GENETICS CYTOGENETICS Definition of Linkage, Coupling and Repulsion hypothesis, Linkage group- Drosophila, maize and man, Types of linkage-complete linkage and incomplete linkage, Factors affecting linkage- distance between genes, age, temperature, radiation, sex, chemicals and nutrition, Significance of linkage. The tendency of two or more genes to stay together (i.e., the co-existence of two or more genes) in the same chromosome during inheritance is known as LINKAGE. The linked genes are present on the same chromosome are said to be SYNTENIC. The linked genes do not show independent assortment. LINKAGE v/s INDEPENDENT ASSORTMENT The frequency of linkage or the strength recombination is influenced by several factors (agents).

1. GENETICS Page 1 of 12
CYTOGENETICS LINKAGE
LINKAGE
Genes (hereditary units) which determines the character of the individual are
carried in the chromosomes. The genes for the different character may be either
situated in the same chromosomes or different chromosomes. When the genes are
situated in different chromosome, the characters they control appear in the next
generation together or apart, depending upon the Mendel’s law of Independent
assortment.
During meiosis, all chromosomes are inherited as one gametic unit and all the
genes (which may specify to the same or various phenotypic traits) located on the
same chromosomes tend to be inherited together. All genes on same chromosomes
are said to be linked to one another and they belong to same LINKAGE GROUP.
The tendency of two or more genes to stay together (i.e., the co-existence of two or
more genes) in the same chromosome during inheritance is known as LINKAGE.
The linked genes are present on the same chromosome are said to be SYNTENIC.
The linked genes donot show independent assortment.
LINKAGE v/s INDEPENDENT ASSORTMENT
LINKAGE INDEPENDENT ASSORTMENT
Gene location Same chromosome Different chromosome
Dihybrid cross
ratio
Highly varies 9:3:3:1
Test cross ratio Highly Varies 1:1:1:1
Example Coloured full seeds (CCSS)
and Colour-less shrunk seeds
of maize
Round yellow peas (RRYY) and
Wrinkled Green peas (rryy)
COUPLING AND REPULSION HYPOTHESIS
• In linkage, there are two phases; they are coupling phase & Repulsion Phase.
• BATESON & PUNNETT (1905) proposed the concept of Coupling and repulsion
phase, but they could not provide exact interpretation of these terms.
• THOMAS H MORGAN (1910) conducted series experimental research on
Drosophila which enabled him to explain that coupling & repulsion are two
aspects of the same phenomenon known as LINKAGE.

2. GENETICS Page 2 of 12
CYTOGENETICS LINKAGE
COUPLING
• The Concept of coupling explains about;
1. Two or more dominant genes which are
present on one of the homologous
chromosomes.
2. Two or more recessive genes which are
present on one of the homologous
chromosomes.
• The linkage between two or more dominant
genes on one homologous chromosome and all
recessive genes on another homologous
chromosome.
• It is also known as Cis-arrangement
• The linkage between two or more dominant
alleles of different genes on one homologous
chromosome and all recessive alleles of
different genes on another homologous
chromosome during the process of
inheritance is called as Coupling.
The best example for Coupling is been reported by HUTCHINSON.
In maize, gene for seed color as dominant allele ‘C’ which produces colored seeds,
while its recessive allele ‘c’ produces colorless seeds. Another gene for seed shape
as dominant allele ‘S’ which produces full – round seeds, while its recessive
allele‘s’ produces shrunken seeds.
HUTCHINSON made a experimental cross between plants having Colored-full seeds
(CCSS) and colorless- shrunken seeds (ccss). The F1 seeds were Colored-full. When
the F1 was test crossed with double recessive parent, the following result were
obtained, instead of 1:1:1:1.
CROSS:
Parental phenotype: Colored-full seeds X colorless- shrunken seeds
Parental genotype : CCSS X ccss
Gametes : CS X cs
F1 generation : CcSs
Colored-full seeds
Test cross : F1 X double recessive parent
Test cross phenotype : Colored-full seeds X colorless- shrunken seeds
Test cross genotype : CcSs X ccss

