Linkage
Linkage
• One Gene One Trait
• Two Genes Two Traits
• Genes on the same chromosome are
“linked”.
Linkage
A a Coupling
AB
B b ab
A a
Ab Repulsion
b B aB
Linkage
If genes are linked, you would expect that
the law of independent assortment would
not apply.
AaBb x AaBb….. coupled
AB Ab aB ab
AB
Ab
aB
ab
Linkage
AB Ab aB ab
AB AABB AaBb
Ab
aB
ab AaBb aabb
Linkage
Banded and Detached are wing phenotypes
in fruit flies. The two genes are linked.
bn dt+ X bn+ dt
P1
bn dt+ bn+ dt
bn dt+ X bn dt
Wild Type +
F1 bn dt bn dt
bn dt+ bn+ dt
bn dt bn dt
Banded Detached
Linkage
• Make the cross and observe…..
• 483 Banded
• 512 Detached
• 2 Banded, Detached
• 3 Wild type
• Where did the wild type and
banded detached phenotypic
classes come from?
Recombination
• Recombination may occur in
the space between 2 linked
genes.
• Recombination results in the
exchange of alleles between
chromatids.
Recombination
• The result of crossing over
(________) formation during
prophase I.
• Segments of nonsister
chromatids may be exchanged.
bn+ dt
bn+ dt
bn dt+
bn dt+
bn+ dt
bn+ dt
bn dt+
bn dt+
bn+ dt
bn+ dt
bn dt+
bn dt+
}
bn+ dt
Non
bn dt+
Crossover
bn+
bn
dt+
dt
} Recombinant
Recombination
• Recombination can occur in many different places
in each meiocyte
• The frequency of recombination between two loci
is a function of the distance between the loci.
• Recombination as measured between markers is
reciprocal….. Both of the recombinant products
occur with equal frequency.
• Occurs during prophase I
483 Banded Nonrecombin bn dt+
ant bn dt
512 Nonrecombin bn+ dt
Detached ant bn dt
2 Banded Recombinant bn dt
Detached bn dt
3 Wild type Recombinant bn+ dt+
bn dt
Map Distance
• Since the frequency of recombination
events is related to distance, we can use
recombination data to determine the
relative distances between genetic loci.
• Nonrecombinant Gametes =
• Recombinant Gametes =
• Frequency of recombination =
• 5/1000 = 0.5 % = 0.5 map units = 0.5 cM
Linked Genes
• Linkage
– Deviation from normal
independent assortment
– How do you tell whether the
deviation is large enough?
• Chi-square test
Example
• AaBb x aabb
• Progeny are
– 120 AaBb
– 120 aabb
– 80 Aabb
– 80 aaBb
• Are these genes linked?
– If yes
Example
• Assume that the
genes are not
linked.
• Null Hypothesis:
The genes are not
linked and
therefore the
cross should
produce 1 AaBb : 1
Aabb : 1 aaBb : 1
aabb
Chi-square Test
Phenotyp Observ Expecte (o-e) (o-e)2/e
ic ed # d#
Classes
AaBb 120 100 20 400/100
=4
Aabb 80 100 -20 4
aaBb 80 100 -20 4
aabb 120 100 20 4
Totals 400 400
Chi-squared Test
• Chi-square =
• Df = n-1 =
• Critical Value =
• 16 > 7.82 …..
• Independent Assortment is not
occurring…. Therefore the
genes must be linked
Example
• Identify the most
common progeny • Progeny are
– These will always –
be the result of the
120 AaBb
union of gametes – 120 aabb
that have not –
undergone 80 Aabb
recombination – 80 aaBb
– AaBb and aabb are
the most common
ab
• Genotypes:
ab
– a b must come from
tester
• The genes are coupled
Given the results, what is
the map distance between
A/a and B/b?
• Recombinants = • Progeny are
80 + 80 = 160 – 120 AaBb
– 120 aabb
• 160/400 = .40 = – 80 Aabb
40 cM between A – 80 aaBb
and B
• A homozygous groucho (gro) is
crossed with a homozygous rough
fly (ro). The F1 females are
testcrossed with the following
offspring produced.
