LINKAGE AND GENETIC

MAPPING IN EUKARYOTES

1
 LINKAGE
• Each chromosome must possess many different genes
to determine thousand of different human
characteristics.
• Any two genes which occur on the same chromosome
are said to be linked.
• All the genes on a single chromosome form a linkage
group.
• Under normal circumstances, all linked genes remain
together during cell division and so pass into the
gamete, and hence the offspring, together.
• They do not therefore segregate in accordance with
Mendel’s Law of Independent Assortment.

2
• In Drosophila, the allele for broad abdomen is
dominant to narrow abdomen, and allele for long wing
is dominant to vestigial wing.
• If a long-winged, broad fly is crossed with vestigial
winged, narrow fly, the F1 offspring all have long wings
and broad abdomens (as expected).
• But if two of these F1 flies are mated, the ratio of the
F2 generation obtained, 3 long winged, broad flies: 1
vestigial winged, narrow flies (instead of getting
9:3:3:1).
• The explanation in fact is that the genes determining
the length of the wings and width of the abdomen are
located on the same chromosome, resulting in their
being transmitted together.
• Genes linked together on the same chromosome
constitute a linkage group.
3
 L L l l
B B X b b
Long wing Vestigial wing, narrow abdomen
broad abdomen
L l L l Long wing
B b X B b broad abdomen

L L L l L l l l
B B B b B b b b

3 Long wing, broad abdomen 1 Vestigial wing, narrow abdomen

4
 CROSSING OVER AND
RECOMBINATION
• Linked genes do not assort independently
because they are located on the same
chromosomes and tend to move together
through meiosis and fertilization.
• But sometimes, a certain proportion of the
offspring show new combinations, as in
independent assortment.

5
• It is known that genes for flower colour and fruit
colour in tomatoes are on the same chromosome.
• Plants with yellow flowers bear red fruit; those with
white flowers bear yellow fruit.

Let R = allele for red fruit (dominant)

r = allele for yellow fruit (recessive)
W = allele for yellow flowers (dominant)
w = allele for white flowers (recessive)

• If the two types are crossed, the F1 would be Yellow

flower with red fruit as expected.

6
• If the F1 generation is intercrossed (i.e. self
pollinated), the following results would be
expected in F2 generation:
3 yellow flowers/red fruits : 1 white flowers/yellow fruits
• When the actual cross is performed, however,
the following results are typical if 100 F2 plants
are produced:
Yellow flowers and red fruit  68
Yellow flowers and yellow fruit  7
White flowers and red fruit  7
White flowers and yellow fruit  18
7
•What then is the explanation? To find out, let us consider the same F1 intercross as before but
assume that in one parent crossing over took place and this plant was subsequently self-pollinated.

Homologous pair of W W w w
chromosomes at R R r r
prophase 1 of meiosis

Crossing over W W w w
occurs between one
chromatid of each R r R r
chromosome

W W w w
R r R r
If the plant is self
fertilized

Recombinants
Wr
F2 WR wR wr
WR WWRR WWRr WwRR WwRr
Wr WWRr WWrr WwRr Wwrr
wR WwRR WwRr wwRR wwRr
wr WwRr Wwrr wwRr wwrr

New combinations or recombinants WWrr and Wwrr (yellow flowers, yellow fruit) wwRR and wwRr
(white flowers, red fruit). 8
• The new combinations are thus the result of
crossing over in prophase I of meiosis.
• These new combinations are called recombinants
and are another source of variation.
• The chance of two alleles being separated by a
crossover depends on their relative position on
the chromosome.
• The closer they are, the less likely they are to be
separated and, conversely, the greater their
distance apart on the same chromosome the
more likely they are to be separated.

9
• It is possible to calculate how often crossovers
occur during meiosis by counting the percentage
of offspring with recombinants features.
• From this knowledge, chromosome maps can be
produced to show the position of alleles along a
chromosome.
• 10% crossovers value  10 map units (mu)
• 40% crossovers value  40 map units (mu)
• A map unit is also called a centimorgan (cM).
• 1 map unit = 1% recombination frequency (COV)
10
• The crossover value (COV) is calculated using this formula

No. of individuals showing recombination X 100

Number of offspring

From the example above the COV is

COV = (7+7) X 100

(68 + 7 +7 + 18)

COV = 14%

• Meaning the distance between genes for flower colour and

genes for fruit colour are 14 units apart on the same
chromosome.
11
 GENE MAPPING
• In 1917, Alfred H. Sturtevant, reasoned that different
recombination frequencies reflect different distances
between genes on a chromosome.
• The major significance of calculating crossover frequencies is
that it enables geneticist to produce maps showing the
relative positions of genes on chromosomes.
• For example: COV of A and B is 4%. This means that A and B
are 4 units apart on their chromosome.

A B
4

12
• If we can find that A and C give a COV of 10% whereas B and C give only 6%, we
conclude that B is located somewhere between A and C as follows:

A B C
4 6
10
• If, on the other hand, A and C give COV of 2%, and B and C 6%, we conclude that
C lies to one side of A:

C A B
2 4
6
• Another possibility might be that A and C, and B and C both give COV of 2%.
From this we could conclude that C lays midway between A and B.
A C B
2 2

13
Three Point Crosses: A faster more
accurate method to map genes

14
vg – b distance 252 + 241 + 131 + 118 X 100 = 17.7 m.u.
4197

vg – pr distance 252 + 241 + 13 + 9 X 100 = 12.3 m.u.

