linkage and crossing over

Linkage and crossing over
LINKAGE INTRODUCTION
Every individual organism bears several heritable characters which are represented
by the innumerable genes present on the chromosomes. During meiosis, the
chromosomes move into the gametes as units, all the genes present on any given
chromosome will segregate as a group and move together from generation to
generation. This tendency of the genes located on the same chromosome, to stay
together in hereditary transmission, is known as linkage. The genes located on the
same chromosome are called linked genes.
HOW IT DIFFER FROM RECOMBINATION
“In linkage, two or more genes linked together are always inherited together in the
same combination for more than two generations, whereas in recombination the
genetic material is exchanged between different organisms which lead to the
production of offspring’s with the combination of traits”.
Key points:
 When genes are found on different chromosomes or far apart on the same
chromosome, they assort independently and are said to be unlinked.
 When genes are close together on the same chromosome, they are said to
be linked. That means the alleles, or gene versions, already together on one
chromosome will be inherited as a unit more frequently than not.
 We can see if two genes are linked, and how tightly, by using data from genetic
crosses to calculate the recombination frequency.
 By finding recombination frequencies for many gene pairs, we can make linkage
maps that show the order and relative distances of the genes on the chromosome.

LINKAGE
• Discovery of linkage
• Meaning of linkage
• Characteristics of linkage
• Genes in linkage
• Theories
• Kinds of linkage
• Linkage group
• Significance
CROSSING OVER
• Discovery of
crossing over
• Meaning of
crossing over
• Characteristics
of crossing over
• Types crossing over
• Mechanisms
• Factors
affecting
crossing over
• Significance
• Differences
between
crossing over
and linkage

Discovery of
Linkage
• The principle of
linkage was
discovered by English
Scientists William
Bateson and R.C.
Punnet in 1906 in
Sweet Pea (Lathyrus
odoratus). However, it
was put forward as a
regular concept by
Morgan in 1910 from
his work on
(Drosophila
melanogaster).

A
B
A
B
Meaning of Linkage
• Linkage is the
phenomenon of
certain genes staying
together during
inheritance through
several generations
without any change or
separation due to their
being present on same
chromosomes.

CHARACTERISTICS OF LINKAGE
• Linkage involves two or more genes which are linked in same
chromosomes in a linear fashion.
• Linkage reduces variability.
• It may involve either dominant or recessive alleles (coupling
phase) or some dominant and some recessive alleles
(repulsion phase).
• It usually involves those genes which are located close to
each other.
• The strength of linkage depends on the distance between the
linked genes.
*Lesser the distance higher the strength of linkage*

When genes are on separate chromosomes, or very far apart on the same
chromosomes, they assort independently. That is, when the genes go
into gametes, the allele received for one gene doesn't affect the allele
received for the other. In a double heterozygous organism (AaBb), this
results in the formation of all 4 possible types of gametes with equal,
or 25%, frequency.
Genes on separate chromosomes assort independently because of the
random orientation of homologous chromosome pairs
during meiosis. Homologous chromosomes are paired chromosomes
that carry the same genes, but may have different alleles of those genes.
One member of each homologous pair comes from an organism's mom,
the other from its dad.

Genes in Linkage
LINKED GENES :
Thes genes do not
show independent
assortment.
It occurs in
same chromosome.
Dihybrid ratio of
linked gene is 3:1
UNLINKED GENE:
These genes showing
Independent assortment.
Dihybrid ratio is 9:3:3:1.

KINDS OF LINKAGE

 ON THE BASIS OF CROSSINGOVER
i. Complete linkage
ii. Incomplete linkage
Complete Linkage:
If linkage is complete, there should be parental combinations only and no
recombination. Morgan (1919) reported a complete linkage in Drosophila.
When ordinary male wild fly with grey body and normal wings was crossed
with female having black body and vestigial wings, in F1, hybrids were all
grey bodied and normal winged (with dominant characters).
But when F1, male is back crossed with recessive female parent only
two types of individuals in F2 generation were produced instead of
expected four. These two types were grey bodied and normal winged
and black bodied and vestigial winged in equal number, thus
indicating the complete linkage.
But how do genes located on same chromosome assort independently?
It may be due to exceptions in Mendel’s second law of independent
assortment or due to some mechanism for genes on the same
chromosome to separate and recombine during meiosis. Both the
cases have been observed.

