Linkage & Mapping in

Eukaryotes
Part I
Linkage & Chi square for linkage
Non-recombinant meiotic cells

These haploid cells contain a

combination of alleles found
in the original chromosomes

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 Recombinant meiotic cells

These are
termed parental
or non-
recombinant
cells
These haploid cells contain
a combination of alleles
NOT found in the original
chromosomes
This new combination
of alleles is a result of
genetic recombination
These are termed non-
parental or recombinant
cells

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Bateson and Punnett

A much greater proportion

of the two types found in
the parental generation

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 Linked Genes In Drosophila
Morgan’s experiment: pr vs. pr+ (purple vs. red eyes)
and vg vs vg+ (vestigial wings vs. normal wings)

The pr and vg loci are located on an autosome

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 P0: pr vg / pr vg X pr+ vg+ /pr+ vg+
F1 pr+ vg+ / pr vg Female X pr vg / pr vg Male

Expected from test cross:

pr vg

pr+ vg+ pr+ vg+ / pr vg

pr vg pr vg / pr vg

Instead in F2:
Red normal 1339
89.3% parental chromosomes
Purple vestigial 1195
Red vestigial 151
10.7% recombinant chromosomes
Purple normal 154 6
 Frequency Of Recombination

The 10.7% recombinant chromosomes (non-

parental) called frequency of recombination

Results from crossing-over of the chromosomes

in meiosis in the F1 females in flies

The recombination frequency can range from 0%

(complete linkage) to 50% (unlinked)

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 Frequency Of Recombination

Genes with recombination frequencies of < 50%

are present in the same chromosome (linked).

Two genes that undergo independent assortment,

indicated by a recombination frequency  50%,
either are on non-homologous chromosomes
(unlinked) or far apart on the same chromosome.

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Two Configuration For Heterozygous Linked Genes

=w+/+m =wm/++
trans or repulsion cis or coupling
configuration configuration
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Linked Genes Behave the Same in Cis or
Trans Configurations
Morgan used w and m in the trans configuration

He also looked at the cis configuration

Parents: pr+ vg / pr+ vg X pr vg+ /pr vg+

F1 pr+ vg / pr vg+ Female X pr vg / pr vg Male

F2
Red eyes vestigial wings 1067
Purple eyes normal wings 965 87.0%
Red eyes normal wings 157
Purple eyes vestigial wings 146 13.0%
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<50% recombination frequency indicates linkage

 Recombinant progeny
occur less frequently than
parental type of progeny

 Does not show expected

1:1:1:1 ratio

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 The Chi-Square Test for Linkage
• If we want to determine
whether 2 genes are linked:

• 25% each class = unlinked

• < 25% for 2 classes = linked

• Can use a chi-square to test

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 AN EXAMPLE
2 genes R & S - performed cross and scored progeny
 Phenotype data:
Phenotypic classes in progeny
395 RS, 382 rs, 223 rS, 247 Rs

 What are the parents of this cross?

 Recombination frequency = 470/1247 = 0.377

 RF = 0.377 between R and S genes

 Does RF = 0.377 fits the hypothesis that it is the same

as RF = 0.5? 13
 AN EXAMPLE: 7 steps to c2
1. Hypothesis:
No linkage = Our data represents a 1:1:1:1 ratio and thus
R and S are unlinked.

Why do we use no linkage as a hypothesis????

2. Prediction = 311.75 of each class (total = 1247; ¼ for

each class predicted if it is a 1:1:1:1)

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 AN EXAMPLE: 7 steps to c2
3. c2 Analysis
395 – 311.75 = 83.25 (83.25)2/311.75 = 22.23
382 – 311.75 = 70.25 (70.25)2/311.75 = 15.83
223 – 311.75 = -88.75 (-88.75)2/311.75 = 25.27
247 – 311.75 = -64.75 (-64.75)2/311.75 = 13.45
c2 = 76.75
4. We have 4 classes of data – how many degrees of
freedom?

p> 0.995 0.975 0.900 0.500 0.100 0.050 0.025 0.010 0.005 <p
3 0.072 0.216 0.584 2.366 6.251 7.815 9.348 11.345 12.838 3

5. p << 0.001
6. Reject hypothesis (much less than 0.05).
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Twin spots caused by mitotic recombination
After mitotic recombination,
daughter cells can have 2
configurations

undetectable

detectable
twin spot

a homozygous in b homozygous in
one cell the other cell
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