3. GENETICS Page 3 of 12
CYTOGENETICS LINKAGE
Test cross progeny:
Phenotype Genotype Progeny count type
Colored-full CS 4032 (~4000) Parental type
Colored- shrunken Cs 149 (~100) Recombinant
type
colorless-full cS 152 (~100) Recombinant
type
colorless- shrunken cs 4035(~4000) Parental type
Total = 8368
INTERPRETATION
In the experimental results;
the phenotypic classes - Colored-full and colorless- shrunken have a much higher
frequency than the expected. These two character combinations are referred as
Parental combination (parental phenotypes or Parental types). (Since, they are the
same character combinations that were present in the two parents of F1
generation).
The remaining other phenotypic classes - Colored- shrunken and colorless-full are
reported in low frequency than expected. These two character combinations are
called Recombinant combination (Recombinant phenotypes or Recombinant
types). (Since, they are obtained by reshuffling of the characters present in two
parents of F1)
Henceforth, the parental combinations are higher than recombinant combinations,
indicating the presence of linkage and it is clear that, if the two dominant genes
‘C’ and ‘S’ have a strong affinity for each other. The frequencies of Colored-full
and colorless- shrunken phenotypes are greater than expected. This situation is
referred as COUPLING PHASE, due to the presence of genes ‘C’ and ‘S’ in the same
chromosome.

4. GENETICS Page 4 of 12
CYTOGENETICS LINKAGE
REPULSION
• The Concept of Repulsion explains about;
Two or more dominant and recessive
alleles of different genes which are
present on one of the homologous
chromosomes.
Vice-versa
• The linkage between two or more dominant
and recessive alleles of different genes on one
homologous chromosome and respective
counter-alleles on another homologous
chromosome.
• Trans arrangement
• The linkage between two or more
dominant and recessive alleles of
different genes on a homologous
chromosome and vice-versa during the
process of inheritance is called as
Repulsion.
The best example for Repulsion is been reported by HUTCHINSON.
In maize, gene for seed color as dominant allele ‘C’ which produces colored seeds,
while its recessive allele ‘c’ produces colorless seeds. Another gene for seed shape
as dominant allele ‘S’ which produces full – round seeds, while its recessive
allele‘s’ produces shrunken seeds.
HUTCHINSON made a experimental cross between plants having Colored- shrunken
seeds (CCss) and colorless- full seeds (ccSS). The F1 seeds were Colored-full. When
the F1 was test crossed with double recessive parent (ccss), the following result
were obtained, instead of 1:1:1:1.
CROSS:
Parent-1 X Parent-2
Parental phenotype: Colored- shrunken seeds X colorless- full seeds
Parental genotype : CCss X ccSS
Gametes : Cs X cS
F1 generation : CcSs
Colored-full seeds
Test cross : F1 X double recessive parent
Test cross phenotype : Colored-full seeds X colorless- shrunken seeds
Test cross genotype : CcSs X ccss

5. GENETICS Page 5 of 12
CYTOGENETICS LINKAGE
Test cross progeny:
Phenotype Genotype Progeny count type
Colored-full CS 639 (~650) Recombinant
type
Colored- shrunken Cs 21,379 (~21,300) Parental type
colorless-full cS 21,906 (~21,500) Parental type
colorless- shrunken cs 672 (~650) Recombinant
type
Total = 44,596
INTERPRETATION
In the experimental results;
the phenotypic classes - Colored-shrunken and colorless- full have a much higher
frequency than the expected. These two character combinations are referred as
Parental combination (parental phenotypes or Parental types). (Since, they are the
same character combinations that were present in the two parents of F1
generation).
The remaining other phenotypic classes - Colored- full and colorless- shrunken are
reported in low frequency than expected. These two character combinations are
called Recombinant combination (Recombinant phenotypes or Recombinant
types). (Since, they are obtained by reshuffling of the characters present in two
parents of F1)
Henceforth, the parental combinations are higher than recombinant combinations,
indicating the presence of linkage and it is clear that, if the dominant allele for
color genes ‘C’ and and recessive allele for seed shape gene ‘s’ have a strong
affinity for each other. The frequencies of Colored- shrunken and colorless- full
phenotypes are greater than expected. This situation is referred as Repulsion
PHASE, due to the presence of genes ‘C’ and ‘s’ in the same chromosome.

