4.3.1: Linkage and Mapping - Biology

4.3.1: Linkage and Mapping - Biology

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Learning Objectives

  • Understand that linked genes do not exhibit independent assortment because recombination will not always occur between the loci.
  • Distinguish between parental and recombinant chromosomes, gametes, and offspring, and identify them in crosses.
  • Calculate the map distance between loci given the phenotypes of offspring or predict phenotypes of offspring given the recombination frequency between loci. Use the distance to construct genetic maps based on data from two-point or three-point testcrosses.

Loci are locations of genes on chromosomes

In many genetic crosses involving one or two genes, the gene can be representing by a name or a letter. However, when considering linked genes the location of each gene and allele often needs to be represented. For example, a dihybrid BbEe can have one chromosome with both dominant alleles (BE) or one chromosome with a dominant allele for one gene and recessive allele for the other (Be for example). The locations of the genes on the chromosomes are loci. For this section, remember that is the distance between loci that influences how often homologous recombination occurs between them between meiosis.

Exercise (PageIndex{1})

In Figure (PageIndex{1}), why is a chromosome with Bb or Ee not shown as a possible arrangement?


The loci are the locations of the genes on chromosomes. The B gene must be on the same position on each homologous chromosome in pair. The B gene is not located at two positions on one chromosome.

Effect of recombination on gamete possibilities

If B and E in the above example (Figure (PageIndex{1})) were on different chromosomes, we would expect to obtain four gamete genotypes (25% each): BE, Be, bE, and be. However, if B and E in the above example were so close that recombination could never occur between them, then all types of gametes will not be observed. The left possibility BE / be could produce only gametes BE and be (50% each). The right possibility Be / bE could produce only gametes Be and bE (50% each).

Homologous recombination during meiosis I breaks and rejoins pieces of homologous chromosomes. If homologous recombination occurs between B and E then all four gametes will be possible. But at what frequency will each gamete be observed? The answer depends on how far apart they are! Recombination frequency is the percent of meioses in which homologous recombination exchanges two loci. In genetic mapping, this number expresses distance in map units (m.u.) or centiMorgans (cM) (named after geneticist Thomas Hunt Morgan).

How do geneticists know if recombination has occurred? Use a testcross. As shown in the next video, the map distance between loci B and E is determined by the number of recombinant offspring.


  • The # of recombinant offspring / total # of offspring x 100% = recombination frequency
  • Recombination frequency = map units = centiMorgan (cM)

Example (PageIndex{1})

In the above example, number of recombinant offspring was used to calculate map distance. However, the map distance can also be used to predict recombinant offspring. What percetnage of f g / f g offspring will be produced from an F g / f G and an f g / f g cross if loci F and G are 30 map units apart?


The homozygous recessive parent can only transmit an f g chromosome, so determine the percentage of f g gametes from the dihybrid parent. The parental chromosomes are F g and f G. The map distance (30 m.u.) is equal to the recombination frequency, so 30% of gametes will be recombinant, but there are two types of recombinants, so 15% will be F G and 15% will be f g. Therefore, we predict 15% of offspring will be f g / f g.

Exercise (PageIndex{1})

Two hypothetical SNPs are 4 map units apart. The allele at SNP1 can be A or T; the allele at SNP2 can be C or G. A man with genotype A G / T C and a woman with genotype A C / A C have a child. What is the probability they have a child with genotype A G / A C?


The woman gives the child an A C chromosome. (Note that recombination still occurs in the mother, but with or without recombination, the outcome is the same for these SNPs.) An A G / A C child must inherit the A G parental chromosome from the father. The map distance (4 m.u.) indicates that 4% of gametes will be recombinant. If 4% are recombinant, then 96% must be parental: 48% A C and 48% T G. Therefore, the probability of an A G / A C child is 48%.

Double crossovers

Especially for large chromosomes, multiple crossover events can occur on the same chromosome. A double crossover occurs when fragments of the chromosome are exchanged in two places. The result of a double crossover is that the two ends of the chromosome are parental, but a region between the crossovers has been "swapped" for another sister chromatid sequence; this is depicted in the video.

