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Chromosome Behavior and Gene Linkage

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Introduction and Goals

Previously we examined the relationship between gene segregation and meiosis. As you should now know, Mendel was able to infer independent assortment between different genes because they were located on different chromosomes (each of which assorts randomly during meiosis). We also mentioned that genes located on the same chromosome may segregate together because they are linked. Next, you will learn why they may, or may not, segregate together. Moreover, you will learn how the frequency at which they become unlinked can be used to construct a genetic map of each chromosome. By the end of this tutorial you should have a basic understanding of:

  • Why genes are linked
  • How genes become  separted by crossing over during prophase I
  • The stochastic nature of crossing over
  • How crossover frequency can be used to map genes
  • How meiotic recombination and independent assortment contribute to generational variation

Performance Objectives:

  • Review the events in meiosis that result in the independent assortment of genes, and the phenomenon of crossing over
  • Describe the relationship of the distance between genes on the same chromosome and the frequency of crossing over between the genes
  • Calculate the recombination frequency between linked genes based upon the frequency of offspring phenotypes
  • Use the recombination frequency between genes to map genes to a chromosome
  • Explain how the position of genes on a chromosome can affect the recombination frequency
  • Discuss how some genes may be completely linked and not assort independently

Historical Background

While at Columbia University in 1909, a young undergraduate student (Alfred Henry Sturtevant, Figure 1) took a class from Dr. Thomas H. Morgan, the famous geneticist who first described the relationship between genes and chromosomes (see Tutorial 32). Sturtevant decided to continue in this line of study due to his life-long interest in genetics. Sturtevant's interest had been fostered by his work on inheritance patterns of coat color in horses; he had spent his youth tabulating the pedigrees of his father's horses and studying the passing of color traits from one generation to the next. Sturtevant approached the distinguished professor and asked for a research position in Morgan's laboratory.

Figure 1. A.H. Sturtevant relaxing at Woods Hole in 1916. (Click image to enlarge)

Intrigued by Sturtevant's work on coat color inheritance (which he later encouraged Alfred to publish in the Biological Bulletin; c. 1910), Morgan offered Sturtevant a desk and research project, in what later became known as "Morgan's Fly Room." Morgan had recently begun working with a relatively new model system for genetic analysis, the fruit fly Drosophila melanogaster. Together with Calvin Bridges and H.J. Muller, Sturtevant became a member of Morgan's lab at a time when the focus of the lab was shifting away from the study of development and embryology in marine invertebrates to the genetics of Drosophila.

Sturtevant was fascinated by his work in the "Fly Room." Over the course of his undergraduate research he spent hours talking about inheritance with his colleagues. One night, after a lengthy discussion about a paper describing coat color inheritance in rabbits, Sturtevant deduced that genes were linked in a series. He was so energized about his idea that he stayed up late that evening constructing experiments that would later demonstrate his theory and provide the basis of linkage analysis. Sturtevant's work (as well as that of his lab mates) was a key component to the demonstration of the chromosome theory of heredity published by Morgan's group. Sturtevant continued his research as a graduate student in the lab, where he published the first genetic map of a chromosome as part of his graduate dissertation in 1913. Still, chromosome theory would not be definitively proven until after the Second World War. Sturtevant had a long career studying the genetics of fruit flies (Figure 2).

Figure 2. Sturtevant in a Drosophila room in Kerckhoff Hall at UCLA in 1949, later in his career. (Click image to enlarge)

Pairing at Prophase I

Chromosomes are linear pieces of DNA that are highly folded and compacted (DNA Packaging).  If all of the DNA strands from each of your 46 chromosomes (23 pairs) were  joined end to end, the DNA would stretch about 2 meters. Therefore, DNA molecules must be highly organized and compacted to fit into the nucleus of a single cell.


As you learned in Tutorial 3, DNA is a double-stranded molecule, containing two antiparallel strands of nucleotides arranged in the form of a double helix (Figure 3). The two strands are held together by hydrogen bonds and contain nitrogenous bases (nucleotides) paired in a complementary way that appear as "rungs" on a spiral ladder. The complementary nucleotides pair specifically, such that adenine and guanine nucleotides, the purines (A and G) pair with corresponding thymine and cytosine nucleotides, the pyrimidines (T and C); A pairs with T, and G pairs with C.  Figure 4 depicts this in two ways. The image on the left clearly shows the base-pairing rules, whereas the image on the right depicts the helical arrangement of the paired polynucleotide strands.

Homologous chromosomes have similar nucleotide sequences but they are not identical. Indeed, it is these subtle differences in nucleotide sequences that form the molecular identity of alternative alleles for a given gene. During Prophase I, homologous chromosomes pair together due to their similarity in structure, length, and gene sequence. This sets up a physical association, synapsis, that enables the exchange of genetic sequences (i.e., pieces of DNA) between homologous chromosomes through crossing over (previously discussed in Tutorial 11).

