Linkage, Morgan’s Experiment, Types of Linkage, Crossing Over, Recombination, Gene mapping, Practice Problems and FAQs

How many times have you been told that you have your mother’s eyes or your father’s nose or something of the sort to draw similarities between you and your parents? I am sure we all hear these comparisons quite often. But the matter of fact is, although we inherit all our genes from our parents and do share similarities with them, we are still quite different from them in many aspects. Do you know why? This is because sexual reproduction brings about variations in offspring. But how?

We know that when gametes form they receive only half the number of chromosomes from the parents and this is possible through a special type of cell division known as meiosis. During meiosis, there is a random assortment as to which member of the homologous pair of chromosomes in our parents will enter into a particular gamete. So each gamete carries a different assortment of chromosomes and this is one of the reasons which leads to variation.

But, the major cause of variation is the crossing over between non-sister chromatids of a homologous pair of chromosomes during meiosis. This leads to exchange of genes between the two non-sister chromatids of the homologous pair and end up producing genetic combinations in the chromosomes that are very different from what the parent had. Thus the chromosomes carried by the gametes end up being quite different from the chromosomes of our parents and hence we end up being different from our parents.

But the distance between the genes is a strong determinant of whether they will be inherited in the parental combination or not, after crossing over. Can you think of why? Let us try and understand this concept through this article.

Table of contents

• Morgan’s experiment
• Linkage
• Linkage and crossing over
• Recombination
• Recombination of linked genes
• Gene mapping
• Practice problems
• FAQ’s

Morgan’s experiment

Thomas Hunt Morgan was an American scientist who had spent his whole research career working and experimenting with Drosophila. Thomas Hunt Morgan was awarded the Nobel Prize for his research on Drosophila, which revealed the importance of chromosomes in inheritance.

                                Fig: T H Morgan

Drosophila- Model organism

He chose Drosophila as a model organism because of the following reasons:

• The life cycle of Drosophila is very short i.e. of two weeks.
• They can easily reproduce in lab conditions by providing synthetic media and this process requires less labour.
• They produce a large number of progeny.
• The male and female sexes are different.
• They possess variations that can be visible under light microscopy.

                    Fig: Drosophila melanogaster

He chose two types of Drosophila variety. The first is the wild type, which is normally present in nature and the other is the mutant type, which is a special type of variety that occurs after mutation. The normal red-eyed fly is a wild type and the special white-eyed fly is a mutant type.

                                                        Fig: Drosophila variety

Gene notation for eye colour

The first letter of the mutant allele, written in small letters, is used to indicate the mutant allele, for example, w for white. Wild type is denoted by the initial letter of the mutant allele in tiny letters followed by a plus sign in superscript, e.g. w⁺ for red eyes.

                                           Fig: Gene notation for eye colour

Gene notation for body colour

The brown body colour is dominant and wild type over yellow body colour. For brown body colour, the gene notation used is y⁺ and for the yellow body colour, it is y.

                                      Fig: Gene notation for body colour

Dihybrid cross

Dihybrid Cross A

Morgan tried a dihybrid cross in Drosophila. The yellow-bodied white-eyed female is crossed with a brown-bodied red-eyed male.

                                            Fig: Parents in Dihybrid Cross A

In the F₁ generation, wild-type females with brown bodies and red eyes along with males with yellow bodies and white eyes are obtained. This result was similar to Mendel's dihybrid cross experiment.

                          Fig: Possible gametes from parents of Dihybrid Cross A

There are two conclusions obtained:

• Male flies are white-eyed and yellow-bodied.
• Female flies are red-eyed and brown-bodied.

The male characters in the paternal generation are shown in the female progeny if the female is homozygous recessive and the male parent is homozygous dominant. However, the male progeny inherits the recessive characteristics of the female parent.

                                       Fig: F₁ generation in Dihybrid cross A

Next the F₁ generation was selfed to obtain the F₂ generation.

                                           Fig: Selfing the F₁ generation

Mendel’s dihybrid cross gave four different phenotypic combinations in the F₂ generation - 9 offspring with both dominant characters (Round and yellow seeds), 3 with dominant character 1 and recessive character 2 (round and green seeds), 3 with recessive character 1 and dominant character 2 (wrinkled and yellow seeds) and 1 with both recessive characters (wrinkled and green seeds). The obtained F₂ generation in Morgan’s experiment had some phenotype as expected just like Mendel obtained in F₂ generation of his dihybrid cross.

