This document discusses chromosome and gene mapping techniques. It describes how gene mapping is used to identify the location of genes and distances between genes on chromosomes. Two main types of maps are discussed - genetic maps based on linkage and physical maps using actual distances in base pairs. Molecular markers are described as polymorphic DNA sequences used to map genes. Methods for genetic mapping like linkage analysis and calculating recombination fractions are explained.

1. Chromosome or Gene
Mapping
&
Linkage Analysis
Mrs.R.Gloria Jemmi Christobel
Assistant Professor
Department of Biochemistry
V.V.Vanniaperumal College for Women
Virudhunagar, Tamil Nadu, India.

2. Chromosome OR Gene Mapping
• Gene mapping describes the methods used to identify the
locus of a gene and the distances between genes.
• The essence of all genome mapping is to place a collection of
molecular markers onto their respective positions on the
genome. Molecular markers come in all forms. Genes can be
viewed as one special type of genetic markers in the
construction of genome maps, and mapped the same way as
any other markers.
• In 1911, by Thomas Hunt Morgan, gene for eyecolor was
located on the X chromosome of fruit fly.
• E.B. Wilson attributed the sex-linked genes responsible for
color-blindness and hemophilia in human beings to be located
on the Xchromosome,similar to the many X-linked factors
being described by the Morgan group in flies.

3. Picture showing loci in chromosome 3
3p21, 3p22.1 are the locus of various genes or sequences

4. What are molecular markers?
• It is a DNA sequence readily detected and
their inheritance is easily monitored.
• It is polymorphic(more than one allele occupy
the locus in a population)
• Includes; Biochemical & genetic markers
• Genetic markers- RFLP, RAPD, SSR,SNP, VNTR
etc….
• Biochemical markers-genes that code for
proteins

5. • There are two distinctive types of "Maps" used in the
field of genome mapping: genetic maps and physical
maps.
• Genetic maps' distances are based on the genetic
linkage information
• Physical maps use actual physical distances usually
measured in number of base pairs.
• While the physical map could be a more "accurate"
representation of the genome, genetic maps often
offer insights into the nature of different regions of the
chromosome, e.g. the genetic distance to physical
distance ratio varies greatly at different genomic
regions which reflects different recombination rates,
and such rate is often indicative of euchromatic
(usually gene-rich) vs heterochromatic (usually gene
poor) regions of the genome.

6. • Genetic mapping
• Usually done by collecting samples (saliva, blood or tissue)
from members with prominent trait or tissue & from
members who doesn’t have the same.
• DNA isolated from the samples
• Examined for the difference in the DNA pattern in person
with disease and person who don’t have the disease.
• Unique DNA pattern is termed as polymorphism or marker
• The important step in building a genetic map is the
development of genetic marker -any sequence feature that
can be faithfully distinguished from the two parents can be
used as a genetic marker
• Closer two markers pass on together to the next
generation.
• “Co-segregation" patterns of all markers can be used to
reconstruct their order

7. • The genotypes of each genetic marker are recorded
for both parents and each individual in the following
generations.
• The quality of genetic map depends on : number of
genetic markers on the map and the size of the
mapping population.
• Linkage for the newly viewed marker with the other
genetic markers are calculated and the actual gene
loci are then bracketed in a region between the two
nearest neighboring markers.
• Process repeated to look for more markers till the
causative locus identified.
• The great advantage of genetic mapping is that it can
identify the relative position of genes based solely on
their phenotypic effect

8. • Genetic mapping is a way to identify exactly which
chromosome has which gene and exactly pinpointing
where that gene lies on that particular chromosome.
• Mapping also acts as a method in determining which
gene is most likely recombine based on the distance
between two genes.
The distance between two genes is measured in units
known as centimorgan. A centimorgan is a distance
between genes for which one product of meiosis in
one hundred is recombinant.
DNA sequence features that satisfy this requirement are
– Restriction Fragment Length Polymorphism (RFLP)
– Simple Sequence Length Polymorphism (SSLP)
– Single Nucleotide Polymorphism (SNP)