6. GENETICS Page 6 of 12
CYTOGENETICS LINKAGE
LINKAGE GROUP
A linkage group is a linearly arranged group of linked genes which are normally
inherited together except for crossing over.
It corresponds to a chromosome which bears a linear sequence of genes linked and
inherited together. Because the two homologous chromosomes which possess
either similar or different allelic genes on the same loci, they constitute to the
same linkage group. Therefore, the number of linkage groups present in an
individual corresponds to number of chromosomes in its one genome (all the
chromosomes if haploid or homologous pairs if diploid). However, the organisms in
which the female or the male have heterogametic chromosomes, the linkage group
is haploid plus one. It is known as principle of limitation of linkage groups.
The size of the linkage group depends upon the size of chromosome: The smaller
chromosome will naturally have smaller linkage group while a longer one has
longer linkage group. This is subject to the amount of heterochromatin present in
the chromosome. Thus Y-chromosome of man possesses 231 genes while human
chromosome 1 has 2969 genes.
Example:
1. LINKAGE GROUPS IN HUMANS
Humans can have 2 linkage groups
based on gender. Male have 22
pairs of autosomes and 1X and 1Y.
So, there are in all 24 linkage
groups. While females have 22
pairs autosomes and 1X pair. So,
total 23 linkage groups
1a) Human Females
= 22 pairs of autosomes + 1 pair of homogametic X-chromosome
= 22 + 1 = 23 linkage groups
1b) Human Males
= 22 pairs of autosomes + 1 pair of heterogametic allosome
= 22 + 1 x-chromosome + 1 Y-chromosome
= 24 linkage groups

7. GENETICS Page 7 of 12
CYTOGENETICS LINKAGE
2. LINKAGE GROUPS IN Drosophila melanogaster
In fruit fly, there are four pair of chromosomes: three are autosomal pairs and
one pair of sex chromosomes. Genes present on one chromosome form a linkage
group. Homologous chromosomes carry same set of genes (the alleles may
differ), hence same linkage group.
2a) Female Drosophila
melanogaster (the fruit fly)
consists of FOUR pairs of
chromosomes and hence they
have FOUR linkage groups,
among which three are large
linkage groups and one is small
linkage group.
2b) The male Drosophila’s have one extra
linkage group (FIVE linkage groups)
because they are heterogametic. This is
because other than the three autosomes
there are a pair of sex chromosomes
which are not homologous, i.e. genes on
X chromosome are not same as the genes
on Y chromosome.
3. LINKAGE GROUPS IN MAIZE (Zea mays)
Corn (Zea mays or maize) has 10 pairs of chromosomes and 10 linkage groups.
Note;
• Pea seven linkage groups (7 pairs of chromosomes)
• Neurospora 7 linkage groups (7 chromosomes)
• Escherichia coli one linkage group (one pro-chromosome or nucleoid)

