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# Lecture 4: When 2 or more genes are on the

## same chromosomeor lets relax the assumption of

independence, central to prediction in Classical
Mendelian Models.
!

In genetics you often use both multiplicative and additive rules in one
problem!

!
What is the probability of having two girls and a
boy ?!
(GGB or GBG or BGG)!
!
a) 1/2!
b) 1/4!
c) 1/8!
d) 1/16!
e) 3/8!
!

## The chromosomal theory of inheritance: first proposed by W. Sutton, T. Boveri

1902, based on correlation between chromosome division into gametes and the
inheritance of sex. For example, W. Sutton wrote that the association of paternal
and maternal chromosomes (of the grasshopper Brachystoma magna) in pairs and
their subsequent separation during the reducing division (of meiosis) may explain
Mendelian segregation and that maternal and paternal pairs are indifferent to
their position relative to others when they assort and segregate in meiosis.

## T.H. Morgan and his student C. Bridges experiments on Drosophila showed

phenotype ratios are informative even when they deviate from Mendel s classic
ratio because they correlate with chromosome segregation.
This work strongly suggested, that units of inheritance of different
phenotypic characters -genes- are in chromosomes

## If n is the basic number of chromosomes.

In humans
2n = 46
n = 23
There are 22 autosome pairs
and
a (1) sex chromosome pair

centromere

## Prophase -Metaphase chromosome

Each diploid human
of DNA in nuclei with
an average diameter of
6 micrometers (10-6 m)

Interphase chromosomes

## To represent the cellular behavior of chromosomes at the cytological

scale in meiosis we use the following model of chromosome structure, a
double stranded DNA molecule with associated histone proteins.!
The centromere is part of a DNA molecule, it is hundreds of kilobases
long, with no functional genes. Count chromosomes by counting
centromeres.!

## Key stages of meiosis and mitosis

Figure 2-15!

Sister Chromatids!

Homologous
chromosomes
Sister chromatids

MEIOSIS
Alleles A and a
at the A locus.
Alleles B and b
at the B locus.
Locus means
place;
Allele means
form or state
Leptotene and Pachytene

## Synaptonemal complexes at meiosis

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(3)Pachytene

(3)Pachytene
(synaptonemal complex,

crossover, recombination).
(synaptonemal
complex,
Recombination
occurs
crossover,
recombination).
where maternal &
Recombination
(1)
paternal chromosomes
occurs
whereand
maternal &
arms break,
paternal
chromosomes
recombine
with their
homologue.!
arms
break, and recombine
with their homologue.
There are genetic
repair mechanisms
Tassociated
here are genetic
with therepair
pairing of chromosomes
mechanisms
associated
in Prophase
1. ! of
with
the pairing

chromosomes in Prophase
1.

## Recombinants (1) are produced by crossovers that

happen in prophase 1 of meiosis!

Synaptonemal complex

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## Crossover, recombination and

repair has finished
in (4)Diplotene, the
chromosomes are beginning to
repel and the chiasmata (points
of recombination) are
beginning to migrate to the
telomeres.
In (5) Diakinesis, chiasmata
have migrated to the
chromosome ends (telomeres)

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## Recombination 2: metaphase: paired homologues

orient randomly on the metaphase plate Mendel 2

13

Understand This !

Genes for
flower, leaf and
stem shape and
color
There is more than
one per
chromosome, or
potentially nonindependent

Linked genes: genes are linked when they are on the same chromosome.
Nomenclature: AB/ab ,

AB//ab or,

AB or
ab

++/ ab,

or

AB

ab

ab

## A/a . C/c (unknown),

chiasma(ta), parentals, recombinants, recombinant frequency, map unit,
centimorgan.

and F1 testcross

## eg. Ab/Ab X aB/aB

AB/ab X ab/ab

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Recombination 1
Gene linkage can be: very close, close or distant

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## Genes on the same chromosome are linked.

(1) Closely linked alleles assort into the same gametes and are more
frequently inherited together than you would expect than if they
were on different chromosomes (not linked).
A B
A
a
a

B
b

b
(2) But, if they are far enough apart on a chromosome, they may
act as if they assort independently

## (1a) Very closely linked alleles usually

assort into the same gametes or, they are
almost always co-inherited.

-2 synapsed replicated chromosomes
AB
AB
ab

AB
AB

ab

ab

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ab

## (1) Dihybrid Parentals (AA BB & aa bb) cross

(2) F1 testcross, showing parental, homozygous test
gametes and the expected F1 offspring genotypes for
(b) a small - sized sample.

tester

ab

AB

ab

AB / ab

ab / ab

ratios ?
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## (2 ) there is a cross-over between the locations (loci) of 2

genes on homologous chromatids in prophase 1 of meiosis.
A

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## Gene linkage Gene recombination in Pachytene, a sub-stage in

prophase 1 of meiosis.
Linked alleles are inherited together, except when there is a
cross-over between linked loci on homologous chromatids
A

chiasma

## There may be a cross-over, but it cannot be detected

unless there are different alleles on each dyad (a pair
of sister chromatids joined at the centromere).
22

23
Gene linkage and recombination in Pachytene
(1) Linked alleles are inherited together except when there is a
cross-over between linked loci on homologous chromatids.
A B

## Crossovers involve the breaking of at least one

chromatid on each dyad and the rejoining of maternal
with paternal fragments.

