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Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.

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Genomes. 2nd edition.

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Chapter 5Mapping Genomes

Learning outcomes

When you have read Chapter 5, you should be able to:

  • Explain why a map is an important aid to genome sequencing
  • Distinguish between the terms ‘genetic map’ and ‘physical map’
  • Describe the different types of marker used to construct genetic maps, and state how each type of marker is scored
  • Summarize the principles of inheritance as discovered by Mendel, and show how subsequent genetic research led to the development of linkage analysis
  • Explain how linkage analysis is used to construct genetic maps, giving details of how the analysis is carried out in various types of organism, including humans and bacteria
  • State the limitations of genetic mapping
  • Evaluate the strengths and weaknesses of the various methods used to construct physical maps of genomes
  • Describe how restriction mapping is carried out
  • Describe how fluorescent in situ hybridization (FISH) is used to construct a physical map, including the modifications used to increase the sensitivity of this technique
  • Explain the basis of sequence tagged site (STS) mapping, and list the various DNA sequences that can be used as STSs
  • Describe how radiation hybrids and clone libraries are used in STS mapping

The next two chapters describe the techniques and strategies used to obtain genome sequences. DNA sequencing is obviously paramount among these techniques, but sequencing has one major limitation: even with the most sophisticated technology it is rarely possible to obtain a sequence of more than about 750 bp in a single experiment. This means that the sequence of a long DNA molecule has to be constructed from a series of shorter sequences. This is done by breaking the molecule into fragments, determining the sequence of each one, and using a computer to search for overlaps and build up the master sequence (Figure 5.1). This shotgun method is the standard approach for sequencing small prokaryotic genomes, but is much more difficult with larger genomes because the required data analysis becomes disproportionately more complex as the number of fragments increases (for n fragments the number of possible overlaps is given by 2n 2 - 2n). A second problem with the shotgun method is that it can lead to errors when repetitive regions of a genome are analyzed. When a repetitive sequence is broken into fragments, many of the resulting pieces contain the same, or very similar, sequence motifs. It would be very easy to reassemble these sequences so that a portion of a repetitive region is left out, or even to connect together two quite separate pieces of the same or different chromosomes (Figure 5.2).

Figure 5.1. The shotgun approach to sequence assembly.

Figure 5.1

The shotgun approach to sequence assembly. The DNA molecule is broken into small fragments, each of which is sequenced. The master sequence is assembled by searching for overlaps between the sequences of individual fragments. In practice, an overlap of (more...)

Figure 5.2. Problems with the shotgun approach.

Figure 5.2

Problems with the shotgun approach. (A) The DNA molecule contains a tandemly repeated element made up of many copies of the sequence GATTA. When the sequences are examined, an overlap is identified between two fragments, but these are from either end (more...)

The difficulties in applying the shotgun method to a large molecule that has a significant repetitive DNA content means that this approach cannot be used on its own to sequence a eukaryotic genome. Instead, a genome map must first be generated. A genome map provides a guide for the sequencing experiments by showing the positions of genes and other distinctive features. Once a genome map is available, the sequencing phase of the project can proceed in either of two ways (Figure 5.3):

Figure 5.3. Alternative approaches to genome sequencing.

Figure 5.3

Alternative approaches to genome sequencing. A genome consisting of a linear DNA molecule of 2.5 Mb has been mapped, and the positions of eight markers (A-H) are known. On the left, the clone contig approach starts with a segment of DNA whose position (more...)

  • By the whole-genome shotgun method (Section 6.2.3), which takes the same approach as the standard shotgun procedure but uses the distinctive features on the genome map as landmarks to aid assembly of the master sequence from the huge numbers of short sequences that are obtained. Reference to the map also ensures that regions containing repetitive DNA are assembled correctly. The whole-genome shotgun approach is a rapid way of obtaining a eukaryotic genome sequence, but there are still doubts about the degree of accuracy that can be achieved.
  • By the clone contig approach (Section 6.2.2). In this method the genome is broken into manageable segments, each a few hundred kb or a few Mb in length, which are short enough to be sequenced accurately by the shotgun method. Once the sequence of a segment has been completed, it is positioned at its correct location on the map. This step-by-step approach takes longer than whole-genome shotgun sequencing, but is thought to produce a more accurate and error-free sequence.

With both approaches, the map provides the framework for carrying out the sequencing phase of the project. If the map indicates the positions of genes, then it can also be used to direct the initial part of a clone contig project to the interesting regions of a genome, so that the sequences of important genes are obtained as quickly as possible.

5.1. Genetic and Physical Maps

The convention is to divide genome mapping methods into two categories.

  • Genetic mapping is based on the use of genetic techniques to construct maps showing the positions of genes and other sequence features on a genome. Genetic techniques include cross-breeding experiments or, in the case of humans, the examination of family histories (pedigrees). Genetic mapping is described in Section 5.2.
  • Physical mapping uses molecular biology techniques to examine DNA molecules directly in order to construct maps showing the positions of sequence features, including genes. Physical mapping is described in Section 5.3.

5.2. Genetic Mapping

As with any type of map, a genetic map must show the positions of distinctive features. In a geographic map these markers are recognizable components of the landscape, such as rivers, roads and buildings. What markers can we use in a genetic landscape?

5.2.1. Genes were the first markers to be used

The first genetic maps, constructed in the early decades of the 20th century for organisms such as the fruit fly, used genes as markers. This was many years before it was understood that genes are segments of DNA molecules. Instead, genes were looked upon as abstract entities responsible for the transmission of heritable characteristics from parent to offspring. To be useful in genetic analysis, a heritable characteristic has to exist in at least two alternative forms or phenotypes, an example being tall or short stems in the pea plants originally studied by Mendel. Each phenotype is specified by a different allele of the corresponding gene. To begin with, the only genes that could be studied were those specifying phenotypes that were distinguishable by visual examination. So, for example, the first fruit-fly maps showed the positions of genes for body color, eye color, wing shape and suchlike, all of these phenotypes being visible simply by looking at the flies with a low-power microscope or the naked eye. This approach was fine in the early days but geneticists soon realized that there were only a limited number of visual phenotypes whose inheritance could be studied, and in many cases their analysis was complicated because a single phenotype could be affected by more than one gene. For example, by 1922 over 50 genes had been mapped onto the four fruit-fly chromosomes, but nine of these were for eye color; in later research, geneticists studying fruit flies had to learn to distinguish between fly eyes that were colored red, light red, vermilion, garnet, carnation, cinnabar, ruby, sepia, scarlet, pink, cardinal, claret, purple or brown. To make gene maps more comprehensive it would be necessary to find characteristics that were more distinctive and less complex than visual ones.

