MEDICAL BIOLOGY

GENE MAPPING

Sual Tatlısulu
 Gene Mapping
• Genetic mapping - also called linkage
mapping - can offer firm evidence that a
disease transmitted from parent to child
is linked to one or more genes. Mapping
also provides clues about which
chromosome contains the gene and
precisely where the gene lies on that
chromosome.
https://www.youtube.com/watch?v=cAFAj
Yq_68I

3
If two genes are on
different chromosomes…

4
If two genes are on
different chromosomes…

Half look like they got a

set of the parents
chromosomes…

And half look like they got

a mix of both parents
chromosomes…
5
Now suppose both gene A
and B were next to each
other on the same
chromosome.

What happens to the ratios

in this diagram?

6
7
8
 Gene Mapping
• Gene mapping determines the order of genes and the relative
distances between them in map units

• 1 map unit = 1 cM (centimorgan)

• Gene mapping methods use recombination

frequencies between alleles in order to determine the relative
distances between them

• Recombination frequencies between genes are inversely

proportional to their distance apart

• Distance measurement: 1 map unit = 1 percent recombination (true

for short distances)
9
Fig. 4.6
Recombination frequency = (number of
recombinant progeny / total number of
progeny) × 100% 10
 Gene Mapping
• Genes with recombination frequencies less than 50 percent are on
the same chromosome = linked)
• Linkage group = all known genes on a chromosome
• 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

11
 Mapping the distance between two genes
Starting with pure breeding lines,
Cross Parent 1(AA BB) with Parent 2(aa bb)

So Parental chromosomes in the F1 have to be AB and ab

Now cross (AB ab) F1 progeny with (ab ab) tester

to look for recombination on these chromosomes.
Suppose you Get……

AB ab 583 <parental

ab ab 597 <parental

Ab ab 134 <recombinant

aB ab 134 <recombinant
total= 1448

so…. 268 recombinants /1448 progeny =

0.185 recombinants/progeny=
18.5% recombinants=
18.5 mu
12
 Q1

The following testcross produces the progeny

shown: AaBb × aabb → 10 AaBb, 40 aaBb, 40
aaBb, and 10 aabb. What is the percentage of
recombination between the A and B loci? Were
the genes in the AaBb parent in coupling or
repulsion?
 Q1

The following testcross produces the progeny

shown: AaBb × aabb → 10 AaBb, 40 aaBb, 40
aaBb, and 10 aabb. What is the percent
recombination between the A and B loci? Were
the genes in the AaBb parent in coupling or
repulsion?
% recombination: 20%; genes in the AaBb parent
were in repulsion
 Mapping (and ordering) three genes
Starting with pure breeding lines, Cross Parent 1(AA BB DD) with Parent 2(aa bb dd)

So you know the Parental chromosomes in the F1 have to be ABD and abc

Cross (ABD abd) F1 progeny with (abd abd) tester

Ab + aB = (45+89)+(94+40)
recom Suppose you Get……
268 recom/1448 total =0.185
A-B =18.5mu ABD abd 580 <parental
ABd abd 3
Bd + bD = (3+40)+(5+45)
93 recom/1448 total= 0.064 abD abd 5 <parental
B-D =6.4mu abd abd 592

AbD abd 45 <recombinant

Ad + aD = (3+89)+(5+94) Abd abd 89
191 recom/1448 total= 0.132
A-D =13.2mu aBD abd 94
aBd abd 40 <recombinant
total= 1448
so the order must be A-----D---B
-13.2--6.4-
----18.5----
15
So How come 13.2 + 6.4 does not equal 18.5?

We missed the double recombinants on the first pass…

Cross (ABD abd) F1 progeny with (abd abd) tester

Ab + aB = (45+89)+(94+40)
recom Suppose you Get……
268 recom/1448 total =0.185
A-B =18.5mu ABD abd 580 <parental
(45+89)+(94+40)+2(3+5) recom ABd abd 3
284recom/1448 total = 0.196
abD abd 5 <parental
A-B =19.6mu
abd abd 592

longer the distance, more AbD abd 45 <recombinant

potential to underestimate Abd abd 89
recomb freq.
aBD abd 94
aBd abd 40 <recombinant
total= 1448
A-----D---B
-13.2--6.4-
----18.5----
16
Chromosome interference: crossovers in one region decrease the
probability of a second crossover close by

Coefficient of coincidence = observed number of double recombinants

divided by the expected number
\ If the two crossovers were independent,
we would expect that the probability of seeing two recombination events occur would be
0.132 between A-D AND 0.064 between D-B
0.132 X 0.064 = 0.008
For every 1448 progeny, this would be (1448x0.008)=12.23 double recombinants
We actually observed only (5+3)= 8 double recombinants

So the Coefficient of coincidence = observed / expected = 8/12.23 =0.65

Interference = 1-Coefficient of coincidence

Interference = 1-Coefficient of coincidence

= 1- 0.65
= 0.35
17
7.14 The results of a three-point testcross can
be used to map linked genes. In this three-point
testcross of Drosophila melanogaster, the
recessive mutations scarlet eyes (st), ebony body
color (e), and spineless bristles (ss) are at three
linked loci. The order of the loci has been
designated arbitrarily, as has the sex of the
progeny flies.
 • Determining the gene
order

• Determining the
location of crossovers

7.15 Writing the results of a three-point

testcross with the loci in the correct order
allows the locations of crossovers to be
determined. These results are from the
testcross illustrated in Figure 7.14, with the loci
shown in the correct order. The location of a
crossover is indicated by a slash (/). The sex of
the progeny flies has been designated arbitrarily.
 Q2

