DNA Marker:

DNA marker
Jitendra Kumar
MFK-1109
Department of Fisheries Resource Management)
College of Fisheries, Mangalore

jitenderanduat@gmail.com

What is molecular marker ?

DNA sequence used to mark a
particular location on a
particular chromosomes
genetic marker

DNA markers = direct reflection of genotype
• Two Fish can display similar phenotypes, but be very different
from a genetic point of view
e.g. Given fish genotypes with similar yield. In each genotype
different genomic regions can be responsible for the high yield
potential
Genotype A

Genotype B

Same Phenotype

How can molecular markers help?
Molecular markers allow working
with genotype information
directly
Analyze the effect of the genotype on
the phenotype

Provide the breeder a tool to look
into the ‘black box’ of the
genotype

Types of Marker by their origin
Soluble Proteins- the gene products
(Isozymes / Allozymes)

DNA Marker (nDNA and mt DNA )

DNA

100%
0%

1%

99%


There are 2 main categories of DNA
marker:
Type I and Type II Markers
Type I

• Type I marker are the coding gene loci
conserved across the species
• Slightly polymorphic

Type II

• Type II marker are derived mostly from noncoding sequences and are highly polymorphic
• exp. Micro & Minisatellites


Two basic types of DNA-markers
Mutations: Exp. the mutation is responsible for the change in the color of the
Fish

Mutation =
Marker
-The most useful

- Difficult to find


Understanding Germplasm Relationships

Markers are useful in four types of
measurements needed in this field:
• Identity: correct label of
Animal?
• Similarity: degree of
relatedness among Animal?
• Structure: is possible to
identify groups of related
Animal?
• Detection: posses some
Animal of the collection a
particular allele of a gene?

Genetic marker
• In Ichthyotaxonomy, DNA based molecular marker (Genetic
Marker) plays an important role to identify the phylogenic
trends of evolution
• 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.

Now a days it is being replaced by various
other methods of DNA-marker like
•
•
•
•
•
•
•
•
•
•

RFLP
SSLP
AFLP
RAPD
VNTR
SNP
STR
SFP
DArT
RAD

Restriction fragment length polymorphism

Simple sequence length polymorphism
Amplified fragment length polymorphism
Random amplification of polymorphic DNA
Variable number tandem repeat
Single nucleotide polymorphism
Short tandem repeat
Single feature polymorphism

Diversity Arrays Technology
markers Restriction site associated DNA
markers

They can be further categorized as dominant or
co-dominant.

Dominant markers allow for
analyzing many loci at one
time, e.g. RAPD.

Co-dominant markers analyze one locus at a time.

Co-dominant markers
(RFLPs, microsatellites, etc)


Markers: desired properties

• Highly polymorphic: able to detect many different alleles

• Highly informative; if one individual carries two different
alleles we can visualize both (co-dominant)

• Easy, fast and inexpensive to screen


Basic functions of all markers
 Genetic markers can be used to study the relationship between
an inherited disease and its genetic cause

 Genetic Markers have also been used to measure the genomic response
to selection in livestock
 Identify the phylogenetic relationship between the different species of
fishes
 Monitoring of inbreeding or other changes in the genetic composition of
the stocks
 Comparisons between hatchery and wild stocks

Conclusion
• To identify the stock accuracy
• To study genetic variation
• To study the phylogenetic relationship


References
•

Ibrahim Okumus and Y. Çiftci / Turk. Turkish Journal of Fisheries and Aquatic Sciences 3: 51-79
(2003)

•

ARIAGNA LARA,* JOSE LUIS PONCE DE, Molecular Ecology Resources (2010) 10, 421–430

•

Handbook of fisheries and Aquaculture, 2006

•

www.google.co.in/dnamarker/wikipedia/in

•

MOLECULAR MARKERS IN ANIMAL GENOME ANALYSIS, Biotechnology in Animal
Husbandry 25 (5-6), p 1267-1284, 2009

•

URL: http://www.jove.com/index/Details.stp?ID=1871

•

http://www.ars.usda.gov/research/docs.htm?docid=7203&pf=1&cg_id=0

•

http://www.google.co.in/imgres?q=gene+marker&hl=en&safe=active&gbv=2&biw=1280&bih=699
&tbm=isch&tbnid=3O8vlSiXUk-IoM:&imgrefurl=http://medicineworld.org/news/newsarchives/research-news/Oct-292007.html&docid=HOgYHw05OJswVM&imgurl=http://medicineworld.org/images/blogs/92007/gene-technology-7830.jpg&w=300&h=249&ei=KukmT9OhK4quiAe4qtjnBA&zoom=1


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