Linked alleles are inherited together except when there
is a cross-over between homologous chromatids or
closely - linked genes sometimes recombine.

AB

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aB
Parentals

Recombinant
gametes
Ab
ab

In GENERAL
(1)There is always at least one chiasma(ta)-(a crossover point) per
chromosome, per meiosis, regardless of chromosome length.
(2)The greater the distance between two gene locations (loci) on a
chromosome the greater the chance of a cross over between them.
(3) The position of the crossover between two loci, is at first
approximation random.

A B

c
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With CLOSE LINKAGE Parental types will be more frequent(in excess of 50 %) than recombinant types (less than 50%).
AB x ab
P AB
ab

F1

AB
ab

Test cross

AB
ab

or AB

ab
ab

or ab

aB
AB x ab
ab
a b
ab
Recombinant
Ab
ab

or aB

<1/4

or Ab

<1/4

Parental

>1/4
>1/4

## Map distance between genes

Complete linkage between loci (absence of a chiasma in
meiosis) decreases with increasing distance between
markers (loci) on a chromosome, or, as the distance
increases between 2 loci on a chromosome, the probability
of a crossover and recombinant gametes increases.
Alfred Sturtevant first suggested using % recombinants as a
linear measure of chromosomal map distance
One map unit = 1% recombinants
1 map unit = 1 centimorgan (cM)
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## Crossover between 2 markers keeping it organized

Testing for linkage between genes for fruit shape (beaked bk)
and internal division number (1 locule Lc

or many lc)

them.

Bk

bk

lc

Lc
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## Measuring linkage between genes for beaked fruit and many

locules in tomatoes.

P:

Bk
Bk /Bk . Lc /Lc x bk /bk . lc/ lc

bk

lc

Lc

Bk bk
Bk bk
bk bk
bk bk

Lclc
lc lc
Lc lc
lc lc

170
26
30
168
400

## The ratio of the 4 classes of

offspring is clearly not
1:1:1:1 suggesting
The two genes are closely
chromosome.

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## Measuring linkage between genes for beaked fruit and many

locules in tomatoes.
Bk
P:

bk

lc

Lc

Bk Lc / Bk Lc x bk lc / bk lc
F1

Bk Lc x bk lc Test cross:
bk lc
bk lc

Bk bk Lc lc 170
bk bk lc lc 168
Bk bk lc lc 26
bk bk Lc lc
30
400

(26 + 30 ) / 400

56 / 400

14%

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SUMMARY

## Dihybrid testcross, showing parental,

recombinant, homozygous test gametes and the
expected genotypes in the F2.
F1: AB/ab

ab

AB
AB/ab

Ab
Ab/ab

aB

ab

aB/ab

ab/ab

## If a & b loci are so far apart that there is always a

crossover between them, then the ratios will be the
same as independent assortment of A & B loci.
If they are close, then recombinants < parentals
If they are very close then all you see is parentals

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## Double crossover between two markers (gene loci), in this

case there will not appear to be a crossover between v and cv.
So all you will see are the genotypes of the F1
and the testers- no recombinants.

32

## Double crossover between v and cv will appear the same

as no crossover, but a third, intermediate marker has
recombined. Use the third intermediate marker to
estimate double frequency crossover.

## The outside markers are still the same as the

parental, but the inside marker changes
chromosome association (switches).
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## Three markers or loci on the same arm of a

chromosome allows you to:
(1) detecting double crossovers between the
outside markers (loci)
(2)estimate the distance between loci
(3) determine the order of loci

34

The three point cross is used, if they are linked, to map the
distance between three genes and determine their order .
Three genes controlling locule form, stem color and stem
hairiness in tomato are linked .
F faciated,
ff - two fascia
A purple stem,
aa green stem
Hl hairless stems hl hl hairy stems
Parents
F1 Test Cross:

F A Hl / F A Hl x f a hl / f a hl
F A Hl // f a hl x f a hl // f a hl
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## The three point cross

P:

ff - two fascia
aa green stem
hl hl hairy stems

F A Hl//F A Hl x f a hl // f a hl

Test X:

36

F fasciated
A purple stem
Hl hairless stems

F A Hl // f a hl x f a hl // f a hl
F A Hl
Parental types f a hl
F a hl
f A Hl
Single recombinants
F A hl
f a Hl
F a Hl
Double crossover gametes
f A hl

302
308
101
109
82
77
10
11
1000

## F fasciated (many locules) ff - two locules

A purple stem
X
aa green stem
Hl hairless stems
hl hl hairy stems

P: F A Hl//F A Hl x f a hl // f a hl
Test X: F A Hl // f a hl x f a hl // f a hl

## F-A- find recombinants

Parental types
F A recombinants are unlike
parental configuration.
% recombination =
101 + 109 + 10 + 11 / 1000 =
231/ 1000 = 23.1 %
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F A Hl
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

