Linkage

and
Crossing over
Dhirendra khare
Plant Breeding and Genetics
JNKVV, Jabalpur (India)
 We consider two traits to test their inheritance
Individually inheritance of each trait follows 3:1 ratio in F 2
Therefore considering both the traits simultaneously should
follow 9:3:3:1 ratio
In F2
four classes are formed as formed in case of simple dihybird
but
the data did not follow 9:3:3:1 ratio
it means
it is not the case of gene interaction
(Generally In gene interaction four classes are not formed)
To follow 9:3:3:1 ratio both the genes under study
should be located on two different chromosomes
A

Location of
A a first gene on chromosome seventh
B b Second gene on chromosome third

When genes are located on two different

chromosomes they follow
B
law of segregation
and
Independent assortment
As dihybrid case
i.e.,
study of both the genes simultaneously 7
3
Chromosome 7 Chromosome 3 genes under study are
located on two different
chromosomes
Chromosome 7 Chromosome 3

Gamete formation
Chromosome 7 Chromosome 3

Gamete formation
Law of segregation
Chromosome 7 Chromosome 3

Gamete formation
Law of segregation

Law of independent assortment

If the genes are located on the same chromosome 3

A a A a

B b

B b
 Genes are located on the same chromosome 3
Considering individual gene separately
Gamete formation

A a
A a B b

A a B b

Allele of individual gene segregates

as per law of segregation

B b
 Genes are located on the same chromosome 3
Considering individual gene separately
F2 for first gene

A a
A a

Gamete formation

Law of segregation

A a

A a
A AA Aa B b

a Aa aa

3:1 Law of independent assortment

 Genes are located on the same chromosome
Considering individual gene separately 3
F2 for second gene

A a
A a B b

Gamete formation

Law of segregation

A a B b

B b
A a
A AA Aa B BB Bb B b

a Aa aa b Bb bb

3:1 Law of independent assortment 3:1

 It shows that when genes are located on different
chromosomes or in the same chromosome they follow
Law of Segregation
&
Independent assortment
When considered individually
 Consider both the genes present on the same
chromosome simultaneously

A a
A a
B b

Gamete formation

A a

B b

Allele of individual gene segregates

but
B b
when we observed both the genes simultaneously then they
do not segregate from each other
because
both are located on the same chromosome
 Gamete formation It means it will follow law of
segregation A a
A a but not
law of independent assortment
B b therefore
new combinations in next
generation will not formed

It shows that A will always

go with B and a with b

Following combination will

not be formed
This type of situation when two
alleles of different genes inherited B b
A a with each other due to their
location on the same
chromosome is known as
b B LINKAGE
 In this case
allele A of first gene and allele B
of second gene are considered
linked A a
Similarly
allele a of first gene and allele b
of second gene are considered
linked

Linkage checks the Independent

assortment
therefore
A is not able to combine with b
and
a not with B B b

Hence in dihybrid study it will not

provide 9:3:3:1 ratio
 Sometimes even in the presence of linkage
four classes are formed
that do not follow simple 9:3:3:1 ratio
Why A a
The new combination i.e., not possible because of linkage
appear in F2
Again we consider the same case

A a

B b
B b

These two are the homologous chromosomes that

pair at stage of prophase during meiosis division
 A a

A a

B b

B b
Homologous chromosomes
pair at ZYGOTENE stage of prophase
 After pairing they form their copy

A a

A A a a

B B b b

B b

Four copies of each gene and two copies of each

allele are formed during Pachytene stage
 A a

Sister chormatid Sister chormatid

A A a a

B B b b

B b
 After pairing they form their copy

Non sister chormatid

A A a a

B B b b

Now four copies of each gene and two copies of

each allele are formed during Pachytene stage
During pairing Non sister chromatids cross over
each other
It means breakage and reunion of only two of the
four strand at any given point on the chromosome

A A a a

B B b b
During pairing Non sister chromatids cross over
each other
It means breakage and reunion of only two of the
four strand at any given point on the chromosome