Three factor crosses

Distances between multiple loci can be determined using three factor testcrosses. Again, we will cross a heterozygous parent to a parent homozygous recessive for all three genes. When solving three factor test crosses, remember that in the heterozygote the dominant and recessive alleles can be on the same or different chromosomes. You will know which chromosomes are parental because they will be the most abundant offspring from the testcross. In contract, the double crossover offspring will be the least abundant, because the double crossover events between the genes of interest are more rare than single crossovers.

Note: Steps for solving a three factor cross

  • Identify the parental offspring (the most abundant).
  • Identify the double crossover offspring (the least abundant).
  • Determine which locus is in the middle (the one that "swaps places" in the double crossover).
  • Determine the recombination frequency between one locus and the middle locus.
  • Determine the recombination frequency between the other locus and the middle locus.
  • Draw the genetic map.

Note that other factors that might influence recombination and double crossovers, such as the position along the chromosome or whether recombination at one site suppresses recombination nearby. These might make the number of observed recombinants different from expected, but we will not consider these factors at this time.

Genotype: the alleles of an organism.

Phenotype: the characteristics of an organism.

Dominant allele: an allele that has the same effect on the phenotype whether it is present in the homozygous or heterozygous state.

Recessive allele: an allele that only has an effect on the phenotype when present in the homozygous state.

Codominant alleles: pairs of alleles that both affect the phenotype when present in a heterozygote.

Locus: the particular position on homologous chromosomes of a gene.

Homozygous: having two identical alleles of a gene.

Heterozygous: having two different alleles of a gene.

Carrier: an individual that has one copy of a recessive allele that causes a genetic disease in individuals that are homozygous for this allele.

Test cross: testing a suspected heterozygote by crossing it with a known homozygous recessive.

4.3.1: Linkage and Mapping - Biology

Genetic maps provide information about which chromosomes contain specific genes and precisely where the genes lie on that chromosome.

Learning Objectives

Describe the different types of genetic markers that are used in generating genetic maps of DNA

Key Takeaways

Key Points

  • Genetic mapping, often called linkage mapping, provides information about the location of a specific gene along a chromosome.
  • Gene linkage describes the phenomenon that certain genes are physically linked by being located on the same chromosome and have a tendency to be inherited together.
  • Genetic recombination involves the production of a novel set of genetic information by breaking and rejoining DNA fragments that have a great distance between them along the chromosome.
  • The construction of genetic maps is reliant on the natural process of recombination which results in the ability to identify genetic markers with variability within a population.
  • Genetic markers that can be used in generating genetic maps include restriction length polymorphisms ( RFLP ) variable number of tandem repeats (VNTRs) microsatellite polymorphisms and single nucleotide polymorphisms ( SNPs ).

Key Terms

  • polymorphism: the regular existence of two or more different genotypes within a given species or population
  • SNP: single nucleotide polymorphism is single base pair of DNA which is polymorphic with respect to a population
  • microsatellite: any of a group of polymorphic loci in DNA that consist of repeat units of just a few base pairs
  • RFLP: restriction fragment length polymorphism is a section of DNA whose length varies among individuals and which is delimited by a base which does not occur within it

Genetic Maps

The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together and, thereby, deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps.

Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant’s pollen were linked traits therefore, the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. If the recombination frequency between two genes is less than 50 percent, they are said to be linked.

Crossovers and Recombination: Crossover may occur at different locations on the chromosome. Recombination between genes A and B is more frequent than recombination between genes B and C because genes A and B are farther apart a crossover is, therefore, more likely to occur between them.

The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population.

Some genetic markers used in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms, and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced “rif-lips”) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases this is sometimes referred to as an individual’s DNA “fingerprint.” Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding DNA has no known biological function however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small thus, it is often referred to as short tandem repeats(STRs). SNPs are variations in a single nucleotide.

Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods.

The Genetic Mapping Includes Following Processes | Biology (1780 Words)

Before starting the genetic mapping of the chromosomes of a species, one has to know the exact number of chromosomes of that species and then, he has to determine the total number of genes of that species by undergoing hybridization experiments in between wild and mutant strains.

By the same hybridization techniques, it can also be easily determined that how many phenotypic traits remain always together or linked and consequently their determiners or genes during the course of inheritance. And thus, the different linkage groups of a species can be worked out.