The answer was to use biochemistry to distinguish phenotypes. This has been particularly important with two types of organisms - microbes and humans. Microbes, such as bacteria and yeast, have very few visual characteristics so gene mapping with these organisms has to rely on biochemical phenotypes such as those listed in Table 5.1. With humans it is possible to use visual characteristics, but since the 1920s studies of human genetic variation have been based largely on biochemical phenotypes that can be scored by blood typing. These phenotypes include not only the standard blood groups such as the ABO series (Yamamoto et al., 1990), but also variants of blood serum proteins and of immunological proteins such as the human leukocyte antigens (the HLA system). A big advantage of these markers is that many of the relevant genes have multiple alleles. For example, the gene called HLA-DRB1 has at least 290 alleles and HLA-B has over 400. This is relevant because of the way in which gene mapping is carried out with humans (Section 5.2.4). Rather than setting up many breeding experiments, which is the procedure with experimental organisms such as fruit flies or mice, data on inheritance of human genes have to be gleaned by examining the phenotypes displayed by members of a single family. If all the family members have the same allele for the gene being studied then no useful information can be obtained. It is therefore necessary for the relevant marriages to have occurred, by chance, between individuals with different alleles. This is much more likely if the gene being studied has 290 rather than two alleles.

Table 5.1. Typical biochemical markers used for genetic analysis of Saccharomyces cerevisiae.

Table 5.1

Typical biochemical markers used for genetic analysis of Saccharomyces cerevisiae.

5.2.2. DNA markers for genetic mapping

Genes are very useful markers but they are by no means ideal. One problem, especially with larger genomes such as those of vertebrates and flowering plants, is that a map based entirely on genes is not very detailed. This would be true even if every gene could be mapped because, as we saw in Chapter 2, in most eukaryotic genomes the genes are widely spaced out with large gaps between them (see Figure 2.2). The problem is made worse by the fact that only a fraction of the total number of genes exist in allelic forms that can be distinguished conveniently. Gene maps are therefore not very comprehensive. We need other types of marker.

Mapped features that are not genes are called DNA markers. As with gene markers, a DNA marker must have at least two alleles to be useful. There are three types of DNA sequence feature that satisfy this requirement: restriction fragment length polymorphisms (RFLPs), simple sequence length polymorphisms (SSLPs), and single nucleotide polymorphisms (SNPs).

Restriction fragment length polymorphisms (RFLPs)

RFLPs were the first type of DNA marker to be studied. Recall that restriction enzymes cut DNA molecules at specific recognition sequences (Section 4.1.2). This sequence specificity means that treatment of a DNA molecule with a restriction enzyme should always produce the same set of fragments. This is not always the case with genomic DNA molecules because some restriction sites are polymorphic, existing as two alleles, one allele displaying the correct sequence for the restriction site and therefore being cut when the DNA is treated with the enzyme, and the second allele having a sequence alteration so the restriction site is no longer recognized. The result of the sequence alteration is that the two adjacent restriction fragments remain linked together after treatment with the enzyme, leading to a length polymorphism (Figure 5.4). This is an RFLP and its position on a genome map can be worked out by following the inheritance of its alleles, just as is done when genes are used as markers. There are thought to be about 105 RFLPs in the human genome, but of course for each RFLP there can only be two alleles (with and without the site). The value of RFLPs in human gene mapping is therefore limited by the high possibility that the RFLP being studied shows no variability among the members of an interesting family.

Figure 5.4. A restriction fragment length polymorphism (RFLP).

Figure 5.4

A restriction fragment length polymorphism (RFLP). The DNA molecule on the left has a polymorphic restriction site (marked with the asterisk) that is not present in the molecule on the right. The RFLP is revealed after treatment with the restriction enzyme (more...)

In order to score an RFLP, it is necessary to determine the size of just one or two individual restriction fragments against a background of many irrelevant fragments. This is not a trivial problem: an enzyme such as EcoRI, with a 6-bp recognition sequence, should cut approximately once every 46 = 4096 bp and so would give almost 800 000 fragments when used with human DNA. After separation by agarose gel electrophoresis (see Technical Note 2.1), these 800 000 fragments produce a smear and the RFLP cannot be distinguished. Southern hybridization, using a probe that spans the polymorphic restriction site, provides one way of visualizing the RFLP (Figure 5.5A), but nowadays PCR is more frequently used. The primers for the PCR are designed so that they anneal either side of the polymorphic site, and the RFLP is typed by treating the amplified fragment with the restriction enzyme and then running a sample in an agarose gel (Figure 5.5B).

Figure 5.5. Two methods for scoring an RFLP.

Figure 5.5

Two methods for scoring an RFLP. (A) RFLPs can be scored by Southern hybridization. The DNA is digested with the appropriate restriction enzyme and separated in an agarose gel. The smear of restriction fragments is transferred to a nylon membrane and (more...)

Simple sequence length polymorphisms (SSLPs)

SSLPs are arrays of repeat sequences that display length variations, different alleles containing different numbers of repeat units (Figure 5.6A). Unlike RFLPs, SSLPs can be multi-allelic as each SSLP can have a number of different length variants. There are two types of SSLP, both of which were described in Section 2.4.1:

Figure 5.6. SSLPs and how they are typed.

Figure 5.6

SSLPs and how they are typed. (A) Two alleles of a microsatellite SSLP. In allele 1 the motif ‘GA’ is repeated three times, and in allele 2 it is repeated five times. (B) How the SSLP could be typed by PCR. The region surrounding the SSLP (more...)

Microsatellites are more popular than minisatellites as DNA markers, for two reasons. First, minisatellites are not spread evenly around the genome but tend to be found more frequently in the telomeric regions at the ends of chromosomes. In geographic terms, this is equivalent to trying to use a map of lighthouses to find one's way around the middle of an island. Microsatellites are more conveniently spaced throughout the genome. Second, the quickest way to type a length polymorphism is by PCR (Figure 5.6B), but PCR typing is much quicker and more accurate with sequences less than 300 bp in length. Most minisatellite alleles are longer than this because the repeat units are relatively large and there tend to be many of them in a single array, so PCR products of several kb are needed to type them. Typical microsatellites consist of 10–30 copies of a repeat that is usually no longer than 4 bp in length, and so are much more amenable to analysis by PCR. There are 6.5 × 105 microsatellites in the human genome (see Table 1.3).

Single nucleotide polymorphisms (SNPs)

These are positions in a genome where some individuals have one nucleotide (e.g. a G) and others have a different nucleotide (e.g. a C) (Figure 5.7). There are vast numbers of SNPs in every genome, some of which also give rise to RFLPs, but many of which do not because the sequence in which they lie is not recognized by any restriction enzyme. In the human genome there are at least 1.42 million SNPs, only 100 000 of which result in an RFLP (SNP Group, 2001).

Figure 5.7. A single nucleotide polymorphism (SNP).

Figure 5.7

A single nucleotide polymorphism (SNP).