Incomplete linkage:
Incomplete linkage produces new combinations of the genes in the
progeny due to the formation of chiasma or crossing over in between
the linked genes present on homologous chromosomes. When a cross
is made between blue and long species (BBLL) with red and round
species (bbll) in F1 expected outcome will be as blue and long (BbLl)
heterozygous condition.
Fig. A case of incomplete linkage.
However, test cross between blue and long (BbLl) and double recessive
(bbll) gave blue long (43.7%), red round (43.7%), blue round (6.3%) and
red long (6.3%). The parent combinations are 87.4% are due to linkage
in genes on two homologous chromosomes, while in case of new
combinations (12.6%) the genes get separated due to breaking of

chromosomes at the time of crossing over in prophase-I of meiosis. New
combinations in the progeny appeared due to incomplete linkage.
Morgan picked Drosophila melanogaster as his subject for the
following reasons:
 He noticed a white-eyed male drosophila instead of the regular red
eyes.
 It was small in size
 They have a short lifespan and so many generations can be studied in
a short time frame.
 They have a high rate of reproduction.
He crossed a purebred white eyed male with purebred red-eyed female. As
expected following Mendel’s laws, the F1 progeny were born with red
eyes. When F1 generation was crossed among each other, the ratio of red-
eyed to white eyed progeny were 3:1. However, he noticed that there was
no white- eyed female in the F2 generation.
To understand further, he performed a cross between a heterozygous red-
eyed female with a white-eyed male. This gave a ratio of 1:1:1:1 in
the progeny (1 white eyed female, 1 red eyed female, 1 white eyed male
and 1 red eyed male). This made Morgan think about the linkage between
the traits and sex chromosomes. He performed many more crosses and
determined that the gene responsible for the eye color was situated on the
X chromosome.

 ON THE BASIS OF CHROMOSOME
INVOLVED
1). Autosomal linkage. 2). Allosomal /Sex linkage
Based on chromosomes involved: Based on the location of genes on the
chromosomes, linkage can be categorized into :-
(a) Autosomal linkage: It refers to linkage of those genes which are
located in autosomes (other than sex chromosomes).
(b) X-chromosomal linkage / allosomal linkage / sex linkage: It refers
to linkage of genes which are located in sex chromosomes i.e. either ‘X’
or ‘Y’ (generally ‘X’)
 ON THE BASIS OF GENE INVOLVED
i. Coupling phase
ii. Repulsion phase
:
 Genes which are closely located show strong linkage & genes which are
located far show weak linkage.
 He stated that Coupling & Repulsion are two aspects of Linkage.
1. Cis -arrangement: dominant alleles of 2 or more genes are present in
one chromosome & its recessive alleles in its homologue. AB/ab. This
is coupling.
2.Trans -arrangement: The dominant allele of one pair & recessive of
the other pair together lie in a chromosome.Ab/aB. This is Repulsion.
Theories of Linkage
 COUPLING AND THEORY (William Bateson)
 CHROMOSOMAL THEORY (Thomas Hunt Morgan)

Coupling and repulsion hypothesis
This theory was proposed by Bateson to explain the phenomenon of
linkage. According to this theory, the set of gametes possessing parental
combinations multiply more rapidly than the set having non- parental
combinations after the segregation of characters during gamete
formation. This results in the formation of a greater number of gametes
with parental combinations.
W. Bateson, in 1905, described a cross in sweet pea, where a deviation
from independent assortment was exhibited. Plants of a sweet pea
variety having blue flowers (B) and long pollen (L) were crossed with
those of another variety having red flowers (b) and round pollen (l).
F1 individuals (BbLl) had blue flowers and long pollen. These were
crossed with plants having red flowers and round pollen (bbll). (In this
case character for blue colour of flowers is dominam over red colour and
long pollen character is dominant over round pollen).
Normally if independent assortment takes place, we should expect
1:1:1:1 ratio in a testcross. Instead, 7:1:1:7 ratios were actually obtained,
indicating that there was a tendency in dominant alleles to remain
together. Similar was the case with recessive alleles. This deviation was,
therefore, explained as gametic coupling by Bateson. Similarly, it was
observed that when two such dominant alleles or two recessive alleles
come from different parents, they tend to remain separate. This was
called gametic repulsion.
In Bateson's experiment in repulsion phase, one parent would have blue
flowers and round pollen (BBll) and the other would have red
flowers and long pollen (bbLL). The results of a testcross in such a
repulsion phase were similar to those obtained in coupling phase giving
1:7:7:1 ratio instead of expected 1:1:1:1. Bateson explained the lack of
independent assortment in the above experiments by means of a
hypothesis known as coupling and repulsion hypothesis. Although

