Crossing over produces new allelic combinations

Meiotic crossovers
- physical exchange of DNA between non-sister chromatids during meiosis I
- small number of crossover events per chromosome per meiosis
- occur with random distribution along the chromosome
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T. Evans S’13
 Forward genetic screen in Drosophila: Identifying recessive mutations

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 Inversion heterozygote during meiosis:
Meiotic recombination events are NOT heritable
diploid
paracentric inversion

1 2 3 4

1 3 2 4

1 2 3 4

1 2 3 1

4 2 3 4

1 3 2 4
3
gametes
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 We can use crossover frequency to measure
distance between genes

Logic behind the “3-point cross”

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 Three Drosophila mutations on the X chromosome

crossveinless cut vermillion

(cv) (ct) (v)

wild type wild type

© Carolina Biological/Visuals Unlimited/Corbis

cv

v 5
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 Linkage mapping in Drosophila:
testcross of triple heterozygote

cv ct v + + +
cv ct v X Y

crossing-over cv ct v cv ct v
will occur
+ + + X Y testcross
during meiosis

how frequently does crossing-over happen

between each pair of genes?

Note: there is NO recombination 6

221 S16 during meiosis in Drosophila males
 Linkage mapping in Drosophila:
sorting progeny by class

cv ct v cv ct v
+ + + X Y
testcross

class genotype number

1 cv ct v 580 Parental chromosomes
2 + + + 592
Recombinant means a different
3 cv + + 45 combination of alleles from the
testcross progeny 4 + ct v 40 parental chromosomes

5 cv ct + 89 recombinant
6 + + v 94 chromosomes
7 cv + v 3* double
* recombinants
8 + ct + 5
1448
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 Comparing parental and double recombinant classes
reveals gene order

cv ct v cv + v Double
Parental middle gene
is swapped recombinant
+ + + + ct +

class genotype number

1 cv ct v 580 Parental chromosomes
2 + + + 592

testcross progeny

* double
* recombinants
7 cv + v 3
8 + ct + 5
1448 8
T. Evans S’13
 Different gene orders predict
different double recombinant genotypes

Double
Gene order
recombinant
cv + v
cv ct v
+ ct +
ct + v
ct cv v
+ cv +
cv + ct
cv v ct
+ v +

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 What is the map distance between cv and ct?

testcross progeny
Parental

class genotype number

cv ct -
1 cv ct v 580 + + -
2 + + + 592
3 cv + + 45
4 + ct v 40 Recombinant
5 cv ct + 89 cv + -
6 + + v 94
+ ct -
7 cv + v 3
8 + ct + 5
1448

45+40+3+5
cv & ct X 100 = 6.4 m.u.
1448
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 Recombination mapping

Recombination # recombinant chromosomes

= RF = X 100
Frequency # total chromosomes

map unit (m.u.)

The “distance” between two linked genes where
1% of the products of meiosis are recombinant

a.k.a. - centimorgan (cM); crossover unit

Note: there is NO recombination

during meiosis in Drosophila11
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 What is the map distance between ct and v?

testcross progeny
Parental

class genotype number

- ct v
1 cv ct v 580 - + +
2 + + + 592
3 cv + + 45
4 + ct v 40 Recombinant
5 cv ct + 89 - ct +
6 + + v 94
- + v
7 cv + v 3
8 + ct + 5
1448

89+94+3+5
ct & v X 100 = 13.2 m.u.
1448
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 What is the map distance between cv and v?
Parental
testcross progeny
cv ct v
Parental
cv - v + + +
class genotype number
two
1 cv ct v 580 + - + crossover
2 + + + 592 events!
3 cv + + 45 Double
4 + ct v 40 Recombinant Recombinant
5 cv ct + 89 cv - + cv + v
6 + + v 94
+ - v + ct +
7 cv + v 3
8 + ct + 5
40+45+ 89 + 94
1448 X 100 = 18.5 m.u.
1448

cv & v 40+45+ 89 + 94 + 2(3+5)

X 100 = 19.6 m.u.
1448 13
T. Evans S’13
 Double crossovers count twice

Recombination # recombination events

= RF = X 100
Frequency # total chromosomes

40+45+89+94+2(3+5)
X 100 = 19.6 m.u.
1448

# events/chromosome # chromosomes with 2 recombination events

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What are the map distances between these genes?

6.4 cM 13.2 cM

cv ct v

19.6 cM

45+40+3+5
cv & ct X 100 = 6.4 m.u.
1448

89+94+3+5
ct & v X 100 = 13.2 m.u.
1448

40+45+
40+45+89
89++94
94 + 2(3+5)
cv & v X 100 = 18.5
X 100
m.u. = 19.6 m.u.
1448 1448

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T. Evans S’13
 The way you write the genotypes does not affect the data
These data sets are identical

class genotype number class genotype number

1 cv ct v 580 1 ct cv v 580
2 + + + 592 2 + + + 592
3 cv + + 45 3 + cv + 45
4 + ct v 40 4 ct + v 40
5 cv ct + 89 5 ct cv + 89
6 + + v 94 6 + + v 94
7 cv + v 3 7 + cv v 3
8 + ct + 5 8 ct + + 5
1448 1448

cv ct v
6.4 cM 13.2 cM

19.6 cM 16
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 Different parental chromosome allele configurations
will not alter the linkage map

These allele configurations will yield identical maps

Parental
chromosomes
cv ct v
cv ct v 6.4 cM 13.2 cM
+ + + 19.6 cM
+ cv v
ct + +
Recombinant does not mean a combination of wild type
cv + ct and mutant alleles
+ cv +
Recombinant means a different combination of alleles
cv ct + from the parental chromosomes
+ + v
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 Drosophila genetic map

Recombination distances
and
physical distances
are additive

66 cM

http://genetics.biol.ttu.edu/genetics/figures/genmap.html
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107 cM 106.2 cM
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 Genes on different chromosomes appear to map 50 cM apart

+;+ X a;b recessive alleles

visible phenotype
+ + a b

a;b X a;b
testcross
+ + a b

a;b a;+ +;b +;+

a;b a;+ +;b +;+
a;b genotypes

a b a b a b a b
1 1 1 1
50% “recombinant” chromosomes

Two genes located > 50 cM apart appear unlinked 19

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 Recombination distance approximates
physical distance in Drosophila

cv ct v
6.4 cM 13.2 cM

cv ct v
1.95 Mb 3.28 Mb

cv ct v
3.28 cM/Mb 4.02 cM/Mb

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 Recombination frequencies vary among organisms
(and chromosomes, and regions within chromosomes...)

genome
chromosome total cM cM/Mbp
Mbp

human #1 (male) 211 247 0.85

#1 (female) 381 247 1.54

all ~3500 ~3100* 1.13

(avg. male & female)

Drosophila all ~280 ~120 2.33

*Homo sapiens (human) genome view

Build 37.1 statistics (August
21 2009)
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
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