9. • Physical mapping
– Uses molecular biology techniques to examine
DNA molecules directly.
– Based on these techniques map construction is
done.
• – These maps show the positions of sequence
features , including genes. The most important
techniques used in physical mapping are as
follows:
– Restriction Mapping
– Fluorescent in situ Hybridization (FISH)
– Sequence Tagged Site (STS) Mapping

10. • There are two methods for scoring an RFLP
– Southern hybridization
– PCR
• Two types of SSLPs are-
– Minisatellites (VNTRs)
– Microsatellites (STRs)
Mapping of SSLPs are done by PCR
• There are some positions in the genome where
some individuals have one nucleotide while
others have another known as SNP
• SNPs enable very detailed genome maps to be
constructed.

11. • Mapping SNPS: These are mainly based on
oliginucleotide hybridization analysis which
includes -
• – DNA Chip Technology
• – Solution Hybridization
• – Oligonucleotide Ligation Assay
• – Amplification Refractory Mutation Assay
(ARMS Test)

12. • Example for mapping the difference in traits of
dominant and recessive in RFLP sequence:

13. Linkage
• Genetic linkage describes the way in which
two genes that are located close to each other
on a chromosome are often inherited
together
• Genes on the same chromosome are said to
be exhibit linkage and are called linked genes
• Linkage is based on crossing over frequency

14. • Chromosomes are inherited as intact units, so it was
reasoned that the alleles of some pairs of genes will be
inherited together because they are on the same
chromosome. This is the principle of genetic linkage,
• Pairs of genes were either inherited independently, as
expected for genes in different chromosomes, or, if
they showed linkage, then it was only partial linkage:
sometimes they were inherited together and
sometimes they were not
• The frequency with which the genes are unlinked by
crossovers will be directly proportional to how far
apart they are on their chromosome. The
recombination frequencyis therefore a measure of the
distance between two genes
• If you work out the recombination frequencies for
different pairs of genes, you can construct a map of
their relative positions on the chromosome

15. • Two types of Linkage: Complete and
incomplete linkage

16. What is linkage anlaysis?
• Genetic Linkage Analysis is a power tool to
detect the chromosomal locations of diseases
genes
• Statistical method for mapping heritable trait
genes to their chromosome locations
Techniques of Linkage Analysis
• Recombination Fraction
• LOD score
• Haldane mapping function

17. Recombination Fraction
• Recombination fraction is a measure of the distance between two
loci.
• Two loci that show 1% recombination are defined as being 1
centimorgan (cM) apart on a genetic map.
• 1 map unit = 1 cM (centimorgan)
• Two genes that undergo independent assortment have
recombination frequency of 50 percent and are located on
nonhomologous chromosomes or far apart on the same
chromosome = unlinked
• Genes with recombination frequencies less than 50 are on the
same chromosome = linked Probability of a marker and a
susceptibility locus segregating independently(may be represented
as θ)
• Ratio of the number of recombined gametes to the total number of
gametes produced
• If θ = 0.5 No linkage
• If θ < 0.5 Linkage

18. • LOD scores
• Statistical measure of the likelihood of genetic
linkage between two loci
• Test to compare the likelihood that two loci are
linked, vs. the likelihood that the two loci are
unlinked
LOD – logarithm of the odd LOD calculations:
• LOD(Z) = log10 ( probability of birth sequences
with a given linkage/probability of birth
sequences with no linkage)
• A LOD score, higher than 3.0 is generally accepted
as evidence for linkage
• A LOD score lower than -2.0 is accepted as
evidence against linkage

19. Haldane’s Mapping functions
• Mapping functions are used to translate
recombination fractions into genetic distances
• A genetic map function M gives a relations i.e. r =
M(d), connecting recombination fraction rand
genetic map
• According to Haldane’s
dM = -1/2ln(1-2r) where
dM is the distance between marker loci,
r is the recombination frequency,
dM is expressed in Morgan, so
r = ½(1-exp (-2dM))

20. Some of the tools for Linkage Analysis
• JoinMap
• Vitesse
• MAPMAKER
• HOMOG
• LOT
• LInkageMapView

21. THANK YOU