coupling and repulsion as explained above were later discovered to be
the two aspects of the same phenomenon called linkage, the
terms coupling phase and repulsion phase are still considered to be
useful terms presents in scientific literature.
Chromosomal theory of linkage: by T. H Morgan.
 Bateson and Punnett failed to explain the exact reasons of
coupling and repulsion.
 Later, T.H. Morgan who found coupling and repulsion hypothesis
incomplete, while performing experiments with Drosophila, in
1910. Therefore, he proposed that the two genes are found in
coupling phase because they are present on same chromosome and
similarly on repulsion phase because they are preset on two
different homologous chromosomes. There genes are then
called linked genes and the phenomenon of inheritance of such
linked genes is called linkage by Morgan.
 And the term coupling and repulsion were replaced by the
terms, cis and trans by (Haldane, 1942).
 Morgan stated the linked genes have the tendency to remain
together in original combination because they are located on same
chromosome. And the strength of linkage depends upon the
distance between the linked genes in the chromosome.
 The concept of linkage given by Morgan established the foundation
of Cytogenetics and developed the theory of linear arrangement of
genes in the chromosomes and helps to construct genetic map of the
chromosome.
 According to Chromosomal theory of linkage:
 Chromosome contains genes and Genes lie in a linear order in a
chromosome and distance between them is variable.
 Each gene has a definite locus in a chromosome. The genes
which are close to each other, shows the phenomenon of
linkage

*The linked genes cannot be separated during gametogenesis
(inheritance process), they inherited together.
*Tendency of genes to remain linked is due to their presence on same
chromosome.
*The distance between the linked genes determines the strength of
linkage. The closer the distance stronger is the linkage strength.
*The linkage is not due to any relation between two genes but is simply
because they happen to be located in the same chromosome.


Linkage and pleiotropy:
A close association between two or more characters may result either
due to linkage or pleiotropy or both. Pleiotropy refers to the control of
two or more characters by a single gene. A tight linkage between two
loci can be often confused with pleiotropy. The only way to distinguish
between linkage and pleiotropy is to find out a crossover product
between linked characters. Intermating in segregating populations may
break a tight linkage, but a huge population has to be raised to find out
the crossover product. If a cross over product is not found in spite of
repeated inter-mating, there seems to be the case of pleiotropic rather
than linkage.
Linkage groups:
Linkage group refers to a group of genes which are present in one
chromosome. In other words, all those genes which are located in one
chromosome constitute one linkage group. The number of linkage
groups is limited in each individual. The maximum number of linkage
groups is equal to the haploid chromosome number of an organism.
For example there are ten linkage groups in corn (2n = 20), seven in
garden pea (2n = 14), seven in barley (2n = 14), four in Drosophila
melanogaster (2n = 8) and 23 in man (2n = 46). Detection of linkage:
Test cross is the most common method of detecting the linkage. In this
method, the F, heterozygous at two loci (AB/ab) is crossed to a double
recessive parent (ab/ab) and the phenotypic ratio of test cross progeny is
examined. If the phenotypic ratio of test crosses progeny shows 1:1:1:1
ratio of parental and recombinant genotypes, it indicates absence of
linkage. If the frequency of parental types and recombinant types deviate

significantly from the normal dihybrid test cross ratio of 1:1:1:1, it
reveals presence of linkage between two genes under study. Another
way to detect the presence or absence of linkage is to self-pollinate the
individual heterozygous at two loci. If there is complete dominance at
each locus and no epistasis, the segregation ratio of the progeny will be
9:3:3:1. Presence of linkage either in coupling or repulsion phase will
lead to significant deviation from 9:3:3:1 ratio.
Significance of linkage:
 Linkage does not permit the breeders to bring the desirable characters in
one variety.
 For this reason, plant and animal breeders find it difficult to combine
various characters.
 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.