Although each SNP could, potentially, have four alleles (because there are four nucleotides), most exist in just two forms, so these markers suffer from the same drawback as RFLPs with regard to human genetic mapping: there is a high possibility that a SNP does not display any variability in the family that is being studied. The advantages of SNPs are their abundant numbers and the fact that they can be typed by methods that do not involve gel electrophoresis. This is important because gel electrophoresis has proved difficult to automate so any detection method that uses it will be relatively slow and labor-intensive. SNP detection is more rapid because it is based on oligonucleotide hybridization analysis. An oligonucleotide is a short single-stranded DNA molecule, usually less than 50 nucleotides in length, that is synthesized in the test tube. If the conditions are just right, then an oligonucleotide will hybridize with another DNA molecule only if the oligonucleotide forms a completely base-paired structure with the second molecule. If there is a single mismatch - a single position within the oligonucleotide that does not form a base pair - then hybridization does not occur (Figure 5.8). Oligonucleotide hybridization can therefore discriminate between the two alleles of an SNP. Various screening strategies have been devised (Mir and Southern, 2000), including DNA chip technology (Technical Note 5.1) and solution hybridization techniques.

Figure 5.8. Oligonucleotide hybridization is very specific.

Figure 5.8

Oligonucleotide hybridization is very specific. Under highly stringent hybridization conditions, a stable hybrid occurs only if the oligonucleotide is able to form a completely base-paired structure with the target DNA. If there is a single mismatch then (more...)

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Box 5.1

DNA microarrays and chips. High-density arrays of DNA molecules for parallel hybridization analyses. DNA microarrays and chips are designed to allow many hybridization experiments to be performed in parallel. Their main applications have been in the screening (more...)

  • A DNA chip is a wafer of glass or silicon, 2.0 cm2 or less in area, carrying many different oligonucleotides in a high-density array. The DNA to be tested is labeled with a fluorescent marker and pipetted onto the surface of the chip. Hybridization is detected by examining the chip with a fluorescence microscope, the positions at which the fluorescent signal is emitted indicating which oligonucleotides have hybridized with the test DNA. Many SNPs can therefore be scored in a single experiment (Wang et al., 1998; Gerhold et al., 1999).
  • Solution hybridization techniques are carried out in the wells of a microtiter tray, each well containing a different oligonucleotide, and use a detection system that can discriminate between unhybridized single-stranded DNA and the double-stranded product that results when an oligonucleotide hybridizes to the test DNA. Several systems have been developed, one of which makes use of a pair of labels comprising a fluorescent dye and a compound that quenches the fluorescent signal when brought into close proximity with the dye. The dye is attached to one end of an oligonucleotide and the quenching compound to the other end. Normally there is no fluorescence because the oligonucleotide is designed in such a way that the two ends base-pair to one another, placing the quencher next to the dye (Figure 5.9). Hybridization between oligonucleotide and test DNA disrupts this base pairing, moving the quencher away from the dye and enabling the fluorescent signal to be generated (Tyagi et al., 1998).
Figure 5.9. One way of detecting an SNP by solution hybridization.

Figure 5.9

One way of detecting an SNP by solution hybridization. The oligonucleotide probe has two end-labels. One of these is a fluorescent dye and the other is a quenching compound. The two ends of the oligonucleotide base-pair to one another, so the fluorescent (more...)

Box Icon

Box 5.1

Why do SNPs have only two alleles? Any of the four nucleotides could be present at any position in the genome, so it might be imagined that each single nucleotide polymorphism (SNP) should have four alleles. Theoretically this is possible but in practice (more...)

5.2.3. Linkage analysis is the basis of genetic mapping

Now that we have assembled a set of markers with which to construct a genetic map we can move on to look at the mapping techniques themselves. These techniques are all based on genetic linkage, which in turn derives from the seminal discoveries in genetics made in the mid 19th century by Gregor Mendel.

The principles of inheritance and the discovery of linkage

Genetic mapping is based on the principles of inheritance as first described by Gregor Mendel in 1865 (Orel, 1995). From the results of his breeding experiments with peas, Mendel concluded that each pea plant possesses two alleles for each gene, but displays only one phenotype. This is easy to understand if the plant is pure-breeding, or homozygous, for a particular characteristic, as it then possesses two identical alleles and displays the appropriate phenotype (Figure 5.10A). However, Mendel showed that if two pure-breeding plants with different phenotypes are crossed then all the progeny (the F1 generation) display the same phenotype. These F1 plants must be heterozygous, meaning that they possess two different alleles, one for each phenotype, one allele inherited from the mother and one from the father. Mendel postulated that in this heterozygous condition one allele overrides the effects of the other allele; he therefore described the phenotype expressed in the F1 plants as being dominant over the second, recessive phenotype (Figure 5.10B). This is the perfectly correct interpretation of the interaction between the pairs of alleles studied by Mendel, but we now appreciate that this simple dominant-recessive rule can be complicated by situations that he did not encounter. One of these is incomplete dominance, where the heterozygous phenotype is intermediate between the two homozygous forms. An example is when red carnations are crossed with white ones, the F1 heterozygotes being pink. Another complication is codominance, when both alleles are detectable in the heterozygote. Codominance is the typical situation for DNA markers.

Figure 5.10. Homozygosity and heterozygosity.

Figure 5.10

Homozygosity and heterozygosity. Mendel studied seven pairs of contrasting characteristics in his pea plants, one of which was violet and white flower color, as shown here. (A) Pure-breeding plants always give rise to flowers with the parental color. (more...)

As well as discovering dominance and recessiveness, Mendel carried out additional crosses that enabled him to establish two Laws of Genetics. The First Law states that alleles segregate randomly. In other words, if the parent's alleles are A and a, then a member of the F1 generation has the same chance of inheriting A as it has of inheriting a (Figure 5.11A). The Second Law is that pairs of alleles segregate independently, so that inheritance of the alleles of gene A is independent of inheritance of the alleles of gene B (Figure 5.11B). Because of these laws, the outcomes of genetic crosses are predictable (Figure 5.11C).

Figure 5.11. Mendel's Laws enable the outcome of genetic crosses to be predicted.

Figure 5.11

Mendel's Laws enable the outcome of genetic crosses to be predicted. (A) Mendel's First Law states that alleles segregate randomly. The example shows inheritance of alleles A and a in a cross involving two heterozygous parents. Each member of the F1 generation (more...)

When Mendel's work was rediscovered in 1900, his Second Law worried the early geneticists because it was soon established that genes reside on chromosomes, and it was realized that all organisms have many more genes than chromosomes. Chromosomes are inherited as intact units, so it was reasoned that the alleles of some pairs of genes will be inherited together because they are on the same chromosome (Figure 5.12). This is the principle of genetic linkage, and it was quickly shown to be correct, although the results did not turn out exactly as expected. The complete linkage that had been anticipated between many pairs of genes failed to materialize. Pairs of genes were either inherited independently, as expected for genes in different chromosomes, or, if they showed linkage, then it was only partial linkage: sometimes they were inherited together and sometimes they were not (Figure 5.13). The resolution of this contradiction between theory and observation was the critical step in the development of genetic mapping techniques.