2. Determination of Map Distance:

The intergene distance on the chromosomes cannot be measured in the customary units employed in light microscopy geneticists use an arbitrary unit to measure the map unit, to describe distances between linked genes. A map unit is equal to 1 per cent of crossovers (recombinants) that is, it represents the linear distance along the chromosome for which a recombination frequency of 1 per cent is observed.

These distances can also be expressed in Morgan units one Morgan unit represents 100 per cent crossing over. Thus, 1 per cent crossing over can also be expressed as 1 centimorgan (1 cM), 10 per cent crossing-over as 1 decimorgan and so on. The Morgan unit is named in honour of T.H. Morgan however, most geneticists prefer map units.

1. If a F1 hybrid having the genotypes Ab/aB produces 8% of cross over gametes AB and ab, then the distance between A and B is estimated to the 16 map units or centimorgan.

2. If the map distance between the gene loci B and C is 12 centimorgan, then 12% of gametes of genotypes BC/bc should be crossover types, i.e., 6% bC.

Because, each chiasma produces 50% crossover products, 50 per cent crossing over is equivalent to 50 map units or centimorgans. If the mean number of Chiasmata is known for a chromosome pair, the total length of the map for that linkage group may be predicted:

Total length = mean number of Chiasmata × 50

The percentage of crossing over between two linked genes is calculated by test crosses in which a F1 Dihybrid is crossed with a double recessive parent. Such crosses because involved crossing over at two points, so called two point test crosses.

For example, a Dihybrid having the genotype Ac/ac is test crossed with a double recessive parent (ac/ac), then among F2 test cross hybrids we may get 37% dominant genes at both gene loci (AC/ac), 37% recessive genes at both gene loci (ac/ac), 13% dominant gene at first gene locus and recessive gene at the second gene locus (Ac/ac).

The last two groups (i.e., 13% Ac/ac) and 13% aC/ac) were produced by crossover gametes (13 + 13) from the Dihybrid parent. Thus 26% of all gametes (13 + 13) were of cross over types and the distance between the loci A and C is estimated to be 26 centimorgans. Because, double crossovers usually do not occur between genes less than 5 centimorgans apart, so for genes further apart, the three point test crosses are used.

Three Point Test Cross:

A three point test cross or trihybrid test cross (involving three genes) gives us information regarding relative distances between these genes, and also shows us the linear order in which these genes should be present on chromosome. Such a three point test cross may be carried out if three points or gene loci on a chromosome pair can be identified by marker genes.

If, in addition to genes A and C indicated above, a third marker gene B is located in fairly close proximity in the same linkage group, all three markers may be used together in conducting a more precise analysis of the map distance and the relative position of the three points.

Suppose that we testcross trihybrid individuals of genotype ABC/abc and find in the progeny the following:

To find the distance A-B we must count all crossovers (both singles and doubles) that occurred in region I = 18% + 2% or = 20% or 20 map units between the loci A and B. To find the distance B-C we must again count all crossovers (both singles and doubles) that occurred in region II = 8%+2% = 10% or 10 map units between the loci B and C. The A-C distance is, therefore, 30 map units when double crossovers are detected in a three point linkage experiment and 26 map units when double crossovers are undetected in the two-point linkage experiment above.

Without the middle marker (B), double crossovers would appear as parental types and hence we underestimate the true map distance (crossover percentage). In this case the 2% double crossovers would appear with the 72% parental types, making a total 74% parental types and 26% recombinant types.

Therefore, for any three linked genes whose distances are known, the amount of detectable crossovers between the two outer markers A and C when the middle marker B is missing is (A-B crossover percentage) plus (B-C crossovers percentage) minus (2 × double crossover percentage).

3. Determination of Gene Order:

After determining the relative distances between the genes of a linkage group, it becomes easy to place genes in their proper linear order. For example, if the linear order of three genes ABC is to be determined, then these three genes may be in any one of three different orders depending upon that which gene is in the middle. For the time being we may ignore left and right end alternatives. If double crossovers do not occur, map distances may be treated as completely additive units. Now, if we suppose that the distance between the genes A-B = 12, B-C = 7, A-C = 5, we can determine the order of genes correctly in the following manner:

Case I. Let us assume that gene A is in the middle (e. g., B-A-C):

In this case because, the distances between B-C are not equitable, genes A cannot be in the middle.