Crossing over Definition
Crossing over is the exchange of genetic material between non-sister
chromatids of homologous chromosomes during meiosis, which results
in new allelic combinations in the daughter cells. The term crossing over
was first used by Morgan and Cattell in 1912. “The exchange of
precisely homologous segments between non-sister chromatids of
homologous chromosomes is called crossing over.”
Each diploid cell contains two copies of every chromosome, one derived
from the maternal gamete and the other from the paternal gamete. These
pairs of chromosomes, each derived from one parent, are
called homologous chromosomes. When diploid organisms
undergo sexual reproduction, they first produce haploid gametes through
meiosis. During prophase I of meiosis, homologous chromosome align
with each other and exchange genetic material, so that some of the
resultant chromosomes are recombinants – containing a mixture of genes
derived from the maternal as well as the paternal chromosomes.
“Crossing over is the swapping of genetic material that occurs in the
germ line. During the formation of egg and sperm cells, also known as
meiosis, paired chromosomes from each parent align so that similar
DNA sequences from the paired chromosomes cross over one another.
Crossing over results in a shuffling of genetic material and is an
important cause of the genetic variation seen among the offspring”.

homologous chromosomes
Homologous chromosomes are two pieces of DNA within a diploid
organism which carry the same genes, one from each parental source. In
simpler terms, both of your parents provide a complete genome. Each
parent provides the same 23 chromosomes, which encode the same
genes.
During meiosis, the two chromosomes in each homologous pair
exchange segments, through a process called crossing over. This process
of crossing over and the resulting recombination, (exchange of gene
alleles across the chromosomes in a pair) enables us to reason about
genetic mapping - that is, about the order of genes on a chromosome and
the distances among the genes.

The next section provides a brief description of crossing over and
recombination. The section that follows introduces the logic that allows
us to reason about genetic mapping.

Feature of Crossing Over:
The main features of crossing over are given below:
1. Crossing over takes place during meiotic prophase, i.e., during
pachytene. Each pair of chromosome has four chromatids at that time.
2. Crossing over occurs between non-sister chromatids. Thus one
chromatid from each of the two homologus chromosomes is involved in
crossing over.
3. It is universally accepted that crossing over takes place at four strand
stage.
4. Each crossing over involves only two of the four chromatids of two
homologus chromosomes. However, double or multiple crossing over
may involve all four, three or two of the four chromatids, which is very
rare.
5. Crossing over leads to re-combinations or new combinations between
linked genes. Crossing over generally yields two recombinant types or
crossover types and two parental types or non-crossover types.
6. Crossing over generally leads to exchange of equal segments or genes
and recombination is always reciprocal. However, unequal crossing over
has also been reported.
7. The value of crossover or recombinants may vary from 0-50%.
8. The frequency of recombinants can be worked out from the test cross
progeny. It is expressed as the percentage ratio of recombinants to the
total population (recombinants + parental types). Thus,

Cases of two strand crossing over, somatic crossing over, sister strand
crossing over and unequal crossing over is also known. However,
frequency of such cases is extremely low, i.e. in fractions. Crossing over
differs from linkage in several aspects are:-
Mechanism of crossing over:
The crossing over, leading to recombination of linked genes, is due to
interchange of sections of homologous chromosomes. At meiosis, the
homologous (maternal and paternal) chromosomes come together and
pair, or synapse, during prophase. The pairing is remarkably precise and
is evidently brought about by mutual attraction of the parts of the
chromosomes that are similar or homologous because they contain
allellic genes.