Figure 5.12. Genes on the same chromosome should display linkage.

Figure 5.12

Genes on the same chromosome should display linkage. Genes A and B are on the same chromosome and so should be inherited together. Mendel's Second Law should therefore not apply to the inheritance of A and B, but holds for the inheritance of A and C, (more...)

Figure 5.13. Partial linkage.

Figure 5.13

Partial linkage. Partial linkage was discovered in the early 20th century. The cross shown here was carried out by Bateson, Saunders and Punnett in 1905 with sweet peas. The parental cross gives the typical dihybrid result (see Figure 5.11C), with all (more...)

Partial linkage is explained by the behavior of chromosomes during meiosis

The critical breakthrough was achieved by Thomas Hunt Morgan, who made the conceptual leap between partial linkage and the behavior of chromosomes when the nucleus of a cell divides. Cytologists in the late 19th century had distinguished two types of nuclear division: mitosis and meiosis. Mitosis is more common, being the process by which the diploid nucleus of a somatic cell divides to produce two daughter nuclei, both of which are diploid (Figure 5.14). Approximately 1017 mitoses are needed to produce all the cells required during a human lifetime. Before mitosis begins, each chromosome in the nucleus is replicated, but the resulting daughter chromosomes do not immediately break away from one another. To begin with they remain attached at their centromeres and by cohesin proteins which act as ‘molecular glue’ holding together the arms of the replicated chromosomes (see Figure 13.23). The daughters do not separate until later in mitosis when the chromosomes are distributed between the two new nuclei. Obviously it is important that each of the new nuclei receives a complete set of chromosomes, and most of the intricacies of mitosis appear to be devoted to achieving this end.

Figure 5.14. Mitosis.

Figure 5.14

Mitosis. During interphase (the period between nuclear divisions) the chromosomes are in their extended form (Section 2.2.1). At the start of mitosis the chromosomes condense and by late prophase have formed structures that are visible with the light (more...)

Mitosis illustrates the basic events occurring during nuclear division but is not directly relevant to genetic mapping. Instead, it is the distinctive features of meiosis that interest us. Meiosis occurs only in reproductive cells, and results in a diploid cell giving rise to four haploid gametes, each of which can subsequently fuse with a gamete of the opposite sex during sexual reproduction. The fact that meiosis results in four haploid cells whereas mitosis gives rise to two diploid cells is easy to explain: meiosis involves two nuclear divisions, one after the other, whereas mitosis is just a single nuclear division. This is an important distinction, but the critical difference between mitosis and meiosis is more subtle. Recall that in a diploid cell there are two separate copies of each chromosome (Chapter 1). We refer to these as pairs of homologous chromosomes. During mitosis, homologous chromosomes remain separate from one another, each member of the pair replicating and being passed to a daughter nucleus independently of its homolog. In meiosis, however, the pairs of homologous chromosomes are by no means independent. During meiosis I, each chromosome lines up with its homolog to form a bivalent (Figure 5.15). This occurs after each chromosome has replicated, but before the replicated structures split, so the bivalent in fact contains four chromosome copies, each of which is destined to find its way into one of the four gametes that will be produced at the end of the meiosis. Within the bivalent, the chromosome arms (the chromatids) can undergo physical breakage and exchange of segments of DNA. The process is called crossing-over or recombination and was discovered by the Belgian cytologist Janssens in 1909. This was just 2 years before Morgan started to think about partial linkage.

Figure 5.15. Meiosis.

Figure 5.15

Meiosis. The events involving one pair of homologous chromosomes are shown; one member of the pair is red, the other is blue. At the start of meiosis the chromosomes condense and each homologous pair lines up to form a bivalent. Within the bivalent, crossing-over (more...)

How did the discovery of crossing-over help Morgan explain partial linkage? To understand this we need to think about the effect that crossing-over can have on the inheritance of genes. Let us consider two genes, each of which has two alleles. We will call the first gene A and its alleles A and a, and the second gene B with alleles B and b. Imagine that the two genes are located on chromosome number 2 of Drosophila melanogaster, the species of fruit fly studied by Morgan. We are going to follow the meiosis of a diploid nucleus in which one copy of chromosome 2 has alleles A and B, and the second has a and b. This situation is illustrated in Figure 5.16. Consider the two alternative scenarios:

Figure 5.16. The effect of a crossover on linked genes.

Figure 5.16

The effect of a crossover on linked genes. The drawing shows a pair of homologous chromosomes, one red and the other blue. A and B are linked genes with alleles A, a, B and b. On the left is a meiosis with no crossover between A and B: two of the resulting (more...)


A crossover does not occur between genes A and B. If this is what happens then two of the resulting gametes will contain chromosome copies with alleles A and B, and the other two will contain a and b. In other words, two of the gametes have the genotype AB and two have the genotype ab.


A crossover does occur between genes A and B. This leads to segments of DNA containing gene B being exchanged between homologous chromosomes. The eventual result is that each gamete has a different genotype: 1 AB, 1 aB, 1 Ab, 1 ab.

Now think about what would happen if we looked at the results of meiosis in a hundred identical cells. If crossovers never occur then the resulting gametes will have the following genotypes:

Image ch5e1.jpg

This is complete linkage: genes A and B behave as a single unit during meiosis. But if (as is more likely) crossovers occur between A and B in some of the nuclei, then the allele pairs will not be inherited as single units. Let us say that crossovers occur during 40 of the 100 meioses. The following gametes will result:

Image ch5e2.jpg

The linkage is not complete, it is only partial. As well as the two parental genotypes (AB, ab) we see gametes with recombinant genotypes (Ab, aB).

From partial linkage to genetic mapping

Once Morgan had understood how partial linkage could be explained by crossing-over during meiosis he was able to devise a way of mapping the relative positions of genes on a chromosome. In fact the most important work was done not by Morgan himself, but by an undergraduate in his laboratory, Arthur Sturtevant (Sturtevant, 1913). Sturtevant assumed that crossing-over was a random event, there being an equal chance of it occurring at any position along a pair of lined-up chromatids. If this assumption is correct then two genes that are close together will be separated by crossovers less frequently than two genes that are more distant from one another. Furthermore, the frequency with which the genes are unlinked by crossovers will be directly proportional to how far apart they are on their chromosome. The recombination frequency is therefore a measure of the distance between two genes. If you work out the recombination frequencies for different pairs of genes, you can construct a map of their relative positions on the chromosome (Figure 5.17).

Figure 5.17. Working out a genetic map from recombination frequencies.

Figure 5.17

Working out a genetic map from recombination frequencies. The example is taken from the original experiments carried out with fruit flies by Arthur Sturtevant. All four genes are on the X chromosome of the fruit fly. Recombination frequencies between (more...)