Case II. Let us assume that gene B is in the middle (e. g., A-B-C):

In this case, because the distance between A-C are not equitable, therefore, gene B cannot be in the middle.

Case III. Let us assume that gene C is in the middle (e. g., A-C-B).

In this case, because the distances between A-B are equitable, therefore, gene C must be in the middle.

Thus, the relative distances and ordering of genes in a linkage group are determined in separate segments by two point test crosses or three point crosses, as the case may be.

4. Combining Map Segments:

Finally, the different segments of maps of a complete chromosome are combined to form a complete genetic map of 100 centimorgans long for a chromosome.

Example: For example, suppose we have to combine following three map segments.

We can superimpose each of these segments by aligning the genes shared in common.

Then finally we may combine the three segments into one map:

The a to d distance = (d to b) – (a to b) = 22 – 8 = 14

The a to e distance = (a to d) – (d to e) = 14 – 2 = 12

Interference and Coincidence:

In most higher organisms it has been found that one chiasma formation reduces the probability of another chiasma formation in an immediately adjacent region of the chromosome, probably because of physical inability of the chromatids to bend back upon themselves within certain minimum distances. The tendency of one crossover to interfere with the other crossover is called interference.

Thus, the proximity of one crossover to another decreases the probability of another very close by. The centromere has a similar interference effect frequency of crossing over is also reduced near the ends of the chromosome arms.

The net result of this interference in the observation of fewer double crossover types than would be expected according to map distances. The strength of interference varies in different segments of the chromosome and is usually expressed in terms of a coefficient of coincidence, or the ratio between the observed and the expected double crossovers.

Coefficient of coincidence = % observed double crossovers / % expected double crossovers

The coincidence is the complement of interference, so:

Coincidence + Interference = 1.0

When interference is complete (1.0), no double crossovers will be observed and coincidence becomes zero. When, interference decreases, coincidence increases. Coincidence values ordinarily vary between 0 and 1. Coincidence is generally quite small for short map distance. There is no interference across centromere.

For explaining interference and coincidence, we can consider the results of one of the experiment of Hutchison (1922). He reported the map distance for three genes, c(colourless aleurone), Sh (shrunken grains), and wx (waxy endosperm) of corn and observed following crossing over frequencies between these genes:

Table 37.4. Crossing over frequencies between genes c, Sh and wx of corn:

Regions Genes Percentage crossovers Map-distances (in map units)
I c-Sh 3.4 3.4 + 0.1 =3.5
II Sh-wx 18.3 18.3 + 0.1 = 18.4
Double corssover c-Sh-wx 0.1

If crossing over in region I and II were independent, we should predict 0.035 × 0.184 = 0.6 per cent double crossovers where as only 0.1 per cent was observed.

So, coincidence = 0.1/0.6 = 0.167

Linkage Maps of different Organisms:

By adopting the above mentioned techniques, geneticists have constructed the linkage or genetic maps of various organisms, such as, viruses, bacteria, fungi, tomato, barley, wheat, rice, sorghum, morning glory, garden pea, maize, Drosophila, chickens, mice man, etc. The first linkage map has been constructed for two chromosomes of Drosophila by Strutevant in 1911. The linkage or genetic mapping in maize has been done by McClintock under the leadership of R. A. Emerson.

If two or more specific human gene products and a given human chromosome are both present in the same hybrid cells, then those genes are located in the same chromosome that is, they are Syntenic.

The term synteny refers to genes that are located on the same chromosome, whether or not they show recombination linkage refers only to genetic loci that have been shown by recombination studies to be in the same chromosome. Syntenic genes may be so far apart in their chromosome that they seem to segregate independently that is, they may show as much as 50 per cent recombination as would be exhibited by non-Syntenic genes.

Linkage Group

In order to define linkage groups or specifically define linkage in biology, one has to understand that genes are located on the chromosomes. These genes can be specific markers that are located on the chromosomes. These also result in certain phenotypes i.e. physical characteristics such as long, short, round, rough, etc.