Write the genotypes of all recombinant and

nonrecombinant progeny expected from the
following three-point cross:
 Q2

Write the genotypes of all recombinant and

nonrecombinant progeny expected from the
following three-point cross:

Answer:
 Q3

A three-point test cross is carried out between

three linked genes. The resulting nonrecombinant
progeny are s+r+c+ and s r c, and the double-
crossover progeny are s r c+ and s+r+c. Which is
the middle locus?
 Q3

A three-point test cross is carried out between

three linked genes. The resulting nonrecombinant
progeny are s+r+c+ and s r c, and the double-
crossover progeny are s r c+ and s+r+c. Which is
the middle locus?

the C locus
• https://www.youtube.com/watch?v=TU4
4tR0hJ8A

30
Q4
Genes A, B, G, and H are located on the same
chromosome. The distances between the genes are below:
What is the most likely order of the genes on the
chromosome?
Relationship Map Unit Distance
A-H 18
A-B 10
B-H 8
A-G 2
H-G 20

A. BHGA
B. HBAG
C. BHAG
D. ABHG 31
Q5
In a species of fly, smooth wings (W) are dominant to
wrinkled wings (w) and red bodies (R) are dominant to yellow
bodies (r).
A WwRr and wwrr fly mate and produce the following
offspring:
What is the percent recombination frequency for this cross?

Phenotype Number of Offspring

Smooth, red 778
Smooth, yellow 162
Wrinkled, red 158
Wrinkled, yellow 785

32
Q6
Genes A, B, C, and D are located on the same chromosome.
The recombination frequencies (RF) are as follows:
What is the order of the genes on the chromosome?
Relationship RF
B-D 14%
C-D 12%
A-D 6%
B-C 2%
A-B 8%

A. BCAD
B. DBAC
C. ACBD
D. CBAD
33
Q7
In pea plants, green pods (G) are dominant to yellow pods (g)
and tall plants (T) are dominant to short plants (t).
A scientist crosses a GgTt pea plant with a ggtt pea plant and
the following offspring are produced:
What is the percent recombination frequency for this cross?

Phenotype Number of Offspring

Green, tall 723
Yellow, short 749
Green, short 48
Yellow, tall 46

34
Mapping Genes in Human Pedigrees
• Methods of recombinant DNA technology are used to
map human chromosomes and locate genes

• Genes can then be cloned to determine structure and

function

• Human pedigrees and DNA mapping are used to

identify dominant and recessive disease genes

• Polymorphic DNA sequences are used in human

genetic mapping. 35
 Genetic Polymorphisms
• The presence in a population of two or more relatively
common forms of a gene or a chromosome is called
polymorphism
• Changes in DNA fragment length produced by presence or
absence of the cleavage sites in DNA molecules are known
as restriction fragment length polymorphism (RFLP)
• A prevalent type of polymorphism is a single base pair
difference, simple-nucleotide polymorphism (SNP)
• A genetic polymorphism resulting from a tandemly repeated
short DNA sequence is called a simple sequence repeat
(SSR)
36
 RFLPs
• Restriction endonucleases are used to map genes as
they produce a unique set of fragments for a gene

• There are more than 200 restriction endonucleases in

use, and each recognizes a specific sequence of DNA
bases

• EcoR1 cuts double-stranded DNA at the sequence

5’-GAATTC-3’ wherever it occurs

37
Fig. 4.18 38
 RFLPs
• Differences in DNA sequence generate different recognition
sequences and DNA cleavage sites for specific restriction enzymes
• Two different genes will produce different fragment patterns when cut
with the same restriction enzyme due to differences in DNA sequence

39
Fig. 4.19
 SNPs
• Single-nucleotide polymorphisms (SNPs) are abundant in
the human genome
• Rare mutants of virtually every nucleotide can probably be
found, but rare variants are not generally useful for family
studies of heritable variation in susceptibility to disease
• For this reason, in order for a difference in nucleotide
sequence to be considered as an SNP, the less-frequent
base must have a frequency of greater than about 5% in
the human population.
• By this definition, the density of SNPs in the human
genome averages about one per 1300 bp
40
 SSRs
• A third type of DNA polymorphism results from differences
in the number of copies of a short DNA sequence that
may be repeated many times in tandem at a particular site
in a chromosome

• When a DNA molecule is cleaved with a restriction

endonuclease that cleaves at sites flanking the tandem
repeat, the size of the DNA fragment produced is
determined by the number of repeats present in the
molecule

• There is an average of one SSR per 2 kb of human DNA

41
Mapping Genes in Human Pedigrees
• One source of the utility of SNPs and SSRs in human
genetic mapping is their high density across the
genome

• Additional source of utility of SSRs in genetic mapping

is the large number of alleles that can be present in any
human population.

42
Mapping Genes in Human Pedigrees

• Human pedigrees can be analyzed for the inheritance

pattern of different alleles of a gene based on differences in
SSRs and SNPs

• Restriction enzyme cleavage of polymorphic alleles that are

different in RFLP pattern produces different size fragments
by gel electrophoresis

43
7.19 Linkage between ABO blood types and
nail–patella syndrome was established by
examining families in whom both traits
segregate. The pedigree shown here is for one
such family. The ABO blood type is indicated in
each circle or square. The genotype, inferred
from phenotype, is given below each circle or
square.