302
308
101
109
82
77
10
11
1000

## The three point cross

F many locules
A purple stem
Hl hairless stems

## Work 2 loci at a time

A, Hl

Parental types
F A recombinants

23.1 %

A Hl recombinants
82 + 77 + 10 + 11 / 1000 =
180 / 1000 = 18%

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ff - two locules
aa green stem
hl hl hairy stems

F A Hl
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

302
308
101
109
82
77
10
11
1000

F many locules
A purple stem
Hl hairless stems

## The three point cross

ff - two locules
aa green stem
hl hl hairy stems

P: F A Hl / F A Hl X f a hl /f a hl
Test X: F A Hl / f a hl X f a hl /f a hl

## Work 2 loci at a time

F-Hl

Parental types
F Hl , % recombinants =
101 + 109 + 82 + 77 / 1000 =369 / 1000
= 36.9%

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F A Hl
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

302
308
101
109
82
77
10
11
1000

## The three point cross

F many locules
A purple stem
Hl hairless stems

F A recombinants

23.1 %

A Hl recombinants

18%

F Hl recombinants

36.9%

## ? Outside loci (markers)

F A Hl
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

ff - two locules
aa green stem
hl hl hairy stems

302
308
101
109
82
77
10
11
1000

40

F many locules
A purple stem
Hl hairless stems

## The three point cross

Hl

F A recombinants

23.1 %

A Hl recombinants

18%

F Hl recombinants

36.9%

F A Hl
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

ff - two locules
aa green stem
hl hl hairy stems

302
308
101
109
82
77
10
11
1000

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## The three point cross

F A Hl 302
f a hl
308
F a hl
101
f A Hl
109
F A hl
82
f a Hl
77
F a Hl
10
2.1%
f A hl
11
1000
F

F many locules
A purple stem
Hl hairless stems

ff - two locules
aa green stem
hl hl hairy stems

F A recombinants

23.1 %

A Hl recombinants

18%

F Hl recombinants

36.9%

## These classes are double cross-overs

for F and Hl and must be counted twice.

A
23.1

Hl
18

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## (1)Why calculate all 3 distances to get the order ?

(2) For the order, identify the double recombinant class,
look at which locus has flipped, relative to the parental
order - this one is in the middle.
F A Hl 302
f a hl
F a hl
f A Hl
F A hl
f a Hl
F a Hl
f A hl

308
101
109
82
77
10
11

F
f

A
a

Hl
hl

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F
f

A
a

Hl
hl

## There are two ways to calculate the F to Hl distance. The answer

should be identical.
1. Add the distances between the outside and middle markers or
loci: F to A distance, and A to Hl distance.
2. Identify the middle locus or marker (A), estimate the distance
between the 2 outside markers (F - Hl recombinants), and add 2
times the number of double recombinants - because double
recombinants have single crossovers in each outside region.
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F
f

A
a

Hl

Parental F A Hl!
45
recombinant!

hl

recombinant!
Parental f a hl!

Mapping and recombination - the 4 step method when you do not have a data table
(1) Pair gametic types by complement & frequency
(2) ID parental chromosomes: F A Hl & f a hl (a) # highest ?
(b) complementary pairs ? (c) # similar ?
(3) Organize a table with the 2 or 3 mutant symbol heading the column tops,
corresponding parentals at the top, below each heading. Remember, you are
always organizing & comparing recombinants with parentals.
(4) If the problem involves 3 markers (loci), identify the double recombinant
chromosomes
F a Hl (a) # lowest ?
(c) complementary pairs ? f A Hl (c) # similar ?
Then you can ID the middle marker (pair that has flipped to parentals)
Then you have the gene order. Put the double -X -over pair at the bottom
(5) Table the single recombinant classes (middle):
(a) # similar ?
Estimate the required distances
(b) complementary pairs ?
2!

## Interference between chiasma may decrease the

observed crossover frequency and the apparent
genetic distance.
1. The coefficient of coincidence is the observed frequency of
double recombinants divided by (standardized by) the expected
number of double recombinants.
2. The expected number of recombinants is the product of the
expectation of a crossover in each region (outside to middle).
3. Interference = 1- coefficient of coincidence
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## In the lab, the numbers will not be pre - paired - Look at 45

magnitudes, check by locus complements (+ + + / cn c px)
P
R1
R2
D
R2
D
P
R1

cn c px
cn c +
cn + +
cn + px
+ c px
+c+
+++
+ + px

296
63
119
10
86
15
329
82
1000

## C- curved wings, px - extra wing veins, cn - cinnabar eyes

1. Calculate the individual distances make the map.
OR
Compare double cross-overs with parental lines, the one gene
that is different is in the middle (order) then estimate the other distances.

## Recombination Mapping in General!

As map distance increases over 10 map units, multiple crossovers
cause recombination frequency to underestimate crossover
frequency or the actual recombination map distance. For example,
when the recombination frequency is 30% the actual map distance is
50 mu in Drosophila. !
!
Mapping functions help (p=1/2 (1-e-2d) d=crossover frequency!
!