8. GENETICS Page 8 of 12
CYTOGENETICS LINKAGE
TYPES OF LINKAGE
COMPLETE LINKAGE AND INCOMPLETE LINKAGE
COMPLETE LINKAGE
• The linked genes on a homologous
chromosome which fail to undergo
crossing over and exhibit absolute
linkage is called complete linkage.
• In this case, the parental combinations
of characters appear together for two or
more generations in a continuous or
regular fashion.
• In this type of linkage, genes are
strongly associated and tend to
transmit together.
X
EXAMPLE: COMPLETE LINKAGE in Male Drosophila
In most of the organisms crossing over takes place between both males and
females. But, in case of male Drosophila and female Silk moth (Bombyx mori),
the crossing over takes place very rarely or not at all. This becomes clear from
T H morgan’s experimental results from Drosophila.
T H morgan’s experiment for complete linkage in male Drosophila
In 1919, T.H.Morgan crossed Gray-bodied and Vestigial-winged fly (b+vg/b+vg)
with Black-body and normal wing (bvg+/bvg+) fly. F1 progeny had gray-body and
normal wings (b+vg/bvg+), thereby indicating these characters are dominant in
nature. For the test cross, The F1 male flies were crossed to double recessive
females (bvg/bvg) black-body and vestigial-wing.
Gray-body Black-body Normal-wing Vestigial-wing
b+ b vg+ vg

9. GENETICS Page 9 of 12
CYTOGENETICS LINKAGE
CROSS:
Parental phenotype : Gray-bodied and Vestigial-winged X Black-body and normal wing
Parental genotype : b+ vg/b+vg X bvg+/bvg+
Gametes : b+ vg X bvg+
F1 generation : b+
vg/bvg+
gray-body and normal wings
TEST CROSS : F1 male X double recessive female parent
Test cross phenotype : gray-body and normal wings X black-body and vestigial-wing
Test cross genotype : b+vg/bvg+ X bvg/bvg
Test cross Gametes: b+vg bvg+ X bvg
Test cross progeny:
bvg
b+vg b+vg/ bvg
Gray-bodied and Vestigial-winged
50% or ½
bvg+ bvg+ / bvg
Black-body and normal wing
50% or ½
Test cross ratio= ½ Gray-bodied and Vestigial-winged : ½ Black-body and normal
wing
There are only two types of Test cross progenies in 1:1 ratio (rather than four
types of test cross progenies in 1:1:1:1 ratio). This is due to the complete linkage
(absolute linkage) and absence of crossing over in male Drosophila.

10. GENETICS Page 10 of 12
CYTOGENETICS LINKAGE
INCOMPLETE LINKAGE
• If some frequency of crossing over takes place among the linked genes, it is
known as Incomplete linkage. In other words, when recombinants are produced
in the test cross progeny, besides parental combinations, it refers to Incomplete
linkage.
• The linked genes which are widely located in a chromosome and have chances
of separation by crossing over are called the incompletely linked genes and the
phenomenon of their inheritance is called Incomplete linkage.
EXAMPLE : INCOMPLETE LINKAGE IN FEMALE Drosophila
T H Morgan’s experiment for Incomplete linkage in female Drosophila
T.H.Morgan crossed Gray-bodied and Vestigial-winged fly ( b+ vg/b+vg) with Black-
body and normal wing fly (bvg+/bvg+). F1 progeny had gray-body and normal wings
(b+vg/bvg+), thereby indicating these characters are dominant in nature. For the
test cross, The F1 female flies were crossed to double recessive males (bvg/bvg)
black-body and vestigial-wing.
CROSS:
Parental phenotype : Gray-bodied and Vestigial-winged X Black-body and normal wing
Parental genotype : b+ vg/b+vg X bvg+/bvg+
Gametes : b+ vg X bvg+
F1 generation : b+
vg/bvg+
gray-body and normal wings
Test cross : F1 female X double recessive male parent
Test cross phenotype : gray-body and normal wings X black-body and vestigial-wing
Test cross genotype : b+vg/bvg+ X bvg/bvg
Test cross Gametes : b+vg bvg+ b+vg+ bvg X bvg
Non crossovers recombinants
Test cross progeny:
bvg Experimental
values
b+vg b+vg /bvg Gray-body and Vestigial-
winged
41.5% 83% parental
combination showing
linkage
bvg+ bvg+/bvg Black-body and normal wing 41.5%
b+vg+ b+vg+/bvg gray-body and normal wings 8.5% 17% recombinants due to
crossover
bvg bvg /bvg black-body and vestigial-wing 8.5%
There was both parental combination and recombinant ones in the test cross
progenies. Henceforth, female Drosophila flies exhibit incomplete linkage.
Different test cross ratios showing complete linkage in male Drosophila and
incomplete linkage in female Drosophila were obtained. Thus, proves the
association of linked genes in different patterns of both genders in Drosophila
flies.