A A a a

B B b b

No cross over take place between sister chromatids

 A A a a

B B b b

A A a a

B B b b

3
A A a a

B B b b

A a A a

B B b b

New combination is due to crossing over

it is not due to law of independent assortment 3
The exchange of genetic martial between sister chromatids
of homologues chromosomes is known as
CROSSING OVER

It is of two types
Two pint test cross
Three point test cross
 Two point test cross
When two genes on the same chromosomes are considered for
crossing over
a b
+ +

a b
a b
+ +

+ +

a b
+ +
a
+

+ b
 Three point test cross
When three genes on the same chromosomes are considered for
crossing over

a b c
+ + +
 Three point test cross
When three genes on the same chromosomes are considered for
crossing over

a b c
+ + +

a b c

a b c

+ + +

+ + +

Four strand stage

 Parental type
a b c

a b c

+ + +

+ + +
Parental type

Chromatid first and four are exactly parental type

No crossing over takes place in these chromatids
therefore producing parental type
 a b c

a b c

+ + +

+ + +

a b c
Non sister
+ + + chromatids

Crossing over may take place between non sister chromatids only
and they may produce other than parental type combination
In a three point test cross two types of crossing over may take place

Single Cross Over

Double Cross Over

 Single Cross Over

Crossing over between any two genes in a chromosome

Non sister chromatids

a b c a c
b
+ + + + + +

a b c a + +

+ + + + b c

SCO I
a b c a b +

+ + + + + c

SCO II
 Double Cross Over

Crossing over among three genes in a chromosome

Non sister chromatids

a b c a c
b
+ + + + + +

+
a b c a c
+ + + + b +
 In a three point test cross following combinations may appear

a b c

+ + +
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type

a b c

+ + +
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type

a a + +
b c

+ + b c
+ +
SCO I
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type

a a + +
b c

+ + b c
+ +
SCO I

a b +

+ + c

SCO II
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type

a a + +
b c

+ + b c
+ +
SCO I

a b +

+ + c

SCO II

+
a c

+ b +
DCO II
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type
Ranking based
on frequency a + +

First (Highest) + b c
Second SCO I

Third a b +
Fourth
+ + c
Fifth (Lowest)
SCO II

+
a c

+ b +
DCO II
 In a population

the two combinations with maximum number of frequency

are considered as
parents

the two combinations with minimum number of frequency

are considered as
Double Cross Over

the two combinations between maximum and minimum

number of frequency are considered as
Single Cross Over
 In a three point test cross following combinations may appear

a b c

+ + +

Parental type
Ranking based Class
on frequency a + +

First (Highest) Parent + b c

Second Parent SCO I

Third SCO a b +
Fourth SCO
+ + c
Fifth DCO
SCO II
Sixth (Lowest) DCO
+
a c

+ b +
DCO II
 Gene Order

The gene are positioned in a linear order on a chromosome

Sequential order of genes under study on the chromosome is
known as gene order

In a three point test cross gene order may be

a b c b a c c a b

a c b b c a c b a

It is determined by making double cross over in DCO

the produce should be same as parent
n(n-1) &
the distance between the genes under consideration
3 (2)=6
 Map distance

It is the determination of relative distance between genes

The unit of map distance is cetimorgan = one unit of map distance

It is equivalent to 1% crossing over

Map distance is used in predicting the probability of

crossing over between genes
 Coefficient of coincidence

CoincidenceChances of happening both the events at a time

In this case it means single cross over between
both the combination at a time i.e., double cross over

An experimental value equal to the observed number of double

cross over divided by the expected double cross over

% observed double cross over

Coefficient of coincidence =

% expected double cross over

 Interference

Crossing over at one place in a chromosome may

change the actual probability of another crossing
over at the adjacent region
This change is known as interference

It is of two types
Positive interference The interaction between cross
over is such that the occurrence of one cross over
reduces the chance of cross over of another.
In this case coefficient of coincidence is less than 1

Negative interference The interaction between cross

over is such that the occurrence of one cross over
enhances the chance of cross over of another.
In this case coefficient of coincidence is greater than 1
Coincidence is the complement of interference