It turns out that Sturtevant's assumption about the randomness of crossovers was not entirely justified. Comparisons between genetic maps and the actual positions of genes on DNA molecules, as revealed by physical mapping and DNA sequencing, have shown that some regions of chromosomes, called recombination hotspots, are more likely to be involved in crossovers than others. This means that a genetic map distance does not necessarily indicate the physical distance between two markers (see Figure 5.22). Also, we now realize that a single chromatid can participate in more than one crossover at the same time, but that there are limitations on how close together these crossovers can be, leading to more inaccuracies in the mapping procedure. Despite these qualifications, linkage analysis usually makes correct deductions about gene order, and distance estimates are sufficiently accurate to generate genetic maps that are of value as frameworks for genome sequencing projects.

Figure 5.22. Comparison between the genetic and physical maps of Saccharomyces cerevisiae chromosome III.

Figure 5.22

Comparison between the genetic and physical maps of Saccharomyces cerevisiae chromosome III. The comparison shows the discrepancies between the genetic and physical maps, the latter determined by DNA sequencing. Note that the order of the upper two markers (more...)

5.2.4. Linkage analysis with different types of organism

To see how linkage analysis is actually carried out, we need to consider three quite different situations:

  • Linkage analysis with species such as fruit flies and mice, with which we can carry out planned breeding experiments;
  • Linkage analysis with humans, with whom we cannot carry out planned experiments but instead make use of family pedigrees;
  • Linkage analysis with bacteria, which do not undergo meiosis.

Linkage analysis when planned breeding experiments are possible

The first type of linkage analysis is the modern counterpart of the method developed by Morgan and his colleagues. The method is based on analysis of the progeny of experimental crosses set up between parents of known genotypes and is, at least in theory, applicable to all eukaryotes. Ethical considerations preclude this approach in humans, and practical problems such as the length of the gestation period and the time taken for the newborn to reach maturity (and hence to participate in subsequent crosses) limit the effectiveness of the method with some animals and plants.

If we return to Figure 5.16 we see that the key to gene mapping is being able to determine the genotypes of the gametes resulting from meiosis. In a few situations this is possible by directly examining the gametes. For example, the gametes produced by some microbial eukaryotes, including the yeast Saccharomyces cerevisiae, can be grown into colonies of haploid cells, whose genotypes can be determined by biochemical tests. Direct genotyping of gametes is also possible with higher eukaryotes if DNA markers are used, as PCR can be carried out with the DNA from individual spermatozoa, enabling RFLPs, SSLPs and SNPs to be typed. Unfortunately, sperm typing is laborious. Routine linkage analysis with higher eukaryotes is therefore carried out not by examining the gametes directly but by determining the genotypes of the diploid progeny that result from fusion of two gametes, one from each of a pair of parents. In other words, a genetic cross is performed.

The complication with a genetic cross is that the resulting diploid progeny are the product not of one meiosis but of two (one in each parent), and in most organisms crossover events are equally likely to occur during production of the male and female gametes. Somehow we have to be able to disentangle from the genotypes of the diploid progeny the crossover events that occurred in each of these two meioses. This means that the cross has to be set up with care. The standard procedure is to use a test cross. This is illustrated in Figure 5.18, Scenario 1, where we have set up a test cross to map the two genes we met earlier: gene A (alleles A and a) and gene B (alleles B and b), both on chromosome 2 of the fruit fly. The critical feature of a test cross is the genotypes of the two parents:

Figure 5.18. Two examples of the test cross.

Figure 5.18

Two examples of the test cross. In Scenario 1, A and B are genetic markers with alleles A, a, B and b. The resulting progeny are scored by examining their phenotypes. Because the double homozygous parent (Parent 2) has both recessive alleles - a and (more...)

  • One parent is a double heterozygote. This means that all four alleles are present in this parent: its genotype is AB/ab. This notation indicates that one pair of the homologous chromosomes has alleles A and B, and the other has a and b. Double heterozygotes can be obtained by crossing two pure-breeding strains, for example AB/AB × ab/ab.
  • The second parent is a pure-breeding double homozygote. In this parent both homologous copies of chromosome 2 are the same: in the example shown in Scenario 1 both have alleles a and b and the genotype of the parent is ab/ab.

The double heterozygote has the same genotype as the cell whose meiosis we followed in Figure 5.16. Our objective is therefore to infer the genotypes of the gametes produced by this parent and to calculate the fraction that are recombinants. Note that all the gametes produced by the second parent (the double homozygote) will have the genotype ab regardless of whether they are parental or recombinant gametes. Alleles a and b are both recessive, so meiosis in this parent is, in effect, invisible when the genotypes of the progeny are examined. This means that, as shown in Scenario 1 in Figure 5.18, the genotypes of the diploid progeny can be unambiguously converted into the genotypes of the gametes from the double heterozygous parent. The test cross therefore enables us to make a direct examination of a single meiosis and hence to calculate a recombination frequency and map distance for the two genes being studied.

Just one additional point needs to be considered. If, as in Scenario 1 in Figure 5.18, gene markers displaying dominance and recessiveness are used, then the double homozygous parent must have alleles for the two recessive phenotypes; however, if codominant DNA markers are used, then the double homozygous parent can have any combination of homozygous alleles (i.e. AB/AB, Ab/Ab, aB/aB and ab/ab). Scenario 2 in Figure 5.18 shows the reason for this.

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Box 5.2

Multipoint crosses. The power of linkage analysis is enhanced if more than two markers are followed in a single cross. Not only does this generate recombination frequencies more quickly, but it also enables the relative order of markers on a chromosome (more...)

Gene mapping by human pedigree analysis

With humans it is of course impossible to pre-select the genotypes of parents and set up crosses designed specifically for mapping purposes. Instead, data for the calculation of recombination frequencies have to be obtained by examining the genotypes of the members of successive generations of existing families. This means that only limited data are available, and their interpretation is often difficult because a human marriage rarely results in a convenient test cross, and often the genotypes of one or more family members are unobtainable because those individuals are dead or unwilling to cooperate.

The problems are illustrated by Figure 5.19. In this example we are studying a genetic disease present in a family of two parents and six children. Genetic diseases are frequently used as gene markers in humans, the disease state being one allele and the healthy state being a second allele. The pedigree in Figure 5.19A shows us that the mother is affected by the disease, as are four of her children. We know from family accounts that the maternal grandmother also suffered from this disease, but both she and her husband - the maternal grandfather - are now dead. We can include them in the pedigree, with slashes indicating that they are dead, but we cannot obtain any further information on their genotypes. Our aim is to map the position of the gene for the genetic disease. For this purpose we are studying its linkage to a microsatellite marker M, four alleles of which - M1, M2, M3 and M4 - are present in the living family members. The question is, how many of the children are recombinants?

Figure 5.19. An example of human pedigree analysis.

Figure 5.19

An example of human pedigree analysis. (A) The pedigree shows inheritance of a genetic disease in a family of two living parents and six children, with information about the maternal grandparents available from family records. The disease allele (closed (more...)