                                      Fig: Expected phenotypes of F₂ generation

But Morgan also found few unique unexpected phenotypes which Mendel had not obtained. These were - Brown bodied White eyed males and females and Yellow bodied Red eyed males and females.

                                            Fig: Unexpected phenotypes of F₂ generation

Morgan called the phenotypes similar to that of the crossed parents as the parental types and he named the unique phenotypes as non-parental types.

Morgan knew that the genes of both of the characters he chose for his study were on the same X chromosome. Mendel, on the other hand, chose characteristics with genes on distinct chromosomes.

Thus, the offspring obtained in F₂ generation are as follows -

                                          Fig: F₂ generation in Dihybrid cross A

He observed that in the F₂ generation the parental types were mainly 98.7% whereas the non-parental types were very less and that is 1.3% only.

 Fig: Percentage of parental and non-parental combination in F₂ generation in Dihybrid cross A

Morgan found that the genotype of non parental type individuals was unique and could be because of the location of the genes on the chromosome. He termed the association between two genes on the same chromosome as linkage. The possibility of the two genes being inherited jointly is described by linkage. He concluded that because of strong linkage between the genes, the non-parental varieties are too less.

Dihybrid Cross B

Let us now see the results of another cross carried out by Morgan in which he considered the wild type characters red eye (w⁺) and normal wings (m⁺) in Drosophila and the mutant characters white eye (w) and miniature wings (m). The genes for both the characters are located on the X chromosome.

                                      Fig: Characters considered for Dihybrid cross B

Thus, he crossed a wild type red eyed, normal winged male fly with a mutant white eyed, miniature winged female fly.

                                        Fig: Parents of Dihybrid cross B

The possible gametes from these parents are -

                             Fig: Possible gametes from parents of Dihybrid Cross B

The possible genotypes and phenotypes of the F₁ generation are -

                                       Fig: F₁ generation of Dihybrid Cross B

The F₂ generation was then obtained by selfing the F₁ generation. Like in dihybrid cross A, Morgan obtained some offspring with parental phenotypes and some with unique non-parental phenotypes.

                          Fig: Parental phenotypes of F₂ generation of Dihybrid Cross B

                      Fig: Non-parental phenotypes of F₂ generation of Dihybrid Cross B

Thus, the genotypic combinations of the offspring obtained in the F₂ generation are -

                                       Fig: F₂ generation in Dihybrid cross B

He observed that in the F₂ generation the parental types were mainly 62.8% whereas the non-parental types were very less and that is 37.2% only.

 Fig: Percentage of parental and non-parental combination in F₂ generation in Dihybrid cross B

Morgan proposed that the linkage between the alleles w and m is not as strong as that between the alleles y and w and hence the percentage of non-parental types was higher in the F₂ generation of dihybrid cross B.

Crossing over and Recombination

But, if genes are associated by linkage, then what causes the occurrence of the non-parental types? Morgan found that there is an occasional shuffling of alleles between the two homologous chromosomes. He coined the term crossing over to depict the exchange of alleles. It produces a new combination of alleles which are known as cross overs or recombinants. The unchanged combination of alleles are called parentals or non-crossovers.

Crossing over is a phenomenon which occurs in the prophase of meiosis, where a part of chromosome is exchanged between the non homologous chromatids of a homologous pair of chromosomes. The non-sister chromatids are called crossovers or recombinants after the exchange of segments and the chromatids which do not take part in the crossing over are called the non-recombinant or non crossover chromatids. Crossing over gives rise to a new combination of alleles and hence new linkage. It occurs at the pachytene stage of prophase I during meiotic the cell division process. Crossing over promotes the recombination of linked genes, which plays an important role in evolution.

                                                Fig: Crossing over

Mechanism of crossing over

As to how crossing over occurs, Morgan hypothesised that exchange could occur through the chiasmata which had already been observed by Jansen (1909) in chromosomes undergoing meiosis. He therefore proposed the chiasma type hypothesis for crossing over.

