7 Linkage&ChiSquare

8/8/2019 7 Linkage&ChiSquare

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Linkage & Mapping in

Eukaryotes

Part I

Linkage & Chi square for linkage


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These haploid cells contain a

combination of alleles found

in the original chromosomes

Non-recombinant meiotic cells

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These are

termed parental

ornon-

recombinant

cellsThese haploid cells contain

a combination of alleles

NOT found in the original

chromosomes

This new combination

of alleles is a result ofgenetic recombination

These are termed non-

parental orrecombinant

cells

Recombinant meiotic cells

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Amuch greater proportion

of the two types found inthe parental generation

Bateson and Punnett

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Linked Genes In Drosophila

Morgans experiment:prvs.pr+

(purple vs. redeyes) and vgvs vg+ (vestigial wings vs. normalwings)

Theprand vg loci are located on an autosomeautosome

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F1pr+vg+ /prvg Female X prvg / prvgMale

P0:prvg /prvg X pr+ vg+ /pr+ vg+

prvg

pr+ vg+ pr+ vg+/ prvg

prvg / prvgprvg

Red normal 1339

Purple vestigial 1195

Red vestigial 151

Purple normal 154

Instead inInstead in F2F2::

89.3% parental chromosomes

10.7% recombinant chromosomes

Expected from test cross:

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Frequency OfRecombination

The 10.7% recombinant chromosomes (non-

parental) called frequency of recombinationfrequency of recombination

Results from crossingcrossing--overoverof the chromosomesin meiosis in the F1 femalesF1 females in flies

The recombination frequency can range from 0%(complete linkagecomplete linkage) to 50% (unlinkedunlinked)

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Frequency OfRecombination

Genes with recombination frequencies of< 50%< 50%are present in the same chromosome (linkedlinked).

Two genes that undergo independentindependentassortmentassortment, indicated by a recombinationfrequency }} 50%50%,, either are on nonnon--homologoushomologouschromosomes (unlinked) orfar apartfar apart on the samechromosome.

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=w+ / + m

transtrans orrepulsionrepulsion

configuration

=wm / + +

ciscis orcouplingcoupling

configuration

Two Configuration For Heterozygous

Linked Genes

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Morgan used wand m in the transtrans configuration

He also looked at the cis configuration

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

F2Red eyes vestigial wings 1067

Purple eyes normal wings 965

Red eyes normal wings 157

Purple eyes vestigial wings 146

87.0%

13.0%

F1pr+vg /prvg+ Female X prvg / prvgMale

Linked Genes Behave the Same in

Cis orTrans Configurations

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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:

y Phenotypic classes in progeny

y 395RS, 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


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1. Hypothesis:1. Hypothesis:

No linkageNo 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; for

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

AN EXAMPLE: 7 steps to G2

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AN EXAMPLE: 7 steps to G2

3.3. GG22 AnalysisAnalysis

395 311.75=83.25 (83.25)2/311.75= 22.23382 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

G2 = 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


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a homozygous in

one cell

b homozygous in

the other cell

undetectable

detectable

twin spot

After mitotic recombination,daughter cells can have 2

configurations

Twin spots caused by mitotic recombination

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7 Linkage&ChiSquare