4197

b – pr distance 131 + 118 + 13 + 9 X 100 = 6.4 m.u.

4197

Correction for Double Crossovers

vg – b distance 252 + 241 + 131 + 118 + 13 + 9 + 13 + 9 X 100.

4197

= 18.7 m.u.
15
Ordered tetrad analysis in fungi: Recovery of all
products of a single meiotic division

• Fungi are haploid for majority of their life cycle

• In ascomycetes, strains of two different mating
types will combine to form a transient diploid cell
• This cell will undergo meiosis, trapping all the
meiotic products within a single structure (ASCUS)

16
 Ordered Tetrad Analysis
• Ordered tetrads or octads have the following key
feature
– The position and order of spores within the ascus is
determined by the divisions of meiosis and mitosis

• This idea is schematically shown in Figure 5.13

– The example depicts ordered octad formation in
Neurospora crassa
• Spores that carry the A allele show orange pigmentation
• Spores that carry the a (albino) allele are white

17
 Mycelia are
Mycelia are
haploid
haploid

heterokaryon

18
 Pairs of daughter All eight cells are
cells are located arranged in a linear,
next to each other ordered fashion

Figure 5.13 19
 TETRAD

mitosis
ASCUS

homologs sister
Each
separate chromatids chromatid chromatid
separate DNA gives rise
replicates to a spore
pair 20
• The genetic content of spores in ordered tetrads
can be determined
– This allows experimenters to map the distance between
a single gene and the centromere

• The logic of this mapping technique is based on

the following features of meiosis
– Centromeres of homologous chromosomes separate
during meiosis I
– Centromeres of sister chromatids separate during
meiosis II

• Refer to Figure 5.14

21
Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
5-85
This 4:4 arrangement of spores within Octad contains a linear arrangement of
the ascus is termed a first-division 4 haploid cells with the A allele which
segregation (FDS) or an M1 pattern are adjacent to 4 with the a allele

Because the A and a alleles have

segregated from each other after
meiosis I

Figure 5.14 (a) No crossing over

22
Mapping between a gene and the centromere….

Detection of crossovers between a

gene and the centromere: Suppose
no crossover occurs...

A = tan spore
color 4:4
a = black pattern
spore color

First division
segregation
23
These arrangement of
spores are termed a The A and a alleles do not
second-division segregation segregate until meiosis II
(SDS) or M2 patterns

Figure 5.14 (b) Single crossing over 24

Detection of crossovers
between a gene and the
centromere: Suppose a
crossover does occur...

2:2:2:2
pattern

A and a alleles do not

end up in separate cells
until chromatids separate…
second division segregation
25
•Crossovers between the gene and the centromere can
show different patterns…
2:2:2:2
or 2:4:2
•depending on random alignment and which chromatid
was involved in exchange

26
Segregation patterns in
ordered asci

27
Segregation patterns in ordered
tetrads

28
• The percentage of M2 asci can be used to calculate the map
distance between the centromere and the gene of interest
– The logic is that a gene is separated from its original centromere only
after a crossover in the region between the gene and the centromere

29
Figure 5.15
• Therefore the chances of getting a 2:2:2:2 or 2:4:2 pattern
depend on the distance between the gene of interest and the
centromere

• To calculate this distance, the experimenter must count the

number of SDS asci, as well as the total number of asci
– In SDS asci, only half of the spores are actually the
product of a crossover
– Therefore
(1/2) (Number of SDS asci) X 100
Map distance =
Total number of asci
SDS = 2ND division segregation (asci with arrangement
2:2:2:2 and 2:4:2)
30
 Mapping the
distance
from a gene
to the
centromere

4:4

2:4:2

2:2:2:2
31
 Octads

A a a A A a
A a a A A a
A a A a a A
A a A a a A
a A a A a A
a A a A a A
a A A a A a
a A A a A a
126 132 9 11 10 12 Total = 300

32
 9 + 11 + 10 + 12 = 42 recombinant asci
300 total asci
Distance between gene and centromere =
percentage of total asci showing second
division segregation pattern…. divided by 2
42/300 (1/2) x 100% = 7 map units

Distance between gene and centromere = ½ (SDS/ total asci) x 100%

33
 TUTORIAL
• In testcross experiments, the frequency of recombination
between genes P and Q is 0.2; between Q and R, 0.3;
between P and R, 0.1. What is the order of the three genes?
A. P-Q-R
B. P-R-Q
C. R-P-Q
D. either A or B
E. Not enough information to decide.

34
 TUTORIAL
• Genes P, Q, R and S occur on the same
chromosome. Investigation of a large
population produced the following cross-over
values between pairs of genes:
• P and R 34%
• P and Q 59%
• R and S 12%
• S and Q 37%
Map these genes on the chromosome.
35
 TUTORIAL
• The following numbers were obtained for
testcross progeny in Drosophila (phenotypes):
+m+ 218
w+f 236
++f 168
wm+ 178
+mf 95
w++ 101
+++ 3
wmf 1

• Find the distance between w-m, w-f, m-f; and

construct a genetic map. 36
 TUTORIAL
• In a cross in Neurospora involving two alleles,
B and b, the following tetrad patterns were
observed. Calculate the distance between the
gene and the centromere.
Tetrad pattern Number
BBbb 36
bbBB 44
BbBb 4
bBbB 6
BbbB 3
bBBb 7
37