These genes, according to Mendel’s Laws of Inheritance, are typically known to assort independently of each other. But some of the phenotypes are known to be combined together as they appear in the species along with one another. This is due to the genetic linkage in which the tendency of the DNA sequences of genes is to be close together and thus leading to the inheritance of the groups of genes occurring together. These clubbed genes that are situated very close together on a chromosome are known as linkage groups.

Concept of Linkage Group

Linkage group is the group of genes that follow the concept of the genetic linkage which is a tendency of the DNA sequences of the genes which are situated very close together on the chromosome and are inherited together during the meiosis phase of the sexual mode of reproduction.

When two or more genetic markers are present physically near to each other on a chromosome and are highly unlikely to be separated on different chromatids when there is chromosomal crossover while the cell is undergoing meiosis cell division, they are said to be linked together with one another. This concept is used to define linkage in biology and answers the question - what is a linkage group?

Linkage Group in Biology

As per the concept that is used to define linkage in biology, a linkage group is the set of all genes present on a single chromosome. Because of their location, they are inherited together as a group.

Due to this, while the cell is undergoing cell division, these sets of genes that define what is a linkage group, move together as a single unit rather than moving as independent and different entities. This is in contrast to Mendel’s law of inheritance which also describes the law of independent assortment. The law of independent assortment states that the genes and their alleles representing different traits or phenotypes are passed independently of one another while moving from one generation to the next.

However, the discovery of linkage groups clarified the reason why certain traits are usually seen to be inherited together. This work provided proof of concept that genes are physical structures that are related by a unit of physical distance.

This unit of physical distance is centimorgans (cm). A distance of 1 cm is said to be the separation of two different markers per 100 meiotic product or 50 meiosis cycle. These linkage groups and linkage concepts are used to construct linkage maps that show the relative distances between two markers.

Linkage Maps and Linkage Analysis

A linkage map is also known as a genetic map. Such a map is a tabular representation of a species or experimental population which states that the position of the known genes or genetic markers is relative to each other in the terms of frequency of recombination instead of a specific physical distance along each of the chromosomes. One of the first such linkage maps to be developed was prepared using the linkage group in drosophila. A linkage map is prepared on the basis of the frequencies of the recombination event between two or more markers during the crossing over of the homologous chromosomes.

Based on the concepts that define linkage in biology, there is a method of linkage analysis that is used to search for the segments of chromosomes that usually segregate together with a specific phenotype through the generations of the same family. Linkage analysis can also be used to determine the linkage maps in cases of both the binary and quantitative traits. But there are certain limitations to the method of linkage analysis.

Although the linkage analysis has been successful in identifying genetic variants in human beings, via the different number of linkage groups in humans, that are the cause of rare disorders like Huntington’s disease, it has failed itself when it is applied for more common disorders like the heart disease and different forms of cancer. An explanation for this sort of occurrence is that the genetic mechanisms that play part in common disorders are different from the mechanisms that play a role in rare disorders.

Common Example of Linkage Groups - Sex Linkage

Sexual phenotypes or sexual characteristics are one prominent example that can be used to state linkage and linkage groups. This concept of sex linkage can explain the linkage group in human male and female and provide explanations for the characteristics to be transferred and carried as linkage groups. Sex linkage is the concept in which certain characteristics or phenotypes can be linked to one sex. The complete set of genes of the X-chromosome is carried together in both human beings and Drosophila flies while the Y-chromosomes carry only a few genes together. Hence, the linkage group in human male is relatively small as compared to the linkage group in human females.

It is well-established that the eggs of the female carry the X-chromosome and the sperm cells may carry either X-chromosome or Y-chromosome. When an egg carrying an X-chromosome is fertilized by a sperm carrying another X-chromosome a female is born, and when an egg is fertilized by the sperm carrying a Y-chromosome a male is born. Hence, in a child carrying XY chromosome pair, any phenotype or trait that is carried by the X-chromosome will be expressed unless and until a corresponding allele is present on the Y-chromosome.

Examples of sex-linked traits in males that follow the linkage group in human male are red and green colour blindness and haemophilia. This is because the phenotypes are controlled by the genes present on the X-chromosome and have a higher frequency of occurrence in males than females because of the absence of a corresponding allele on the Y-chromosome.

Watch the video: Mapping Eukaryote Chromosomes by Recombination Chapter 4 (August 2022).