic tests
for complex neurodegenerative disorders, such as Alzheimer's
disease. Non-biological molecular markers are also used, for
example, in environmental studies.
1 Genetic markers
1.1 Types of genetic markers
2 Mapping of genetic markers
3 Application in plant sciences
3.1 Applications of markers in cereal breeding
4 Biochemical markers
5 See also
Main article: Genetic marker
In genetics, a molecular marker (identified as genetic marker) is a
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
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". These types of markers may
also identify dominance and co-dominance within the genome.
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).
List of Markers
Restriction Fragment Length Polymorphism
Random Amplified Polymorphic DNA
Amplified Fragment Length Polymorphism
Variable Number Tandem Repeat
Single Nucleotide Polymorphism
Allele Specific Associated Primers
Inverse Sequence-tagged Repeats
Inter-retrotransposon Amplified Polymorphism
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. Different markers may also
require different amounts of DNA. RAPD's may only need 0.02ug of DNA
while an RFLP marker may require 10ug of
DNA extracted from it to
produce identifiable results. currently, SNP markers have turned
out to be a potential tool in breeding programs in several crops.
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. 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.
When developing a map it is beneficial to identify several polymorphic
distinctions between two species as well as identify similar sequence
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.
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
that 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). QTL's 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 pesticides, fungicides and insecticides. 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
Assessing variability of genetic differences and characteristics
within a species.
Identification and fingerprinting of genotypes.
Estimating distances between species and offspring.
Identifying location of QTL's.
DNA sequence from useful candidate genes
It has 5 applications in fisheries and aquaculture:
Genetic variation and population structure study in natural
Comparison between wild and hatchery populations
Assessment of demographic bottleneck in natural population
markers assisted breeding
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
Require prior information.
Low polymerrphism power.
They are very useful to know the genetic stability of a particular
^ Bradley, Linda A.; Johnson, Dorene A.; Chaparro, Carlos A.;
Robertson, Nancy H.; Ferrie, Richard M. (January 1998). "A Multiplex
ARMS Test for 10 Cystic Fibrosis (CF) Mutations: Evaluation in a
Prenatal CF Screening Program". Genetic Testing. 2 (4): 337–341.
^ Zimmer, Carl (January 22, 2015). "Even Elusive Animals Leave DNA,
and Clues, Behind". New York Times. Retrieved January 23, 2015.
^ 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):
^ 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.
^ Maheswaran, M. (2004). "Molecular Markers: History, Features and
Applications". Department of Plant Molecular Biology and
^ a b "Traditional Molecular Markers - eXtension".
articles.extension.org. Retrieved 2015-12-13.
^ Maheswaran, M. (August 2014). "Molecular Markers: History, Features
and Applications". Advanced Biotech.
^ "Molecular Breeding and Marker-Assisted Selection". International
Service For The Acquisition of Agri-Biotech Applications. ISAAA.
^ 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. 2: 1–22 – via Web of Sciences. CS1 maint: Multiple
names: authors list (link)
^ Griffiths, Anthony JF; Miller, Jeffrey H.; Suzuki, David T.;
Lewontin, Richard C.; Gelbart, William M. (2000-01-01). "Mapping with
^ "Molecular Linkage Maps". forages.oregonstate.edu. Retrieved
^ "Molecular breeding and marker-assisted selection". International
Service For The Acquisition of Agri-Biotech Applications. ISAAA.
^ a b c Korzun, Viktor. "Molecular markers and their applications in
cereals breeding" (PDF). Session I: MAS in Plants. Retrieved
Molecular Markers and Genotypi