Dominant and codominant markers30nov

Presented by :
Ankit Tiwari
M.Sc. (MBT)
Final year
Pt. J.N.M. Medical College, Raipur
Department of Biochemistry
Session:2018-19
1

 Introduction
 Genetic Markers
 Dominant and Codominant Marker
 Restriction Fragment Length Polymorphism (RFLP)
 Random Amplified Polymorphic DNA (RAPD)
 Amplified Fragment Length Polymorphism (AFLP)
 Microsatellites
 Applications
 References
2

 What are markers ?
 In 1980, scientists studying human genetics observed that variation
in the pattern of DNA fragments generated by restriction enzyme
digestion of genomic DNA could be used as Genetic Marker.
 Markers are genetically linked with the gene of interest.
 If the gene of interest in not known, markers linked to the gene of
interest can still be used to select for individuals with desirable
alleles of the gene of interest.
3

Genetic marker is a gene or DNA
sequence with known location on
chromosome that can be used to
identify individuals or species.
Generally they do not
represent the target genes
themselves but act as signs or
flags.
Fig. 1 : Genetic Makers
Source : http://usda-ars-beaumont.tamu.edu/dblhelix.jpg
All genetic markers occupy
specific genomic position within
the chromosome called ‘loci’.
4

Dominant Marker :
 Dominant marker can't differentiate the homozygous and
heterozygous.
 Indicate difference on the basis of present and absent.
Examples : RAPD, AFLP.
Codominant Marker :
 Codominant marker can differentiate the homozygous and
heterozygous.
 Indicate differences in size.
Examples : RFLP, Microsatellites.
5

 RFLPs were the first type of DNA marker to be studied.
 Restriction Fragment Length Polymorphism (RFLP) is a difference in
homologous DNA sequences that can be detected by the presence of
fragments of different lengths after digestion of the DNA samples with
specific restriction endonucleases.
Fig.2 A Restriction Fragment Length Polymorphism
Source: Genomes, Brown TA ;2002.
6

Fig.3 Workflow of RFLP
Source:
https://www.slideshare.net/search/slideshow?searchfrom=header&q=Gentic+marker+&
ud=any&ft=all&lang=**&sort= 7

 PCR based technology.
 RAPD is a DNA polymorphism assay based on the amplification of
random DNA segments with single primers of arbitory nucleotide
sequence.
 It do not require any specific knowledge of DNA sequence of target
organism.
 The primers will or will not amplify a segment of DNA depending
on positions that are complementary to the primers sequence.
 Therefore, if a mutation has occurred in template DNA at site
that was previously complementary to primer, a PCR product will
not be produced. This results in different pattern of amplified
DNA segments on gel.
8

Fig.6 Workflow of RAPD
Source : https://www.researchgate.net/figure/The-principle-of-
RAPD-PCR-technique-Arrows-indicate-primer-annealing-sites-
modified_fig4_44684171
9

Fig. 7 Analysis of RAPD
Source :https://pmblab.wordpress.com/2013/09/22/qa-in-
agh635-course-in-rapd-marker-analysis-what-is-called-the-
locus-and-what-is-the-allele/
10

 AFLP is based on the selectively amplifying the subset of restriction
fragments from a complex of DNA fragments obtained after the
digestion of genomic DNA with restriction endonucleases.
 This is the combination of RFLP and RAPD.
 Typically, two different restriction enzymes are used to cut the
genomic DNA to produce large number of fragments.
 Restricted fragments are ligated with adapters (25-30 bp long).
Primers are used to amplify the restricted fragments. These primers
are complementary to adapters.
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Fig.8 Workflow of AFLP
Source: https://www.researchgate.net/figure/Schematic-representation-
of-AFLP-workflow_fig2_298971868
12

 Microsatellites are also known as short tandem repeats.
 Microsatellites, or short tandem repeats/simple sequence repeats
are polymorphic loci present in DNA that consist of repeating units
of one to six base pairs in length.
 The repeated sequence is often simple, consisting of two, three or
four nucleotides (di-, tri-, and tetra-nucleotide repeats) and can be
repeated many times.
 Microsatellites can be amplified for identification by PCR using the
unique sequences of flanking regions as primers.
13

14
Fig.9 Variation in microsatellite alleles can be detected by analyzing polymerase chain
reaction (PCR) products using agarose gel electrophoresis.
Source : Genetic Linkage and Recombination through Mapping with Molecular
Markers, Lisa M McDonnell and Jennifer Klenz,2014.

 RFLPs have been widely used in gene mapping studies because of
their high genomic abundance due to ample availability of different
restriction enzymes and random distribution throughout the
genome.
 RAPDs have been used for many purpose, ranging from studies at
the individual level (e.g. Genetic identity) to studies involving closely
related species.
 The AFLP technology has the capability to detect various
polymorphism in different genomic regions simultaneously.
 Microsatellites are very informative markers that can be used for
many population genetics studies, ranging from the individual level
to that of closely related species.
15

16
Genetic Maker Dominant(D) or
Codominant (C)
Advantages Disadvantages
Restriction
Fragment length
polymorphism
(RFLP)
C Robust,
Reliable.
Transferable across
populations
Time consuming,
laborious and
expensive
Large amount of
DNA required
Random Amplified
Polymorphic DNA
(RAPD)
D Quick and simples,
Inexpensive
Generally not
transferable
Simple Sequence
Repeats (SSR) or
microsatellites
C Technically simple,
Reliable
Large amount of
time and labour
required
Amplified Fragment
length
polymorphism
(AFLP)
D Multiple loci,
High level of polymorphism
generated
Large amount of
DNA required
Complicated

 Satyanarayana U. Biotechnology. Book and allied (p) Ltd; 2013.
4:649-52.
 Lewin Benjamin. Genes VIII. Pearson Education International; 2004.
54-55.
 Brown TA. Genomes.Oxford: Wiiley-Liss; 2002 ISBN-10: 0-471-
25046-5
 Lodish H, Berk A, Matsudaira P et al. Molecular cell biology; 2004. 5:
396-97.
 Pierce BA. Genetics: a conceptual approach. WH.Freeman and
company; 2012. 4:186.
 Collard BCY, Jahufer Z and Kyong Pang EC. An introduction to
markers, quantitative trait loci (QTL) mapping and marker- assisted
selection for crop improvement: the basic concepts. Euphytica; 2005.
142: 169-196.
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 I would like to express my sincere gratitude to Dr. Abhigyan
Nath sir and Dr. Khushboo Bhange Ma’am for their guidance
and help in preparation of this presentation. I would also like
to thanks Dr. G.K. Sahu sir, Dr. Abhigyan Nath sir and Dr.
Khushboo Bhange Ma’am for providing me the opportunity to
present a seminar at this level.
 This power point presentation has been prepared from
various text books (Biochemistry by U. Satyanarayan, Genes
VIII by Lewin, Genetics by Benjamin A. Pierce etc.) and review
articles.
 I am also thankful to my classmates for their support in
completion of the assignment.
18

Dominant and codominant markers30nov

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