Figure 3. DNA Structure. (Click image to enlarge)

Crossing Over Produces Recombinant Chromosomes

The pairing of homologous chromosomes at Prophase I is different than the pairing that occurs between complementary strands of DNA., The DNA of nonsister chromatids becomes precisely aligned when the synaptonemal complex is formed. When the homologues pair, both a maternal copy and a paternal copy of genetic information line up against each other. While the chromosomes are in synapsis, the two homologues may swap genetic material in a process called crossing over.
This process is a source of genetic recombination and produces recombinant chromosomes (Fig. 4). That is, a piece of a maternal chromatid exchanges with a piece of the paternal chromatid on the homologous chromosome. There can be multiple crossovers between the nonsister chromatids of homologous chromosomes. Furthermore, crossover configurations can occur in any combination and can lead to different outcomes. Recall, crossing over was introduced in Tutorial 11.

Figure 4. Crossing over and recombination during meiosis. In the gametes, two chromosomes have a parental genotype (abc and ABC), while two are recombinant (ABc and abC). (Click image to enlarge)

Only two nonsister chromatids are involved in any single crossover event, and crossing over occurs at different points along the chromosome during each meiosis. Every meiotic process does not involve crossing over in the same set of genes each time, but there is at least one crossover per homologous pair. Still, when crossing over is observed in a meiotic division, up to half of the products of that division result in a recombination of DNA between the homologues, producing novel chromsomes. This recombination means the homologues are now different than the parental chromosomes, therefore, each may carry  different  genetic information.


View this animation to observe how recombinants arise from crossing over between genes on nonsister chromatids. 

Crossing Over is Random

Many factors affect crossing over,  and the position on the chromosome where crossing over will occur is unpredictable. Crossing over is a random event. While the location of the break points on the DNA sequence of the chromosomes are  fairly random, the recombination frequency is relatively constant between homologous chromosomes. (For a given chromosome, N number of  cross overs will occur, but where they will occur is random.)

The probability of crossing over between genes on a chromosome is dependent on the distances between the genes. This shouldn't surprise you because the greater the distance between two genes, the greater the chance a break will occur.

Genes that are located on the same chromosome and that tend to be inherited together are  called linked genes because the DNA sequence containing the genes is passed along as a unit during meiosis unless they are separated by crossing over. The closer together that genes  are located on a particular chromosome, the higher the probability that they will be inherited as a unit, since crossing over between two linked genes is less frequent the closer together the two genes are (genes with complete linkage are close enough together on a chromosome that they never recombine and are always inherited as a unit).

Because of this, linked genes do not follow the expected inheritance patterns predicted by Mendel's Theory of Independent Assortment when observed across several generations of crosses. For two heterozygous genes that are unlinked and undergoing independent assortment, you expect to see parental and recombinant gametes in a ratio of 1:1:1:1 (if you don’t remember why, please review Tutorial 29). 

When two genes are linked on a chromosome,crossing over between the two genes will be less common than having no crossing over, so fewer recombinant chromosomes will be produced. Under this circumstance, a ratio that deviates from the usual 1:1:1:1 will be observed, indicating that the genes are linked.  The number of parental genotypes in the gametes will be higher and the number of recombinant genotypes will be lower.

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Evidence for Linked Genes in Drosophila

Figure 5 demonstrates a test cross between flies differing in two characters: body color (b) and wing size (vg). The females are heterozygous at both genes and their phenotypes are wild type, so they display gray bodies and normal wings (b b vg vg). The males are homozygous recessive and express the mutant phenotypes for both characteristics, black bodies and vestigial wings (b b vg vg). When T.H. Morgan scored this particular experiment and classified the offspring according to phenotype, he found that the parental phenotypes were disproportionately represented among offspring. If the two characters were on different chromosomes and assorted independently, Morgan would have expected to see a ratio of recombinant phenotypes to parental phenotypes of 1:1:1:1. Yet Morgan's observation of disproportionate offspring led him to conclude that the genes for body color and wing size in Drosophila were usually transmitted together from parents to offspring because they were located on the same chromosome. Therefore, the black body color gene and the vestigial wing gene are linked. This means these genes are located close to one another on the same chromosome.

Figure 5. Crossing over accounts for recombinant phenotypes. (Click image to enlarge)

Problem 10: Exceptions to the 9:3:3:1 ratio of offspring? - Go over this question from The Biology Project Website. You may recall having seen this problem previously when you learned about dihybrid crosses, but it is particularly applicable to this tutorial.


Using Cross Over Frequencies to Map Genes

Alfred H. Sturtevant hypothesized that the frequency at which linked genes become unlinked through crossing over (recombination frequencies; calculated from experiments similar to the one in Figure 6) could be used to determine the distances between genes on a chromosome. He predicted that the farther apart two genes were on a particular chromosome, the higher the probability that crossing over would occur between them, and subsequently, a higher recombination frequency would be observed. 