Coincidence + interference = 1

When interference is complete (1.0), no double cross over will

be observed and coincidence becomes zero

When all the expected cross over occur actually than

interference becomes zero
 Problems on Linkage

In maize following allelic pairs have been identified

on chromosome number 3.
+/b= plant color booster vs. non booster
+/lg+ Liguled vs. ligule-less
+/v = Green plant vs. Virescent ( turning green)
A tri-hybrid test cross produces following data

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275
Determine
A. Gene Order
B. Map distance
C. Coefficient of coincidence
D. Interference
E. Gene map
 Parents
The off springs with maximum
frequency are considered as parents
The maximum frequency is of

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275
 Parents
The off springs with maximum
frequency are considered as parents
The maximum frequency is of

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275

+ v lg
= 305
= 275
b + +
 Double Cross Over (DCO)
The off springs with minimum frequency are considered as DCO
The minimum frequency is of

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275
 Double Cross Over (DCO)
The off springs with minimum frequency are considered as DCO
The minimum frequency is of

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275
+ + +
= 22
= 18
v b lg
 Double Cross Over (DCO)
Application of double cross over in selected DCO
should form offspring of parental type

+ + +

v b lg
 Double Cross Over (DCO)
Application of double cross over in selected DCO
should form offspring of parental type

DOC type Parental type

+ + + + b +

v b lg v + lg
 DOC type Parental type

b++ 275
+ + + + b +

v b lg v + lg

+ v lg 305
 Single Cross Over (SCO)
SCO I
SCO II

Remaining Off springs are considered as SCO

+ v lg 305 bv+ 66
b + lg 128 +++ 22
v b lg 18 +v+ 112
+ + lg 74 b++ 275
b v + b + lg
= 66 = 128
= 74 = 112
+ + lg + v +
 Correct gene sequence

The correct gene sequence means

the sequence of genes on parents should be
such that after double cross over it produces
correct DCO
 Parental type DCO type

+ v lg
v b lg

+++
b + +
 Parental type DCO type

Correct DCO
+ v lg
v b lg

+++
b + +
 Parental type DCO type

Correct DCO
+ v lg + + lg
v b lg

+++
b v +
b + +
 Parental type DCO type

Correct DCO
+ v lg + + lg
v b lg

+++
b v +
b + +

These two are not correct DCO type

therefore
sequence of gene on parental type has to be changed
 Parental type DCO type

Correct DCO
v + lg
v b lg

+++
+ b +
 Parental type DCO type

Correct DCO
v + lg
v b lg

+++
+ b +
 Parental type DCO type

Correct DCO
v + lg v b lg
v b lg

+++
+ + +
+ b +

This is the correct DCO type

therefore
it is the correct gene sequence
Correct gene sequence of the Parental type

v + lg
305
128
+ b +

DCO type

v + lg v b lg
18

22
+ b + + + +
Correct gene sequence of the Parental type

v + lg
305
128
+ b +
Single Cross Over I

v + lg v b +
66

74
+ b + + + lg
Correct gene sequence of the Parental type

v + lg
305
128
+ b +
Single Cross Over II

v + lg v + +
112

128
+ b + + b lg
Map distance
For this calculate percentage of parental type, DCO and SCO

Frequency Total Percentage

Parental type

DCO

SCO I
(v-b)

SCO II
(b-lg)
Total
Map distance

Frequency Total Percentage

Parental type 275
305

DCO

SCO I
(v-b)

SCO II
(b-lg)
Total
Map distance

Frequency Total Percentage

Parental type 275
305

DCO 22
18

SCO I
(v-b)