Morgan believed that chiasmata cause crossing over although it is now known that they are the product of crossing over. The mechanism of crossing over is also called the modern breakage reunion theory. The various steps involved are -

• The chromosomes replicate in the interphase before meiosis. However, they appear unsplit due to the presence of a nucleoprotein core between the chromatids.
• During zygotene of meiosis I, the homologous chromosomes undergo pairing or synapsis and a synaptonemal complex develops between them. At this stage, each chromosome has a duplicate sister chromatid attached but the chromatids are prominent as the chromosomes aren’t condensed enough. The pairs of homologous chromosomes are termed as bivalents at this stage.
• During the pachytene stage, further coiling of the chromosomes makes the chromatids prominent and each member in a pair of homologous chromosomes now has a sister chromatid and the pairs appear as a tetrad.

                               Fig: Pachytene of Prophase I

• Recombination nodules develop at places. These are multienzyme complexes and the chromatids break at these points.

                                                        Fig: Recombination nodule

• If the broken segments of non-sister chromatids happen to lie exactly opposite, they exchange places and get attached to their new positions. This physical exchange of segments between non-sister chromatids of a homologous pair of chromosomes is called crossing over. It leads to recombination of genes due to their reshuffling.

                                                             GIF: crossing over

Recombination

Recombination is the process of creating new allele combinations by recombining DNA molecules. Because genetic material (DNA) is exchanged between two separate chromosomes or between different portions of the same chromosome, it is also known as genetic recombination. The phenomenon of recombination is against the law of independent assortment. Both eukaryotes and prokaryotes go through this procedure. It boosts the genetic diversity of sexually reproducing organisms.

Types of recombination

The different types of recombination are as follows:

Homologous recombination

During meiosis, homologous recombination takes place between chromosomes that have similar sequences.

Non-homologous recombination

This type of recombination occurs between those chromosomes that are not similar.

Site-specific recombination

Site-specific recombination occurs between very short sequences that have a lot of similarities.

Mitotic recombination

During interphase, mitotic recombination occurs. But, mitotic recombination is detrimental and can lead to malignancies. It rises when cells are exposed to radiation.

Explanation for non-parental types

Crossing over and recombination between the non-sister chromatids of the homologous pairs chromosomes in the F₁ hybrids resulted in the formation of recombinant alleles in the gametes which resulted in the formation of non-parental types in the F₂ generation, upon self crossing.

As the linkage between the y and w alleles tested in dihybrid cross A was stronger, the frequency of crossing over was less and hence only 1.3% of the offspring produced in F₂ generation were recombinants or non-parental types.

                                Fig: Gametes produced by F₁ hybrids in dihybrid cross A

In dihybrid cross B, independent assortment could not take place because the genes were linked together. But, the linkage between the alleles w and m, which were being tested, was not as strong which resulted in more frequency of crossing over. Thus, the offspring showing parental types were 62.8% and the offsprings showing non-parental types 37.2%.

                          Fig: Gametes produced by F₁ hybrids in dihybrid cross B

Linkage

Mendel said that the assortment of one gene into the gametes is independent of the assortment of another. But the concept of linkage defies Mendel’s law of independent assortment.

Linkage is the staying together of genes and their en bloc (as a whole) inheritance from generation to generation. Bateson and Punnett identified linkage in sweet peas (Lathyrus odoratus) for the first time in 1906. Morgan's breeding efforts in the fruit fly Drosophila melanogaster were essential in proving and defining linkage. Morgan invented the term "linkage." Morgan’s experiments distinguished genes into linked and unlinked genes.

Linkage groups

They are groups of linearly arranged genes as are present over chromosomes. One linkage group occurs over one type of chromosome. The two homologous chromosomes are similar in the arrangement and number of gene loci. Therefore they have the same type of linkage group. It is known as the limitation of linkage groups. Total number of linkage groups present in an organism is equal to the number of chromosomes present in a genome or number of homologous chromosome pairs in a diploid organism.

Some examples of linkage groups are given below:

Linked genes

These genes are found on the same chromosome and do not exhibit independent assortment, but remain together and are inherited en bloc (as a whole). The progeny receives only one parental type. Recombinants are absent in linked genes.