If we look at the genotypes of the six children we see that numbers 1, 3 and 4 have the disease allele and the microsatellite allele M1. Numbers 2 and 5 have the healthy allele and M2. We can therefore construct two alternative hypotheses. The first is that the two copies of the relevant homologous chromosomes in the mother have the genotypes Disease-M1 and Healthy-M2; therefore children 1, 2, 3, 4 and 5 have parental genotypes and child 6 is the one and only recombinant (Figure 5.19B). This would suggest that the disease gene and the microsatellite are relatively closely linked and that crossovers between them occur infrequently. The alternative hypothesis is that the mother's chromosomes have the genotypes Healthy-M1 and Disease-M2; this would mean that children 1–5 are recombinants, and child 6 has the parental genotype. This would mean that the gene and microsatellite are relatively far apart on the chromosome. We cannot determine which of these hypotheses is correct: the data are frustratingly ambiguous.

The most satisfying solution to the problem posed by the pedigree in Figure 5.19 would be to know the genotype of the grandmother. Let us pretend that this is a soap opera family and that the grandmother is not really dead. To everyone's surprise she reappears just in time to save the declining audience ratings. Her genotype for microsatellite M turns out to be M1M5 (Figure 5.19C). This tells us that the disease allele is on the same chromosome as M1. We can therefore conclude with certainty that Hypothesis 1 is correct and that only child 6 is a recombinant.

Resurrection of key individuals is not usually an option open to real-life geneticists, although DNA can be obtained from old pathology specimens such as slides and Guthrie cards. Imperfect pedigrees are analyzed statistically, using a measure called the lod score (Morton, 1955). This stands for logarithm of the odds that the genes are linked and is used primarily to determine if the two markers being studied lie on the same chromosome, in other words if the genes are linked or not. If the lod analysis establishes linkage then it can also provide a measure of the most likely recombination frequency. Ideally the available data will derive from more than one pedigree, increasing the confidence in the result. The analysis is less ambiguous for families with larger numbers of children, and, as we saw in Figure 5.19, it is important that the members of at least three generations can be genotyped. For this reason, family collections have been established, such as the one maintained by the Centre d'Études du Polymorphisme Humaine (CEPH) in Paris (Dausset et al., 1990). The CEPH collection contains cultured cell lines from families in which all four grandparents as well as at least eight second-generation children could be sampled. This collection is available for DNA marker mapping by any researcher who agrees to submit the resulting data to the central CEPH database.

Genetic mapping in bacteria

The final type of genetic mapping that we must consider is the strategy used with bacteria. The main difficulty that geneticists faced when trying to develop genetic mapping techniques for bacteria is that these organisms are normally haploid, and so do not undergo meiosis. Some other way therefore had to be devised to induce crossovers between homologous segments of bacterial DNA. The answer was to make use of three natural methods that exist for transferring pieces of DNA from one bacterium to another (Figure 5.20):

Figure 5.20. Three ways of achieving DNA transfer between bacteria.

Figure 5.20

Three ways of achieving DNA transfer between bacteria. (A) Conjugation can result in transfer of chromosomal or plasmid DNA from the donor bacterium to the recipient. Conjugation involves physical contact between the two bacteria, with transfer thought (more...)

  • In conjugation two bacteria come into physical contact and one bacterium (the donor) transfers DNA to the second bacterium (the recipient). The transferred DNA can be a copy of some or possibly all of the donor cell's chromosome, or it could be a segment of chromosomal DNA - up to 1 Mb in length - integrated in a plasmid (Section 2.1.2). The latter is called episome transfer.
  • Transduction involves transfer of a small segment of DNA - up to 50 kb or so - from donor to recipient via a bacteriophage.
  • In transformation the recipient cell takes up from its environment a fragment of DNA, rarely longer than 50 kb, released from a donor cell.

After transfer, a double crossover must occur so that the DNA from the donor bacterium is integrated into the recipient cell's chromosome (Figure 5.21A). If this does not occur then the transferred DNA is lost when the recipient cell divides. The only exception is after episome transfer, plasmids being able to propagate independently of the host chromosome.

Figure 5.21. The basis of gene mapping in bacteria.

Figure 5.21

The basis of gene mapping in bacteria. (A) Transfer of a functional gene for tryptophan biosynthesis from a wild-type bacterium (genotype described as trp +) to a recipient that lacks a functional copy of this gene (trp -). The recipient is called a tryptophan (more...)

Biochemical markers are invariably used, the dominant or wild-type phenotype being possession of a biochemical characteristic (e.g. ability to synthesize tryptophan) and the recessive phenotype being the complementary characteristic (e.g. inability to synthesize tryptophan). The gene transfer is usually set up between a donor strain that possesses the wild-type alleles and a recipient with the recessive alleles, transfer into the recipient strain being monitored by looking for acquisition of the biochemical function(s) specified by the genes being studied. The precise details of the mapping procedure depend on the type of gene transfer that is being used. In conjugation mapping the donor DNA is transferred as a continuous thread into the recipient, and gene positions are mapped by timing the entry of the wild-type alleles into the recipient (Figure 5.21B). Transduction and transformation mapping enable genes that are relatively close together to be mapped, because the transferred DNA segment is short (< 50 kb), so the probability of two genes being transferred together depends on how close together they are on the bacterial chromosome (Figure 5.21C).

5.3. Physical Mapping

A map generated by genetic techniques is rarely sufficient for directing the sequencing phase of a genome project. This is for two reasons:

  • The resolution of a genetic map depends on the number of crossovers that have been scored . This is not a major problem for microorganisms because these can be obtained in huge numbers, enabling many crossovers to be studied, resulting in a highly detailed genetic map in which the markers are just a few kb apart. For example, when the Escherichia coli genome sequencing project began in 1990, the latest genetic map for this organism comprised over 1400 markers, an average of one per 3.3 kb. This was sufficiently detailed to direct the sequencing program without the need for extensive physical mapping. Similarly, the Saccharomyces cerevisiae project was supported by a fine-scale genetic map (approximately 1150 genetic markers, on average one per 10 kb). The problem with humans and most other eukaryotes is that it is simply not possible to obtain large numbers of progeny, so relatively few meioses can be studied and the resolving power of linkage analysis is restricted. This means that genes that are several tens of kb apart may appear at the same position on the genetic map.
  • Genetic maps have limited accuracy . We touched on this point in Section 5.2.3 when we assessed Sturtevant's assumption that crossovers occur at random along chromosomes. This assumption is only partly correct because the presence of recombination hotspots means that crossovers are more likely to occur at some points rather than at others. The effect that this can have on the accuracy of a genetic map was illustrated in 1992 when the complete sequence for S. cerevisiae chromosome III was published (Oliver et al., 1992), enabling the first direct comparison to be made between a genetic map and the actual positions of markers as shown by DNA sequencing (Figure 5.22). There were considerable discrepancies, even to the extent that one pair of genes had been ordered incorrectly by genetic analysis. Bear in mind that S. cerevisiae is one of the two eukaryotes (fruit fly is the second) whose genomes have been subjected to intensive genetic mapping. If the yeast genetic map is inaccurate then how precise are the genetic maps of organisms subjected to less detailed analysis?

