Genome Mapping

1. Submitted By-:
Priya Chaturvedi
M.Sc 3rd
Sem
Roll No.-:1634016

2. Introduction
Types
Genetic mapping
Markers for genetic mapping
DNA markers
RFLP
SSLPs
SNPs
Physical mapping
Techniques
Importance of genetic mapping
-:Contents

3. • Genome mapping is the process of finding
the location of genes on each chromosome.
• It is a critical step in identifying the genes
involved in a genetic disease.
• Once a disease gene is accurately located,
we can determine its DNA sequence and
study its protein product.
Introduction

4. Genome mapping methods can be
divided into two categories-:
Genetic mapping
Physical mapping
Types

5. 1- Genetic Mapping
Uses genetic techniques to construct maps
showing the positions of genes and other sequence
features on a genome.
 Genetic techniques include cross-breeding
experiments or, in the case of humans, the
examination of family histories (pedigrees).

6. • The first genetic maps, constructed in the
organisms such as the fruit fly, used genes as
markers.
• The only genes that could be studied were those
specifying phenotypes that were distinguishable by
visual examination. Eg. Eye colour, height.
• Some organisms have very few visual
characteristics so gene mapping with these
organisms has to rely on biochemical phenotypes.
Markers For Genetic Mapping

8. Markers In Human
• In human the biochemical phenotypes that can be
scored by blood typing.
• These include the standard blood groups such as the
ABO series and also the human leukocyte antigens (the
HLA system).

9. Drawbacks of using gene as marker
Genes are very useful markers but they
are by no means ideal.
One problem, especially with larger
genomes such as those of vertebrates and
flowering plants, is that a map based
entirely on genes is not very detailed.

10. DNA markers
As with gene markers, a DNA marker must have
at least two alleles to be useful.
There are three types of DNA sequence feature
that satisfy this requirement:
Restriction Fragment Length Polymorphisms
(Rflps),
Simple Sequence Length Polymorphisms (Sslps),
and
 Single Nucleotide Polymorphisms (Snps).

11. RFLP
The DNA molecule on the left has a polymorphic restriction
site (marked with the asterisk) that is not present in the
molecule on the right. The RFLP is revealed after treatment
with the restriction enzyme because one of the molecules is cut
into four fragments whereas the other is cut into three
fragments.

12. Simple Sequence Length Polymorphisms
( )Sslps
• SSLPs are arrays of repeat sequences that display length
variations, different alleles containing different numbers of
repeat units
• Unlike RFLPs that can have only two alleles, SSLPs can be
multi-allelic as each SSLP can have a number of different
length variants.
• There are two types of SSLP, both of which were described
in
• Mini satellites , also known as variable number of tandem
repeats(VNTRs), in which the repeat unit is up to 25 bp in

13. Single nucleotide
( )polymorphisms SNPs
These are positions in a genome where some
individuals have one nucleotide (e.g. a G) and
others have a different nucleotide (e.g. a C)).
There are vast numbers of SNPs in every
genome, some of which also give rise to RFLPs,
but many of which do not because the sequence in
which they lie is not recognized by any restriction
enzyme.

14. Advantages Of SNPs
 The advantages of SNPs are their
abundant numbers and the fact that they
can be typed by methods that do not
involve gel electrophoresis.
 This is important because gel
electrophoresis has proved difficult to
automate so any detection method that
uses it will be relatively slow and labour-
intensive.
 SNP detection is more rapid because it is
based on oligonucleotide hybridization

15. Oligonucleotide hybridization
 Oligonucleotide hybridization can therefore
discriminate between the two alleles of an SNP.
 Various screening strategies have been devised
including DNA chip technology and
solution hybridization techniques

16. -2 Physical Mapping
Uses molecular biology techniques to examine DNA
molecules directly in order to construct maps showing the
positions of sequence features, including genes.

17. ..Conti
• A map generated by genetic techniques is
rarely sufficient for directing the sequencing
phase of a genome project. This is for two
reasons:
 The resolution of a genetic map depends on
the number of crossovers that have been
scored.
 Genetic maps have limited accuracy

18. Techniques
 Restriction mapping, which locates the
relative positions on a DNA molecule of the
recognition sequences for restriction
endonucleases;
 Fluorescent in situ
hybridization(FISH), in which
marker locations are mapped by hybridizing a
probe containing the marker to intact
chromosomes;
 Sequence tagged site (STS)
mapping, in which the positions of short
sequences are mapped by PCR and/or

19. The basic methodology for
restriction
mappingThe simplest way to construct a restriction map is
to compare the fragment sizes produced when a
DNA molecule is digested with two different
restriction enzymes that recognize different target
sequences.

20. Limitations of Restriction
mapping
The limitations of restriction mapping can
be eased slightly by choosing enzymes
expected to have infrequent cut sites
( )rare cutter .in the target DNA molecule

21. Rare Cutters
• These ‘rare cutters' fall into two categories-:
 Enzymes with seven- or eight-nucleotide
recognition sequences
 Enzymes whose recognition sequences
contain motifs that are rare in the target
DNA

22. el stretching and molecular combi

23. Fluorescent in situ hybridizati

24. Importance of gene mapping
 Gene map is the anatomy of human genome. It
is a per requisite to understand functioning of
human genome.
 Helps in analysis of the heterogeneity and
segregation of human genetic diseases.
 Helps to develop methods for gene therapy.
 Provides clinically useful information about
linkage