What is molecular marker ? DNA sequence used to mark a particular location on a particular chromosomes

1. DNA marker
Jitendra Kumar
MFK-1109
Department of Fisheries Resource Management)
College of Fisheries, Mangalore
jitenderanduat@gmail.com

2. What is molecular marker ?
DNA sequence used to mark a
particular location on a
particular chromosomes
genetic marker
jitenderanduat@gmail.com

3. jitenderanduat@gmail.com

4. 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
jitenderanduat@gmail.com

5. 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
jitenderanduat@gmail.com

6. Types of Marker by their origin
Soluble Proteins- the gene products
(Isozymes / Allozymes)
DNA Marker (nDNA and mt DNA )
DNA
100%
0%
1%
99%
jitenderanduat@gmail.com

7. 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
jitenderanduat@gmail.com

8. 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
jitenderanduat@gmail.com

9. 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?
jitenderanduat@gmail.com

10. 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.
jitenderanduat@gmail.com

11. Now a days it is being replaced by various
other methods of DNA-marker like
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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
jitenderanduat@gmail.com

12. 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)
jitenderanduat@gmail.com

13. 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
jitenderanduat@gmail.com

14. 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
jitenderanduat@gmail.com

15. Conclusion
• To identify the stock accuracy
• To study genetic variation
• To study the phylogenetic relationship
jitenderanduat@gmail.com

16. 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
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http://www.ars.usda.gov/research/docs.htm?docid=7203&pf=1&cg_id=0
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jitenderanduat@gmail.com

17. jitenderanduat@gmail.com