These two limitations of genetic mapping mean that for most eukaryotes a genetic map must be checked and supplemented by alternative mapping procedures before large-scale DNA sequencing begins. A plethora of physical mapping techniques has been developed to address this problem, the most important being:

  • Restriction mapping, which locates the relative positions on a DNA molecule of the recognition sequences for restriction endonucleases;
  • Fluorescent in situ hybridization (FISH), in which marker locations are mapped by hybridizing a probe containing the marker to intact chromosomes;
  • Sequence tagged site (STS) mapping, in which the positions of short sequences are mapped by PCR and/or hybridization analysis of genome fragments.

5.3.1. Restriction mapping

Genetic mapping using RFLPs as DNA markers can locate the positions of polymorphic restriction sites within a genome (Section 5.2.2), but very few of the restriction sites in a genome are polymorphic, so many sites are not mapped by this technique (Figure 5.23). Could we increase the marker density on a genome map by using an alternative method to locate the positions of some of the non-polymorphic restriction sites? This is what restriction mapping achieves, although in practice the technique has limitations which mean that it is applicable only to relatively small DNA molecules. We will look first at the technique and then consider its relevance to genome mapping.

Figure 5.23. Not all restriction sites are polymorphic.

Figure 5.23

Not all restriction sites are polymorphic.

The basic methodology for restriction mapping

The simplest way to construct a restriction map is to compare the fragment sizes produced when a DNA molecule is digested with two different restriction enzymes that recognize different target sequences. An example using the restriction enzymes EcoRI and BamHI is shown in Figure 5.24. First, the DNA molecule is digested with just one of the enzymes and the sizes of the resulting fragments are measured by agarose gel electrophoresis. Next, the molecule is digested with the second enzyme and the resulting fragments again sized in an agarose gel. The results so far enable the number of restriction sites for each enzyme to be worked out, but do not allow their relative positions to be determined. Additional information is therefore obtained by cutting the DNA molecule with both enzymes together. In the example shown in Figure 5.24, this double restriction enables three of the sites to be mapped. However, a problem arises with the larger EcoRI fragment because this contains two BamHI sites and there are two alternative possibilities for the map location of the outer one of these. The problem is solved by going back to the original DNA molecule and treating it again with BamHI on its own, but this time preventing the digestion from going to completion by, for example, incubating the reaction for only a short time or using a suboptimal incubation temperature. This is called a partial restriction and leads to a more complex set of products, the complete restriction products now being supplemented with partially restricted fragments that still contain one or more uncut BamHI sites. In the example shown in Figure 5.24, the size of one of the partial restriction fragments is diagnostic and the correct map can be identified.

Figure 5.24. Restriction mapping.

Figure 5.24

Restriction mapping. The objective is to map the EcoRI (E) and BamHI (B) sites in a linear DNA molecule of 4.9 kb. The results of single and double restrictions are shown at the top. The sizes of the fragments given after double restriction enable two (more...)

A partial restriction usually gives the information needed to complete a map, but if there are many restriction sites then this type of analysis becomes unwieldy, simply because there are so many different fragments to consider. An alternative strategy is simpler because it enables the majority of the fragments to be ignored. This is achieved by attaching a radioactive or other type of marker to each end of the starting DNA molecule before carrying out the partial digestion. The result is that many of the partial restriction products become ‘invisible’ because they do not contain an end-fragment and so do not show up when the agarose gel is screened for labeled products. The sizes of the partial restriction products that are visible enable unmapped sites to be positioned relative to the ends of the starting molecule.

The scale of restriction mapping is limited by the sizes of the restriction fragments

Restriction maps are easy to generate if there are relatively few cut sites for the enzymes being used. However, as the number of cut sites increases, so also do the numbers of single, double and partial restriction products whose sizes must be determined and compared in order for the map to be constructed. Computer analysis can be brought into play but problems still eventually arise. A stage will be reached when a digest contains so many fragments that individual bands merge on the agarose gel, increasing the chances of one or more fragments being measured incorrectly or missed out entirely. If several fragments have similar sizes then even if they can all be identified, it may not be possible to assemble them into an unambiguous map.

Restriction mapping is therefore more applicable to small rather than large molecules, with the upper limit for the technique depending on the frequency of the restriction sites in the molecule being mapped. In practice, if a DNA molecule is less than 50 kb in length it is usually possible to construct an unambiguous restriction map for a selection of enzymes with six-nucleotide recognition sequences. Fifty kb is of course way below the minimum size for bacterial or eukaryotic chromosomes, although it does cover a few viral and organelle genomes, and whole-genome restriction maps have indeed been important in directing sequencing projects with these small molecules. Restriction maps are equally useful after bacterial or eukaryotic genomic DNA has been cloned, if the cloned fragments are less than 50 kb, because a detailed restriction map can then be built up as a preliminary to sequencing the cloned region. This is an important application of restriction mapping in sequencing projects with large genomes, but is there any possibility of using restriction analysis for the more general mapping of entire genomes larger than 50 kb?

The answer is a qualified ‘yes’, because the limitations of restriction mapping can be eased slightly by choosing enzymes expected to have infrequent cut sites in the target DNA molecule. These ‘rare cutters’ fall into two categories:

  • Enzymes with seven- or eight-nucleotide recognition sequences . A few restriction enzymes cut at seven- or eight-nucleotide recognition sequences. Examples are SapI (5′-GCTCTTC-3′) and SgfI (5′-GCGATCGC-3′). The seven-nucleotide enzymes would be expected, on average, to cut a DNA molecule with a GC content of 50% once every 47 = 16 384 bp. The eight-nucleotide enzymes should cut once every 48 = 65 536 bp. These figures compare with 46 = 4096 bp for six-nucleotide enzymes such as BamHI and EcoRI. Seven- and eight-nucleotide cutters are often used in restriction mapping of large molecules but the approach is not as useful as it might be simply because not many of these enzymes are known.
  • Enzymes whose recognition sequences contain motifs that are rare in the target DNA . Genomic DNA molecules do not have random sequences and some are significantly deficient in certain motifs. For example, the sequence 5′-CG-3′ is rare in human DNA because human cells possess an enzyme that adds a methyl group to carbon 5 of the C nucleotide in this sequence. The resulting 5-methylcytosine is unstable and tends to undergo deamination to give thymine (Figure 5.25). The consequence is that during human evolution many of the 5′-CG-3′ sequences that were originally in our genome have become converted to 5′-TG-3′. Restriction enzymes that recognize a site containing 5′-CG-3′ therefore cut human DNA relatively infrequently. Examples are SmaI (5′-CCCGGG-3′), which cuts human DNA on average once every 78 kb, and BssHII (5′-GCGCGC-3′) which cuts once every 390 kb. Note that NotI, an eight-nucleotide cutter, also targets 5′-CG-3′ sequences (recognition sequence 5′-GCGGCCGC-3′) and cuts human DNA very rarely - approximately once every 10 Mb.
Figure 5.25. The sequence 5′-CG-3′ is rare in human DNA because of methylation of the C, followed by deamination to give T.