Unlinked genes

These are the genes that occur on different chromosomes and are thus free to undergo independent assortment. Such genes after independent assortment result in the formation of 50% parental types and 50% non-parental recombinants.

Arrangement of linked genes

The linked genes are arranged in two ways:

• Cis-arrangement
• Trans-arrangement

Cis-arrangement

In cis-arrangement, the dominant alleles of both the linked genes are situated on one chromosome. On the other hand, the recessive alleles are situated on its homologous chromosome (AB/ab). In this type of arrangement, genes are said to be in a coupling state.

                                    Fig: Cis-arrangement

Trans-arrangement

Trans-arrangement is a type of arrangement in which the dominant and recessive alleles get mixed. The dominant allele of one pair (A) and the recessive allele of another pair (b) is situated on one chromosome and the recessive allele (a) of the first pair and dominant allele (B) of the second pair are situated on the other homologous chromosome (Ab/aB). In this type of arrangement, genes are said to be in a repulsive state.

                               Fig: Trans-arrangement

Factors affecting linkage

• Distance: Strength of linkage between two genes is inversely proportional to the distance between them.

Strength of linkage ∝ 1∕distance

• Age: Strength of linkage increases with age. The frequency of crossing over is reduced.
• Sex: The sex having heteromorphic chromosomes has stronger linkage than the other, e.g, male Drosophila.
• Temperature: Variation in temperature as well as rise in temperature decreases the strength of linkage.
• X-Rays: They decrease the strength of linkage and increase the frequency of crossing over.
• Chemicals: A number of different chemicals can alter the strength of linkage and the frequency of crossing over

Recombination of linked genes

The linkage is inversely proportional to the recombination.

Recombination ∝ 1∕Linkage

• The closer the genes, tighter the linkage and lesser the chance of recombination.
• The farther the genes, the less the linkage and higher the chance of recombination.

The recombination of linked genes is seen in freckles and red hair. People get freckles and red hair because the genes that regulate these characters are situated on the same chromosome. DNA is rarely split between the two genes during homologous recombination. Although homologous recombination happens frequently, the two traits are usually inherited together because the chances of the DNA coding for these two genes splitting up are extremely low. As a result, genes are frequently inherited combined.

Types of linkage

The absence or presence of non-parental combinations or new combinations can be used to classify linkage into two categories:

• Complete linkage
• Incomplete linkage

Complete linkage

Complete linkage occurs when two or more characteristics are inherited and generally appear in two or more generations in their parental or original combinations. There are no non-parental combinations generated by these genes. The genes that show these linkages are found on the same chromosome.

A pure breeding red eyed and normal winged female Drosophila (PV/PV) is crossed with a pure breeding purple eyed and vestigial winged male fly (pv/pv). F₁ generation is red eyed and normal winged showing that both these traits are dominant. The F₁ hybrid males are test crossed with purple eyed and vestigial winged females. The offspring obtained were only of two types, red eyed normal winged and purple eyed vestigial winged in the ratio 1:1. There was no crossing over indicating that the linkage in male Drosophila was complete

                                          Fig: Cross showing complete linkage

Incomplete linkage

It is the phenomenon of an occasional crossing over between two homologous chromosomes so that one or more alleles present in a linkage group are replaced by other alleles. It produces both parental and recombinant individuals. The percentage of each parental type is more than 25% while that of each recombinant type is less than 25%, that is, parental types are more than 50% and recombinant types are less than 50%.

A pure breeding red eyed and normal winged female Drosophila (PV/PV) is crossed with a pure breeding purple eyed and vestigial winged male fly (pv/pv). F₁ generation is red eyed and normal winged showing that both these traits are dominant. The F₁ hybrid females (PV/pv) are crossed with purple eyed and vestigial winged males. 90.7% offspring were found to be parental types and 9.3% were found to be non-parental or recombinant types.

The ratio comes to 9:1:1:8 while it should have been 1:1:1:1 in case of independent assortment of genes and 1:1 in case of complete linkage.

                              Fig: Cross showing incomplete linkage

Gene mapping

The technique of finding and mapping genes on chromosomes in a relative order is termed as gene mapping. It is also known as linkage mapping. The linear sequence of genes and their relative distances on a chromosome are depicted graphically. Alfred Sturtevant was the first person to build a genetic map, which was a turning point in genetics.