SCO II
(b-lg)
Total
Map distance

Frequency Total Percentage

Parental type 275
305

DCO 22
18

SCO I 74
(v-b) 66

SCO II
(b-lg)
Total
Map distance

Frequency Total Percentage

Parental type 275
305

DCO 22
18

SCO I 74
(v-b) 66

SCO II 128
(b-lg) 112
Total
Map distance

Frequency Total Percentage

Parental type 275
305

DCO 22
18

SCO I 74
(v-b) 66

SCO II 128
(b-lg) 112
Total 1000
Map distance

Frequency Total Percentage

Parental type 275 580
305

DCO 22
18

SCO I 74
(v-b) 66

SCO II 128
(b-lg) 112
Total 1000
Map distance

Frequency Total Percentage

Parental type 275 580
305

DCO 22 40
18

SCO I 74
(v-b) 66

SCO II 128
(b-lg) 112
Total 1000
Map distance

Frequency Total Percentage

Parental type 275 580
305

DCO 22 40
18

SCO I 74 140
(v-b) 66

SCO II 128
(b-lg) 112
Total 1000
Map distance

Frequency Total Percentage

Parental type 275 580
305

DCO 22 40
18

SCO I 74 140
(v-b) 66

SCO II 128 240

(b-lg) 112
Total 1000
Map distance

Frequency Total Percentage

Parental type 275 580
305

DCO 22 40
18

SCO I 74 140
(v-b) 66

SCO II 128 240

(b-lg) 112
Total 1000 1000
Map distance

Frequency Total Percentage

Parental type 275 580 58%
305

DCO 22 40
18

SCO I 74 140
(v-b) 66

SCO II 128 240

(b-lg) 112
Total 1000 1000
Map distance

Frequency Total Percentage

Parental type 275 580 58%
305

DCO 22 40 4%
18

SCO I 74 140
(v-b) 66

SCO II 128 240

(b-lg) 112
Total 1000 1000
Map distance

Frequency Total Percentage

Parental type 275 580 58%
305

DCO 22 40 4%
18

SCO I 74 140 14%

(v-b) 66

SCO II 128 240

(b-lg) 112
Total 1000 1000
Map distance

Frequency Total Percentage

Parental type 275 580 58%
305

DCO 22 40 4%
18

SCO I 74 140 14%

(v-b) 66

SCO II 128 240 24%

(b-lg) 112
Total 1000 1000
Map distance

Frequency Total Percentage

Parental type 275 580 58%
305

DCO 22 40 4%
18

SCO I 74 140 14%

(v-b) 66

SCO II 128 240 24%

(b-lg) 112
Total 1000 1000 100
 Distance between genes

v b lg

Distance between gene v-b

= % SCO I + DCO %
= 14 + 4
= 18%
 Distance between genes

v b lg

Distance between gene v-b Distance between gene b-lg

= % SCO I + DCO % = % SCO II + DCO %
= 14 + 4 = 24 + 4
= 18% = 28%
 Distance between genes
v b lg

Distance between gene v-b Distance between gene b-lg

= % SCO I + DCO % = % SCO II + DCO %
= 14 + 4 = 24 + 4
= 18% = 28%

Distance between gene v-lg

Distance between Distance between

gene v-b + gene b-lg = 46 map unit
18 28
Coefficient of coincidence

Percent observed DCO frequency

=
Percent expected DCO frequency
Percent expected
DCO frequency
= Expected DCO Frequency at SCO I X Expected DCO Frequency at SCO II

SCO I + DCO
Expected DCO Frequency at SCO I =
100

14+4 18
= = = 0.18%
100 100

SCOII + DCO
Expected DCO Frequency at SCO II =
100

24+4 28
= = = 0.28%
100 100
Coefficient of coincidence

Percent observed DCO frequency

Percent expected DCO frequency

Percent observed DCO frequency = 0.04%

Percent expected DCO frequency = 0.18X 0.28

0.04
Coefficient of coincidence = = 0.7936
0.18X 0.28

Coefficient of coincidence = 0.7936 X 100 = 79.36 %

Interference

= 1- Coefficient of coincidence
= 1- 0.7936
= 0.2064
= 20.64%
 Gene map

v b lg
Gene map
Gene map

46map unit

v b lg
Gene map
Gene map

46map unit

v b lg

18 map unit
Gene map
Gene map

46map unit

v b lg

18 map unit 28 map unit