11. GENETICS Page 11 of 12
CYTOGENETICS LINKAGE
FACTORS AFFECTING LINKAGE
• The frequency of linkage or the strength recombination is influenced by several
factors (agents).
• Most of the influential agents or factors data documented based on experiments
conducted on Drosophila
1. DISTANCE BETWEEN GENES
• The strength of linkage between two genes would increase with the decrease in
distance between them.
• Crossing over will be relatively more frequent, if distance between two genes is
more.
• The less distance between the genes the more is the linkage strength, greater
the distance between genes lower is a chance of linkage.
• 𝟏/∝
• CO ∝ Distance between genes
• Linkage 𝟏/∝ C.O
• Linkage 𝟏/∝ Distance between genes
2. AGE
• Generally, the linkage increases with advancement in the age in the female
Drosophila.
• Crossing over shows a progressive decline with advancing age of female
Drosophila this was experimentally proved Drosophila crosses.
• Age ∝ Linkage in female Drosophila
3. TEMPERATURE
• H H Plough (a student of T H Morgan) identified that the rate of linkage remains
constant in 22 degree Celsius.
• In Drosophila, the lowest frequency of recombination (strongest linkage) is
observed when female drosophila flies are cultured at 22 degrees Celsius.
• Above and below 22 degree Celsius there is fluctuation in linkage, showing
increased Recombinant progenies.
4. RADIATION
• An increase in crossing over is observed when Drosophila females and many
other organisms are irradiated with X-rays and gamma-rays.
• The irradiation reduces the frequency of linkage.
• Drosophila male provides evidences for destruction of linkage after irradiation
with X-rays.
• Radiation 𝟏/∝ linkage strength

12. GENETICS Page 12 of 12
CYTOGENETICS LINKAGE
5. SEX / GENDER
• Linkage is markedly influenced by gender or sex of an organism and varies in
heterozygotes.
• Heterochromatic genders show relatively stronger linkage when compared to
homogametic genders of the same species.
• There is lack of crossing over in Drosophila male and female Silk moth, which
means rate of linkage also varies among different genders for a given species.
Female Drosophila exhibit incomplete linkage.
6. CHEMICALS
• Treatment with mutagenic chemicals like alkylating agents would decrease the
frequency of linkage in female Drosophila
• For example; When female Drosophila’s are injected with certain antibiotics like
actinomycin D have reported to reduce linkage, while promoting the crossing
over.
7. NUTRITION
• Presence of metallic ions like calcium (Ca2+) and magnesium (Mg2+) in the food&
nutrition will result in reduction of recombination in Drosophila.
• For example; When female Drosophila’s are fed with high calcium ions diet, the
subsequent generation showed reduced recombinants.
• However, removal of such ions from the diet increased the rate of crossing over.
Note:
1. Centromeric effect: genes located adjacent to the centromere show enhanced frequency of
linkage
2. Cytoplasmic genes/plasmogenes: in some species presence of cytoplasmic genes would
reduce the linkage strength.
3. Chromosomal aberrations / structural changes: they enhance linkage
SIGNIFICANCE OF LINKAGE.
• The phenomenon of linkage has one of the great significance for the living
organisms in that it reduces the possibility of variability in gametes unless
crossing over occurs. (Linkage prevents the incidence of recombination)
• Linkage plays an important role in determining the nature of scope of
hybridization and selection programme.
• Linkage reduces the chance of recombination of genes and thus helps to hold
parental characteristics together. It thus helps organism to maintain its
parental, racial and other characters. For this reason plant and animal breeders
find it difficult to combine various characters.