gen linkage mapping

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Linkage Mapping and Crossing-over

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Independent assortment vs linkage.

Independent assortment occurs when the genes for two different traits

or genetic markers are located on different chromosomes. Mendel was

lucky enough to have chosen such a configuration.

Assuming pea plants have approximately, !,!!! genes and seven

chromosomes, then each chromosome might carry around ,"!!genes. #hese genes are not expected to assort independently during

meiosis. In other words, there is a roughly "$ chance of the genes

%eing linked.

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Comparison of independent and linked genetic

markers.

&A

A

'

'

a

a

%

%( )

'

a %

A

Independent

#estcross*

a

a

%

%

'

a %

A

&a

a

%

%

a

A %

%a

a

'

%

+!$ parental

phenotypes

+!$ recom%inant

phenotypes

'

a %

A

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&A

A

a

a c

)

Linked genetic markers

#estcross*

cC

C

A C

a c

A C

a c

a

a c

c

&

A C

a c

A

a c

c

a c

Ca

reater than +!$

of progeny with parental

phenotype

less than +!$

of progeny with recom%inant

(henotype resulting from crossing over.

a

a c

c

#rans, or repulsion

Cis-configuration

or coupling

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&s/ s

)

#estcross*

In female flies

%%/

&

s/0 long wings

%/ 0gray %odies

s 0 short wings

% 0%lack %odies

s/ %/ s %

s/ %/

%

s/ %/

s/ %/

s

%s

%s

%s

%s

s/ %

%s %s

%s

%s

"$

"$

1$

1$

Long wing, gray %odies

Long wing, gray %odies short wing, %lack %odies

Long wing, gray %odies

short wing, %lack %odies

short wing, gray %odies

Long wing, %lack %odies

(arental

com%inations

2ecom%inant

com%inations

)ruit flies

%/s

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&s/ s

)

% %/

&

s/0 long wings

%/ 0gray %odies

s 0 short wings

% 0%lack %odies

s/ %/s%

s/ %

s/ %/

s

%s

%s

%s

%s

%s

1$

1$

Long wing, gray %odies

Long wing, gray %odies short wing, %lack %odies

Long wing, gray %odies

short wing, %lack %odies

(arental

com%inations

2ecom%inant

com%inations

%/

s/ %

s %/

%s

%s

s/ %

"$

"$ short wing, gray %odies

Long wing, %lack %odies

s %/

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A C

a c

a

a c

c

A

A

C

C

All even num%er of exchanges %etween two segregating loci will yield

parental com%inations and thus go undetected.

In general the maximum fre9uency of recom%ination for two genes located

8n the same chromosome is +!$.

Two stranded double crossover

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A B

#wo-stranded dou%le crossover

#hree stranded dou%le crossover

)our-stranded dou%le crossover

:ou%le crossovers occur in the following ways

All

parental

p

p

r

r

p

p

r

r

A '

a %a %A %

All

2ecom

%inant

a '

A %

5

; p

; rec

; p

; rec

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If one looks at all the different possibilities of double crossovers one

arrives

at a similar conclusion, again at most 50 will be recombinant. !see

ne"t slide#.

6ven if crossovers did not occur %y chance %ut all the time, +!$ would still

%e the limit. 7imilarly, if one went through all the possi%ilities of triple

crossovers, one would again arrive at a theoretical maximum of +!$.etc.

8nly if nature had some kind of %ias toward four-stranded dou%le

crossovers, would the ratio come out to more than +!$

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C$%C&'(I$%) If over 50 of the gametes produced b* a + cross contain

parentalcombinations of genetic markers, this is an indication that genes are

linked. 3hen a large num%er of genes is analy5 average

num%er of all cross-overs per interval in a meiotic cell.

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If one assumes proportionality %etween the distance %etween two loci and the

average num%er of crossovers per chromatid then*

%umber of crossovers / !distance#,

3here ? is a proportionality constant. In that case one would also predict that the

map distances would also %e additive.

A CB

&$

recom

%ination

@$ recom%ination

&/@$ recom%ination

3hen distances are large B! - 5! map units the results are less then the

additivity would predict.

In that case dou%le or even num%ered crossovers occur almost as fre9uently

as single or uneven num%ered crossover. 6ven num%ered crossovers are not

phenotypically detected as recom%inant events, as the second event

apparently cancels the first.

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If p is the fre9uency for

one crossover in interval I

and 9 the fre9uency

)or interval two, the

fre9uency for a dou%le

crossover is p9 >" or

; x. ;,

7ince p or 9 are ;

each.

#he a%ility to identify theparental and the two

reciprocal dou%le

crossover

classes also allows one to

determine the order of theD genetic markers.

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Three-factor crosses

.If one uses three markersto map a chromosome it %ecomes possi%le todetect and uantif* double crossovers, and it %ecomes possible to orderthe markers relative to each other. In diploid organisms three factor

crosses are used in analogous fashion to two-factor crosses. #hat is,homo

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In a three-factor cross for three linked genes* how are the gametes formed4

1 2 3

x y a%c +!

A'c>a%c 5a%C>a%c D

A%C>a%c F+

a'c>a%c F!

#otal !!!

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:etermining the order of three linked markers.

#he dou%le crossover results in an interchange of the center marker. #hus,

#he recom%inant class with the lowest fre9uency indicates the identity of

central marker.

enotype Eum%er of progeny

A'C>a%c DF!

a%c>a%c DG+

A%c>a%c "+

a'C>a%c +!

A'c>a%c 5a%C>a%c D

A%C>a%c F+

a'c>a%c F!

(arental configuration all cis

7ingle crossover in interval I

7ingle crossover in interval II

:ou%le crossover* one in interval I

and one in interval II

#otal !!!

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7ince the recom%ination class A'c, a%C occurs with the lowest fre9uency

it must %e marker C>c that is located in the center, since marker C is

recom%inant in that class. #hat is the order of the markers must %e AC'.

#he linkage distances can now %e calculated as follows*

:istance %etween A and C* add fre9uencies of single and dou%le crossover

in

interval AC* A%c, a'C, is "+/+!/ 5/D>!!! 0 !. or !$.

Linkage distance in interval II, i.e. 'C* F+/F!/5/D>!!! 0 !.+ or +$.

#he dou%le crossovers are included in the calculation %ecause one of the 5

crossovers occurred in the interval.

! map units + map units

A,a C,c ',%

I t f

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Interference*

In a three factor testcross the o%served fre9uency of a

dou%le crossover was + out of a thousand or !.!!+. If the two crossovers

in a dou%le crossover had %een completely independent, the expected

fre9uency would have %een !.+ & !.0 !.!+. #he o%servation thatactually fewer dou%le crossovers occur than expected was called chromosome

interference or chiasma interference. #his is o%served in most dou%le crossovers. #his

is not to %e confused with chromatid interference.

#he degree of interference is measured %y the coefficient of coincidence*

Coefficient of coincidence 0 o%served dou%le crossover fre9uency

expected dou%le crossover fre9uency

Coefficient of interference 0 - coefficient of coincidence.

6xample one gives a coefficient of coincidence of !.!!+>!.!+0.DDD

Coeff. of interference 0 H !.DDD 0 !.F

A positive coefficient of interference %etween ! and indicates that the first crossover

interferes with a second.

In %acteria the coefficient of coincidence can %e greater than one negative interference

indicating that the occurrence of one crossover increases thero%a%ilit of a second.

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4ore reasons wh* recombination freuencies are not linearand additive over all

distances* ecombi