                                          Fig: Alfred Sturtevant

The centiMorgan (cM) or map unit (m.u) is used to measure the distance between genes. Each map unit represents a physical length of the chromosome where crossing occurs. The frequency of crossing over is directly proportional to the distance between genes.

One centiMorgan is equal to 1% recombination frequency. Due to the fact that the frequency of crossing over is related to the distance between genes. As a result, the percentage of recombination is used to reflect the relative distance between genes.

Recombination Frequency = Recombinants / Total number of offspring

Recombination Frequency% = (Recombinants / Total number of offspring) X 100

The gene mapping of a chromosome of Drosophila is as follows:

                                              Fig: Gene map of Drosophila

Practice Problems

1. In a normal Mendel dihybrid cross, the ratio between parental types and recombinants is

1. 6:10
2. 5:3
3. 3:1
4. 1:1

Solution: In a dihybrid cross between pure breeding pea plants having round and yellow seeds (RRYY) and wrinkled and green seeds (rryy), the F₁ hybrids are all round and yellow hybrids (RrYy) showing parental phenotypes. Four different types of gametes are produced by the F₁ hybrids due to independent assortment of genes: RY, Ry, rY, ry. In the F₂ generation, 16 combinations of alleles are possible and each of them is equally probable. The F₂ generation shows four different types of phenotypes. These are: Yellow round (9) and green wrinkled (1) are parental combinations. Yellow wrinkled (3) and green round (3) are recombinants. Therefore, the ratio is calculated as

(9+1):(3+3) = 10:6 which is then simplified as 5:3.

Hence, the correct option is b.

2. At which stage of meiosis I, recombination occurs?

1. Leptotene
2. Pachytene
3. Zygotene
4. Diplotene

Solution: The interchange of fragments of non-sister chromatids of homologous chromosomes happens at the pachytene stage. Recombination is the term for this process. Genes on the same chromosome have a tendency to be split during this process, especially if they are positioned far apart. Hence, the correct option is b.

3. Why did Morgan choose fruit fly as an experimental material?

1. they have a life cycle of about 10 weeks
2. single mating produces a large number of progeny flies
3. all the characteristics exhibited by flies can only be viewed under a compound microscope
4. male and female flies are indistinguishable from each other

Solution: He chose Drosophila as a model organism because of the following reasons:

• The life cycle of Drosophila is very short i.e. two weeks.
• They can easily reproduce in lab conditions by providing synthetic media and this process requires less labour.
• They produce a large number of progeny.
• The male and female sexes are different.
• They possess variations that can be visible under light microscopy.

Hence, the correct option is b.

4. Morgan's dihybrid cross in Drosophila which considered body colour and eye colour found that 98.7 percent of the progenies had parental combination flies and 1.3 percent had non-parental kinds. This suggests that the genes that determine the body and eye colour are

1. Located far on the same chromosome
2. Located very near on the same chromosome
3. Present on different chromosomes
4. Located on autosomes

Solution: The association of two genes on the same chromosome is known as linkage. The possibility of the two genes being inherited jointly is described by linkage. In the given condition, the number of Drosophila obtained in the F₂ generation contained parental types and non-parental types. The parental types were mainly 98.7% whereas the non-parental types were very less and that is 1.3% only. He concluded that because of tightly linked genes which lie very close to each other on the same chromosome, the recombination varieties are too less. Hence, the correct option is b.

FAQs

1. Linkage violates the law of independent assortment in what ways?

Answer: According to the law of independent assortment, the genes are inherited independent of each other at the time of gamete formation. But, linked genes are inherited together because they are located very close to each other.

2. How can linked genes become unlinked?

Answer: Linked genes become unlinked through a process called recombination. Recombination is the probability of separating genes on the basis of their distance from each other.

3. Does recombination occur in mitosis?

Answer: Recombination is used to repair double-stranded breakage or single-stranded gaps in chromosomes during mitosis.

4. Can recombination cause mutation?

Answer: Recombination is the source of variation but if any error occurs during meiotic recombinations, it leads to mutation.