Linkage

1
Linkage

• Genes linked on the same chromosome may segregate
  together.

2
Independent Assortment2 chromosomes
P AABB x aabb
A
b
a
B
Parental Gametes AB ab

F1
A
A
a
B
b
B
a
b

R
R
3
MeiosisOne Chromosome No Cross Over
2n 2
A
a
Parent Cell
B
b
A
A
a
a
B
B
b
b
Daughter Cells Have Parental Chromosomes
4
MeiosisOne Chromosome With Cross Over
2n 2
A
a
Parent Cell
B
b
A
A
a
a
B
b
B
b
Daughter Cells Have Recombinant Chromosomes
5
Meiosis Prophase I
If genes are linked, crossing over must occur for
there to be recombination.
6
Linkage?
P AABB x aabb
F1 AaBb
Test cross AaBb x aabb
1/4 AaBb
? AaBb
1/4 Aabb
? Aabb
1/4 aaBb
? aaBb
1/4 aabb
? aabb
7
Recombination Frequency

• or Linkage Ratio the percentage of recombinant
  types,
• if 50, then the genes are not linked,
• if less than 50, then linkage is observed.

8
Linkage

• Genes located on the same chromosome do not
  recombine,
• unless crossing over occurs,
• The recombination frequency gives an estimate of
  the distance between the genes.

9
Recombination Frequencies

• Genes that are adjacent have a recombination
  frequency near 0,
• Genes that are very far apart on a chromosome
  have a linkage ratio of 50,
• The relative distance between linked genes
  influences the amount of recombination observed.

10
a
b
a
c
11
Linkage RatioP GGWW x ggwwTestcross F1 GgWw
x ggww
GW
Gw
gW
gw

• recombinant
• total progeny

Linkage Ratio
12
Linkage Ratio Units

• mu (map units)
• - or -
• cm (centimorgan)

13
a
b
a
c
14
cis coupling
15
trans repulsion
16
Fly Crosses(white eyes, minature, yellow body)
Study Figs 4.2, 4.3, and 4.5

• In a white eyes x miniature cross, 900 of the
  2,441 progeny were recombinant, yielding a map
  distance of 36.9 mu,
• In a separate white eyes x yellow body cross, 11
  of 2,205 progeny were recombinant, yielding a map
  distance of 0.5 mu,
• When a miniature x yellow body cross was
  performed, 650 of 1706 flies were recombinant,
  yielding a map distance of 38 mu.

17
Simple Mapping

• white eyes x miniature 36.9 mu,
• white eyes x yellow body 0.5 mu,
• miniature x yellow body 38 mu,

18
Do We have to Learn More Mapping Techniques?

• Yes,
• three point mapping,
• Why,
• Certainty of Gene Order,
• Double crossovers.

19
Gene Order

• It is often difficult to assign the order of
  genes based on two-point crosses due to
  uncertainty derived from sampling error.
• A x B 37.8 mu,
• A x C 0.5 mu,
• B x C 37.6 mu,

20
Double Crossovers

• More than one crossover event can occur in a
  single tetrad between non-sister chromatids,
• if recombination occurs between genes A and B 30
  of the time,
• (p 0.3),
• then the probability of the event occurring twice
  is 0.3 x 0.3 0.09, or nearly 10 map units.
• If there is a double cross over, does
  recombination occur?
• how does it affect our estimation of distance
  between genes?

21
Why Me? Why Map?

• Over 4000 human diseases have a genetic
  component,
• knowing the protein produced at specific loci
  facilitates the treatment and testing,
• Facilitates both classical and molecular analysis
  of organisms.

22
Classical Mapping
Cross an organism with a trait of interest to
homozygous mutants of known mapped genes.

• Then, determine if segregation is random in the
  F2 generation,
• if not, then your gene is linked (close) to the
  known mapped gene.

What recombination frequency do you expect beteen
the target and HY2?
What recombination frequency do you expect beteen
the target and TT2?
23
Three Point Testcross

• Triple Heterozygous
• (AaBbCc )
• x
• Triple Homozygous Recessive
• (aabbcc)

24
Three Point Mapping Requirements

• The genotype of the organism producing the
  gametes must be heterozygous at all three loci,
• You have to be able to deduce the genotype of the
  gamete by looking at the phenotype of the
  offspring,
• You must look at enough offspring so that all
  crossover classes are represented.

25
w g d

• Representing linked genes...
• W G D
• w g d
• x
• w g d
• w g d

P
WwGgDd
Testcross
wwggdd
26
w g d

• Representing linked genes...
• w g d
• x
• w g d
• w g d

P
WwGgDd
Testcross
wwggdd
27
Phenotypic Classes
W-G-D-
W-G-dd
W-
W-gg-D
W-gg-dd
wwG-D-
wwG-dd
ww
wwggD-
wwggdd
28
Crossovers

W-G-D-
0
179
wwggdd
173
0
W-G-dd
1
46

• W G D
• w g d

wwggD-
1
52
wwG-D-
22
1
W-gg-dd
22
1
W-gg-D
2
2
wwG-dd
2
4
29

W-G-D-
179
Parentals
wwggdd
173
W-G-dd
46
Recombinants 1 crossover, Region I
I
II

• W G D
• w g d

wwggD-
52
wwG-D-
22
Recombinants 1 crossover, Region II
W-gg-dd
22
W-gg-D
2
Recombinants, double crossover
wwG-dd
4
30

I
W-G-D-
179

• W G D
• w g d

Parentals
wwggdd
173
W-G-dd
46
Recombinants 1 crossover, Region I
wwggD-
52

Region I
wwG-D-
22
Recombinants 1 crossover, Region II
W-gg-dd
22
46 52 2 4 500
x 100
W-gg-D
2
Recombinants, double crossover
wwG-dd
4
20.8 mu
Total 500
31

II
20.8 mu
W-G-D-
179

• W G D
• w g d

Parentals
wwggdd
173
W-G-dd
46
Recombinants 1 crossover, Region I
wwggD-
52

Region II
wwG-D-
22
Recombinants 1 crossover, Region II
W-gg-dd
22
22 22 2 4 500
x 100
W-gg-D
2
Recombinants, double crossover
wwG-dd
4
10.0 mu
Total 500
32
10.0 mu
20.8 mu

• W G D
• w g d

0.1 x 0.208 0.0208
NO GOOD!
6/500 0.012
33
Interference

• the affect a crossing over event has on a second
  crossing over event in an adjacent region of the
  chromatid,
• (positive) interference decreases the
  probability of a second crossing over,
• most common in eukaryotes,
• negative interference increases the probability
  of a second crossing over.

34
Gene Order in Three Point Crosses

• Find either double cross-over phenotype, based on
  the recombination frequencies,
• Two parental alleles, and one cross over allele
  will be present,
• The cross over allele fits in the middle...

35

2001
A-B-C-
1786
aabbcc
46
A-B-cc
Which one is the odd one?
52
aabbC-
990
aaB-cc
887
A-bb-C-
600
A-bb cc
589
aaB-C-
36

Region I
A-B-C-
2001
aabbcc
1786
A-B-cc
46
aabbC-
52
aaB-cc
990
I
A-bb-C-
887

• A C B
• a c b

A-bb cc
600
aaB-C-
589
37

Region II
A-B-C-
2001
aabbcc
1786
A-B-cc
46
aabbC-
52
aaB-cc
990
28.4 mu
II
A-bb-C-
887

• A C B
• a c b

A-bb cc
600
aaB-C-
589
38
Today

• Coefficient of Confidence,
• Gene mapping in humans,
• Problems, problems, problems,
• Be sure to at least try them before Friday.