Types of Crossing Over:
Depending upon the number of chiasmata involved, crossing over may
be of three types, viz., single, double and multiple as described below:
i. Single Crossing Over:
It refers to formation of a single chiasma between non-sister
chromatids of homologous chromosomes. Such cross over involves
only two chromatids out of four.
ii. Double Crossing Over:
It refers to formation of two chiasmata between non-sister chromatids
of homologous chromosomes. Double crossovers may involve either
two strands or three or all the four strands. The ratio of recombinants
and parental types under these three situations are observed as 2:2:3:1
and 4 : 0, respectively.
iii. Multiple Crossing Over:
Presence of more than two crossovers between non-sister chromatids
of homologous chromosomes is referred to as multiple crossing over.
Frequency of such type of crossing over is extremely low.

Further, during the transition between the pachytene and the diplotene of
the prophase of meiosis, the paired chromosomes divide each into two
chromatids, so that the bivalent is now composed of four chromatids. At
about the time when the chromosomes are first seen to be divided, the
chromatids establish one or more exchange, or Chiasmata, per bivalent.
The following points highlight the four theories proposed for the
mechanism of crossing over.
The theories are: 1. Janssen’s Classical Theory 2. Belling’s Copy
Choice Theory 3. Uhl’s Theory 4. Darlington’s Theory of Crossing
Over.
Theory # 1. Janssen’s Classical Theory:
Janssen (1909) believed that prior to the formation of chiasmata the
homologous maternal and paternal chromosomes come in pair and in
pachytene stage they become coiled round each other and become
doubled.
He further suggested that in order to derive chiasmata from such a coil,
the paternal and maternal chromatids made contacts at intervals and then
one chromatid of chromosome penetrated that of the other until they
were broken, where upon they rejoined in new ways; paternal to
maternal and vice versa, forming the typical chiasmata between them.
The theory did not suggest a satisfactory mechanism by which two
chromatids break at precisely equivalent points.

Theory # 2. Belling’s Copy Choice Theory:
In 1931, a cytologist named J. Belling proposed “the copy choice
theory”. According to this theory, the paired chromosome in first
meiotic prophase duplicates their genes before the fibres that join them
in tandem are developed.
During the process, if the chromosomes are twisted around each other,
the connecting fibres may connect genes of one chromosome at some
points and adjacent genes produced by other chromosome at the other.
In brief, the theory assumes that the crossing over is the direct result of
the new chromatids copying partly from one strand and partly from other
homologous strand.

There are two main defects in the copy choice theory:
(i) The theory does not properly account for the fact that crossing over
can involve all the four chromatids and not just the two chromatids,
though three strands and four strands double cross overs (i.e., successive
cross-overs involving three or four different strands) are also known to
occur.
(ii) The second shortcoming of this hypothesis is that it requires
singleness of leptotene threads and duplication of genes must occur
during meiosis. But the synthesis of new chromosome material, at least
the DNA, occurs during the interphase and thus the gene duplication
takes place before the prophase of first meiosis begins.
Hence, copy choice theory must assume that crossing over occurs in the
interphase rather than in pachytene, the only known time at which most
chromosomes regularly pair and duplicate themselves.
Theory # 3. Uhl’s Theory:
Uhl (1965) proposed a mechanism some-what similar to that of Belling.
According to him, a chromosome consists of many small strands of
DNA which are joined successively end to end by linkers. At the time of
DNA replication, the linkers remain single and go with one or the other
complementary strand.
Formation of linkers to fill the vacant spaces after synapsis, sometimes
results in the linking of segments from homologous chromosomes rather
than linking the sister chromatids and thus it eventually results in
crossing over and chiasmata. The basic sequence is shown in Fig. 16.4.
The theory has only a few defects but many merits.

Demerits:
(a)The linkers should be so close that telophase chromosomes should
appear single, but it is not so.
(b)The cistron (constitutional gene) must be interrupted by linkers or be
unreasonably long since intragenic crossing over does take place, unless
this kind of crossing over has different
Merits:
(a) The theory goes far toward reconciling the multi-stranded nature of
the chromosomes with unitary behaviour of chromatids.
(b) In this theory, stress has been given on the bond exchange between
the adjacent DNA strands of the two homologues and no stress is laid on
the physical breakage and reunion.
(c) The theory restricts rejoining to successive segments and does not
allow for lateral exchange. Presumably, very specific bonds are involved
in reunion.
(d) Broken chromosome and chromatid ends resulting from the action of
radiation or chemicals have apparently free choice and they can rejoin
with any other broken end regardless of the direction.