Figure 6. Calculating Recombination Frequencies. (Click image to enlarge)

By considering a chromosome a linear sequence of genes, Sturtevant assigned each gene he was studying in fruit fly crosses a position on the chromosome using recombination frequencies.  Figure 7 illustrates one of Sturtevant's genetic maps, where three genes that are linked to each other (body color (b), wing size (vg) and an eye color gene called cinnabar (cn)) are positioned based on recombination frequencies determined through test crosses. This type of genetic map is called a linkage map because it portrays the sequence of genes along a chromosome, but it does not give the precise location of the genes.

To determine the distance between two genes, Sturtevant divided the number of gametes with recombinant chromosomes by the total number of gametes observed. In the figure above, the recombination frequency between cn and b is 9%, and the recombination frequency between cn and vg is 9.5%. Therefore, crossovers between cn and b, and between cn and vg, are about half as frequent as crossovers between b and vg (17%). A map that places cn between b and vg (approximately half-way) is consistent with these observations. Sturtevant expressed the distance between genes in map units. By definition, one map unit (1 m.u.) is equivalent to a 1% recombination frequency. In honor of Morgan, one map unit, or a 1% frequency, is also called one centimorgan (cM).

Figure 7. Illustration of a Genetic Map. (Click image to enlarge)

Thus, using crossover data, Sturtevant and his coworkers mapped other Drosophila genes in linear arrays at particular genetic locations. Figure 8  shows an abbreviated genetic map of chromosome II in Drosophila.

As with many rules, there are exceptions. The maximum recombination frequency that can be calculated between two genes is 49%.  Once two genes are 50 map units apart, or further, the number of recombinant offspring produced would be equal to the number of offspring with the parental pehnotypes.  These genes would appear to assort independently and may mistakenly be thought to be located on different chromosomes because they are far enough apart on their chromosome that linkage is not observed in genetic crosses. These genes are mapped by adding the recombination frequencies from crosses involving intermediate genes, and by determining the approximate distance of each gene from the intermediates. For example, in Figure 8, the genes for black body and brown eyes are move than 50 map units apart, so if you performed a test cross you would see a 1:1:1:1 ratio of phenotypes in the offspring.  However, the genes for vestigial wings and cinnabar eyes are between these two genes at a distance of less than 50 map units, and you can to crosses to determine the recombination frequency between those genes and either black body or brown eyes, allowing you to construct a linkage map.

Figure 8. Genetic Map of Chromosome II in Drosophila. (Click image to enlarge)

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This tutorial examined the consequences of gene linkage and how crossing over in meiosis can alter the segregation pattern of genes that are located on the same chromosome. During Prophase I, homologous chromosomes pair up, gene-for-gene. Occasionally this pairing leads to breakage and rejoining of regions of homologous chromosomes. In other words, portions of a maternally derived chromatid can exchange and become physically connected with regions of a paternally derived chromatid (and vice-versa). Any gene located on either side of this  break point will become unlinked. The absolute point where crossover occurs cannot be predicted with certainty (although some regions of the chromosome are more prone to this than others); however, the greater the distance that two genes are from one another on the same chromosome, the greater the likelihood that crossing over will occur between them.

If the probability for crossing over increases proportionately with the distance between two linked genes, then the frequency at which they become unlinked (due to crossovers) is an indirect measure of how far apart these genes are from one another. If you don't understand why this is so, you might find it helpful to draw a couple of cartoons of chromosomes with two hypothetical genes at different distances from one another. Draw one set with the two genes 1/2 inch apart, and the other set with them one inch apart. If, on average, a crossover occurs once every four inches, then 25% of the time the two genes located one inch apart will become unlinked. However, the two genes located 1/2 inch apart will only become unlinked 12.5% of the time.

The relationship between gene distance and recombination frequency can be used to map the relative location of a gene on a chromosome. Be sure that you understand the logic behind this process that allows geneticists to map the relative order of genes on a chromosome.



After reading this tutorial, you should have a working knowledge of the following terms:

  • complete linkage
  • genetic map
  • genetic recombination
  • linkage map
  • linked genes
  • map unit
  • nucleotide
  • recombinant chromosome
  • recombination frequency 

Case Study for Chromosome Behavior and Gene Linkage

Crossing-over in meiosis is typically described as a random event and for genes that reside on most areas of the chromosomes this is a true statement. However, it is observed that the crossing-over process becomes suppressed as one examines genes that lie progressively closer to the centromere (i.e., that region of the chromosome where sister chromatids remain attached until the onset of Anaphase II). Consider four genes in a
heterozygotic state that lie on the same chromosome prior to the onset of meiosis (as shown in Figure 9).

  • If you examine the gametes of individuals having this arrangement, would you expect to see a higher proportion of gametes with AB compared to CD? Why or why not?
  • If a cross-over takes place at the location indicated with an arrow, what are the possible gametes that can be produced?


Figure 9.  A pair of homologous chromosomes in the replicated state.  


Now that you have read this tutorial and worked through the case study, go to ANGEL and complete the tutorial practice problems to test your understanding.  Questions?  Either send your instructor a message through ANGEL or attend an online office hour (the times are posted on ANGEL).