Seminar topic about DNA Markers

1. DNA Marker
Presented by
Satyaveer
(Department of Fisheries Resource Management)
College of Fisheries Mangalore

2. Marker
Biochemical Molecular
Morphological
Based on
Hybridization
Based on PCR
Protein banding
pattern
Isozyme

3.  These are related to shape, size , colour and surface of
various plants parts.
 Such characters used for the varietal identification.
Advantages
 Readily available
 Usually require only simple equipment
 From the most direct measure of phenotype
Disadvantage
 Require expertise on crop or species
 Subject to environmental influences
 Limited in number
1- Morphological markers

4. • Such markers are related to the variation in protein and
amino acid banding pattern.
• Gel Electrophoretic studies used for identification of
biochemical markers.
E.g.- Peroxidase, Acid Phosphatic , Esterase etc.
Advantages :
 Require simple equipment
 A vigorous complement to the morphological assessment
of variation.
Disadvantages:
 Subjected to environment influences
 Limited in number
2. Protein (biochemical) Markers

5.  DNA Sequence used to mark a particular location on a
particular chromosomes.
 Molecular marker are polymorphic DNA or protein
sequences that can be used to identify a chromosomal
region.
 Two type of maker based on their origin
1- soluble protein (the gene products
Isozymes/Allozymes).
2- DNA Marker
used for genetic stock identification and
for resolving taxonomic ambiguity in fisheries.
3. Molecular Marker

6.  Identity
Correct label of animals.
 Similarity
Degree of relatedness among animals.
 Structure
Is possible to identify groups of related
animals.
 Detection
Possess some animal of the collection of
particular allele of gene.
Marker are useful in 4 types of
measurement

7. 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.
How can molecular markers help

8.  The first priority for such research is the identification of
genetic marker.
 Expertise has been developed for various classes of
molecular markers, namely protein (allozymes)and DNA
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 makers 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.
Genetic Markers

9.  “The green section indicates the
presence of a desirable gene in an
organism’ genetic code that
associated with two genetic markers
(red flags).
Conti……..

10. DNA Marker
The DNA marker s are based on polymorphism,
detected at DNA level. Hence these are called as
nuclear DNA markers or polymorphic DNA markers.
Polymorphic DNA markers which can
identification and analysis of new loci or gene in
the genome (Chromosome).

11. 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.

12. Type I
• Type I markers are the coding gene loci
conserved across the species.
• Ex. Slightly polymorphic.
There are 2 main categories of Nuclear DNA
Marker:
Type I and type II Marker
Type II
• Type II marker are derived mostly from non-
coding sequences and are highly polymorphic .
• exp. Micro & Minisatellites.
i. NBFGR (Lucknow)
ii. CMFRI (Kochi)
iii. CIFA (Bhubaneshwar)
iv. NIO (Goa)
are the leading institution in India carrying out
research in this field.

13. i. Minisatellites
ii. Microsatellites
iii. Random amplified polymorphic DNA(RAPD)
iv. Amplified fragment length polymorphism (AFLP)
v. Single nucleotide polymorphism(SNP)
vi. Internal transcribed spacers(ITS)
vii. Mitochondria DNA (which in maternally inherited,
Circular with genes in the 16-18 kilo base pair).
Type II Markers are:-

14. Mutation :
exp. The mutation is responsible for the change in the
color of the fish.
Basic type of DNA markers

15.  RFLP Restriction fragment length polymorphism
 SSLP Simple sequence length polymorphism
 AFLP Amplified fragment length polymorphism
 RAPD Random amplification of polymorphic DNA
 VNTR Variable number tandem repeat
 SNP Single nucleotide polymorphism
 STR Short tandem repeat
 SFP Single feature polymorphism
 DArT Diversity Arrays Technology
 RAD marker Restriction site associated DNA marker
Now a days it is being replaced by various other
method of DNA- marker like

16.  Dominant markers allow for analyzing
many loci at one time, e.g. RAPD
 Co- dominant markers analyze one
locus at a time
CO-dominant marker
(RFLPs, Microsatellites,etc)
They can be further categorized as dominant
or co- dominant

17.  Highly polymorphic – able to detect many different
alleles.
 Highly informative – if one individual carries two
different alleles we can visualize both.
 Easy, fast & inexpensive to screen.
 Easy availability.
 High reproducibility.
 Easy exchange of data between laboratories.
 Frequent occurrence in genome.
Properties of marker

18.  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.
Basic function of all marker

19.  Polymorphism information content (PIC) is the most
important characteristics of a marker.
 From the allelic frequencies, the variability in the
population can be assessed.
 A PIC value greater than 0.5 is considered highly
informative, o.25-0.5 is reasonably informative and <0.25
is slightly informative other method such as Restriction
endonuclease (RE) banding and fluorescent in situ
hybridization (FISH) techniques are used for
identification of fish population stock, species and sex
chromosome in fish.
Characteristics of Marker

20.  To identify the stock accuracy
 To study genetic variation
 To study the phylogenetic relationship
Conclusion

21.  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_i
d=0
References