Theory # 4. Darlington’s Theory of Crossing Over:
A more probable and easy hypothesis of mechanism of crossing over has
been advanced by C. D. Darlington in 1935. This is called “breakage
and reunion theory.” Darlington postulated that the homologous
chromosomes are intertwined during the four stranded stage of first
meiosis. The twisting exerts strain on the chromatids.
If the stresses are great enough one or more chromatids of the
homologues will be broken at one or more points. If more than one
chromatid break, there is possibility that the broken chromatids of one
chromosome will unite with broken ends of different chromatid forming
a chiasma.
If the union takes place between sisters chromatid parts (i.e., paternal to
paternal and maternal to maternal) no genetic consequence is
anticipated. However, if the break and reunion occur between non- sister
chromatids (i.e., paternal to maternal or vice versa) recombinants would
result.
This hypothesis represents the best explanation to date to account for the
formation of recombinants. Diagrams showing the stages involved in
this hypothesis are given.

Previously it was thought that the mechanical stress produced the breaks
before the recombination but now scientists believe that some enzymes
are involved in the processes of breakage and reunion. The idea that
some enzymatic processes bring about breakage and rejoining of DNA
strands was first put-forth by Howard Flanders and Boyce in 1964.
Reproduction of bacterial chromosome, for instance, during conjugation
indicates that the ring structure of DNA may be broken without any
known mechanical stress.
There is also no known twisting of bacterial chromosomes in the
recombination process. While considering the reunion of broken DNA
strands, regardless of breaks occurred, one must hypothesize an
enzymatic process in the formation of covalent bonds necessary to repair
the sugar phosphate backbone of the DNA molecule. Other important
points in the theory are:
I. Exchange takes place between chromatids without any breakage.
ii. Precision in the process.
iii. Positive interference, i.e., successive chiasmata will be minimal
distances apart.
iv. Three and four strands double cross-overs and chiasmata can be
explained.

v. The synthesis of almost all DNA is supposed to occur prior to
synapsis.
Stem and Hotta (1969) are of the opinion that two nuclear enzymes
namely endonuclease and ligase bring about crossing over. The enzyme
endonuclease helps in the breaking of the chromatids while the ligase
helps in the reunion of the chromatid segments. They have also reported
the synthesis of a small amount of DNA during the period of crossing
over which is used in the repairing of the broken chromatids.
Somatic Crossing Over:
The pairing and crossing over take place not only in gonad cells but also
in somatic cells. The process of somatic crossing over is known to occur
in a number of organisms including Drosophila and maize. In the
Diptera insect, the homologous chromosomes have been observed to
pair in the early mitotic prophase.
The crossing over takes place when the chromosomal threads are
plectonemically arranged. Although the somatic crossing over is difficult
to detect, there is no doubt that it occurs. The exact mechanism is not yet
clears.
The somatic crossing over may bring several changes in the structure
and physiology of the organisms. Majority of individuals are
heterozygous for many genes. Somatic crossing over may result in the
malfunctioning of parts or organs on account of presence of recessive

genes in homozygous condition. The influence of this process may
sometimes be very serious and fatal.
Factors Affecting Crossing Over:
It has been proved experimentally that the frequency of crossing over
between two genes is not completely dependent on their distance but
several other physiological and environmental factors can also influence
it. Temperature, x-ray and chemical composition of food may change the
frequency of crossing over. In Drosophila melanogaster it may be
reduced with the increase of the age of flies.
Significance of Crossing Over:
Crossing over is a widespread phenomenon which is known to occur in
all the higher organisms, as well as in most bacteria and viruses. The
exchange of genes between non -sisters chromatids of homologous
chromosomes in this process leads to the production of recombinants.
Hence, it is of great importance in the evolution.
The phenomenon of crossing over is of paramount importance in plant
breeding because new varieties with valuable characters can be evolved
by eliminating undesirable genes through this process. Study of crossing
over is very much helpful in mapping of genes on the chromosomes.

linkage and crossing over

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