• Groucho 518
• Rough 471
• Groucho, Rough 6
• WT 5
• What is the linkage arrangement
and the map distance between loci?
• If the F1 were intermated, what
would be the proportion of
phenotypes produced?
– Male flies do not go through
Linkage
• F1
Heterozygous
Female x Tester
male
– Groucho
518
– Rough 471
– Groucho, Rough
6
– WT 5
gro+ ro gro ro+
(.5) (.5)
gro+ ro gro+gro+ ro gro+ gro
(.4945) ro ro+ ro
(.4945 * .5) (.24725)
(518 + 471) /
(.24725)
1000 / 2 gro ro+ gro+ gro gro gro ro+
(.4945) ro+ ro ro+
(.24725) (.24725)
gro+ ro+ gro+ gro+ gro+ gro
(.0055) ro+ ro ro+ ro+
(6 + 5) / 1000
/2 (.00275) (.00275)
gro ro gro+ gro ro gro gro ro+
(.0055) ro ro
(.00275) (.00275)
Linkage
• Issues
– What if genes are 50 cM apart?
• Nonrecombinant = 50%
• Recombinant = 50%
• Looks like independent assortment therefore will
not pass chi square test
• Solution?
– Add third gene
Linkage
• Adding a third gene creates a new
complication
– What is the correct gene order?
AB ab
X ab
ab
A B 165 a b 191
Nonrecombina
ab ab nt
Ab aB Recombinants
23 21
ab ab
Map Distance = (23 + 21) / 400 = 0.11 = 11
cM between A and B
AC ac
X ac
ac
A C 120 a c 120
Nonrecombinant
ac ac
Ac aC Recombinants
80 80
ac ac
Map Distance = (80 + 80) / 400 = 0.4 = 40 cM
between A and C
Distance A to B = 11
Distance A to C = 40
Two Possibilities
Possibility 1 B 11 A 40 C
Possibility 2 A 11 B 29 C
Which Arrangement is correct?
Another Issue: What happens if two
crossover events occur?
A B C
a b c
If double crossovers occur the original
parental linkage will be restored, causing
us to underestimate the distance between
B and C
The solution to both problems: Three
Point Testcross
ABC abc
X abc
abc
A B C a b c
1 2
a b c a b c
Gametes Produced
A B C a b c
A b c a B C
a b C A B c
a B c A b C
A B C
1 2
a b c
Nonrecombina
nt, no A B C a b c
crossover or
double
crossover in
Recombinant,
regions 1 or 2 A b c a B C
single
crossover in
region 1
Recombinant, a b C A B c
single
crossover in
region 2
Double cross,
crossover a B c A b C
events in
Linkage
Three Point Test Cross
Example
hh – Hairy – growth of bristles on the fly
thth – threaded – thread shape antenna
ryry – rosy – reddish brown eye
Cross h+h ry+ry th+th x hh thth ryry
Phenotype #
Thread 359
Rosy,threa 47
d
Hairy 4
rosy,
thread
Hairy, 98
thread
Rosy 92
Hairy, 351
rosy
Wild type 6
Hairy 43
Phenotype #
Thread 359
Rosy,thread 47
Hairy rosy, 4
thread
Hairy, thread 98
Rosy 92
Hairy, rosy 351
Wild type 6
Hairy 43
Phenotype #
Thread 359
Rosy,thread 47
Hairy rosy, 4
thread
Hairy, thread 98
Rosy 92
Hairy, rosy 351
Wild type 6
Hairy 43
Phenotype #
Thread 359
Rosy,thread 47
Hairy rosy, 4
thread
Hairy, thread 98
Rosy 92
Hairy, rosy 351
Wild type 6
Hairy 43
Phenotype #
Thread 359
Rosy,thread 47
Hairy rosy, 4
thread
Hairy, thread 98
Rosy 92
Hairy, rosy 351
Wild type 6
Hairy 43
Linkage
• Interference = 1 –
coefficient of coincidence
• Some regions of
chromosome less likely
to go through
recombination
– Chromatin structure
– Centromere
– Recombination Hot
Spots