Figure 5.25

The sequence 5′-CG-3′ is rare in human DNA because of methylation of the C, followed by deamination to give T.

The potential of restriction mapping is therefore increased by using rare cutters. It is still not possible to construct restriction maps of the genomes of animals and plants, but it is feasible to use the technique with large cloned fragments, and the smaller DNA molecules of prokaryotes and lower eukaryotes such as yeast and fungi.

If a rare cutter is used then it may be necessary to employ a special type of agarose gel electrophoresis to study the resulting restriction fragments. This is because the relationship between the length of a DNA molecule and its migration rate in an electrophoresis gel is not linear, the resolution decreasing as the molecules get longer (Figure 5.26A). This means that it is not possible to separate molecules more than about 50 kb in length because all of these longer molecules run as a single slowly migrating band in a standard agarose gel. To separate them it is necessary to replace the linear electric field used in conventional gel electrophoresis with a more complex field. An example is provided by orthogonal field alternation gel electrophoresis (OFAGE), in which the electric field alternates between two pairs of electrodes, each positioned at an angle of 45° to the length of the gel (Figure 5.26B). The DNA molecules still move down through the gel, but each change in the field forces the molecules to realign. Shorter molecules realign more quickly than longer ones and so migrate more rapidly through the gel. The overall result is that molecules much longer than those separated by conventional gel electrophoresis can be resolved. Related techniques include CHEF (contour clamped homogeneous electric fields) and FIGE (field inversion gel electrophoresis).

Figure 5.26. Conventional and non-conventional agarose gel electrophoresis.

Figure 5.26

Conventional and non-conventional agarose gel electrophoresis. (A) In standard agarose gel electrophoresis the electrodes are placed at either end of the gel and the DNA molecules migrate directly towards the positive electrode. Molecules longer than (more...)

Direct examination of DNA molecules for restriction sites

It is also possible to use methods other than electrophoresis to map restriction sites in DNA molecules. With the technique called optical mapping (Schwartz et al., 1993), restriction sites are directly located by looking at the cut DNA molecules with a microscope (Figure 5.27). The DNA must first be attached to a glass slide in such a way that the individual molecules become stretched out, rather than clumped together in a mass. There are two ways of doing this: gel stretching and molecular combing. To prepare gel-stretched DNA fibers (Schwartz et al., 1993), chromosomal DNA is suspended in molten agarose and placed on a microscope slide. As the gel cools and solidifies, the DNA molecules become extended (Figure 5.28A). To utilize gel stretching in optical mapping, the microscope slide onto which the molten agarose is placed is first coated with a restriction enzyme. The enzyme is inactive at this stage because there are no magnesium ions, which the enzyme needs in order to function. Once the gel has solidified it is washed with a solution containing magnesium chloride, which activates the restriction enzyme. A fluorescent dye is added, such as DAPI (4,6-diamino-2-phenylindole dihydrochloride), which stains the DNA so that the fibers can be seen when the slide is examined with a high-power fluorescence microscope. The restriction sites in the extended molecules gradually become gaps as the degree of fiber extension is reduced by the natural springiness of the DNA, enabling the relative positions of the cuts to be recorded.

Figure 5.27. Optical mapping.

Figure 5.27

Optical mapping. The image shows a 2.4-Mb segment of the Deinococcus radiodurans genome after treatment with the restriction endonuclease NheI. The positions of the cut sites are visible as gaps in the white strand of DNA. Reprinted with permission from (more...)

Figure 5.28. Gel stretching and molecular combing.

Figure 5.28

Gel stretching and molecular combing. (A) To carry out gel stretching, molten agarose containing chromosomal DNA molecules is pipetted onto a microscope slide coated with a restriction enzyme. As the gel solidifies, the DNA molecules become stretched. (more...)

In molecular combing (Michalet et al., 1997), the DNA fibers are prepared by dipping a silicone-coated cover slip into a solution of DNA, leaving it for 5 minutes (during which time the DNA molecules attach to the cover slip by their ends), and then removing the slip at a constant speed of 0.3 mm s-1 (Figure 5.28B). The force required to pull the DNA molecules through the meniscus causes them to line up. Once in the air, the surface of the cover slip dries, retaining the DNA molecules as an array of parallel fibers.

Optical mapping was first applied to large DNA fragments cloned in YAC and BAC vectors (Section 4.2.1). More recently, the feasibility of using this technique with genomic DNA has been proven with studies of a 1-Mb chromosome of the malaria parasite Plasmodium falciparum (Jing et al., 1999), and the two chromosomes and single megaplasmid of the bacterium Deinococcus radiodurans (Lin et al., 1999; see Table 2.9).

5.3.2. Fluorescent in situ hybridization (FISH)

The optical mapping method described above provides a link to the second type of physical mapping procedure that we will consider - FISH (Heiskanen et al., 1996). As in optical mapping, FISH enables the position of a marker on a chromosome or extended DNA molecule to be directly visualized. In optical mapping the marker is a restriction site and it is visualized as a gap in an extended DNA fiber. In FISH, the marker is a DNA sequence that is visualized by hybridization with a fluorescent probe.

In situ hybridization with radioactive or fluorescent probes

In situ hybridization is a version of hybridization analysis (Section 4.1.2) in which an intact chromosome is examined by probing it with a labeled DNA molecule. The position on the chromosome at which hybridization occurs provides information about the map location of the DNA sequence used as the probe (Figure 5.29). For the method to work, the DNA in the chromosome must be made single stranded (‘denatured’) by breaking the base pairs that hold the double helix together. Only then will the chromosomal DNA be able to hybridize with the probe. The standard method for denaturing chromosomal DNA without destroying the morphology of the chromosome is to dry the preparation onto a glass microscope slide and then treat with formamide.

Figure 5.29. Fluorescent in situ hybridization.

Figure 5.29

Fluorescent in situ hybridization. A sample of dividing cells is dried onto a microscope slide and treated with formamide so that the chromosomes become denatured but do not lose their characteristic metaphase morphologies (see Section 2.2.1). The position (more...)

In the early versions of in situ hybridization the probe was radioactively labeled but this procedure was unsatisfactory because it is difficult to achieve both sensitivity and resolution with a radioactive label, two critical requirements for successful in situ hybridization. Sensitivity requires that the radioactive label has a high emission energy (an example of such a radiolabel is 32P), but if the radiolabel has a high emission energy then it scatters its signal and so gives poor resolution. High resolution is possible if a radiolabel with low emission energy, such as 3H, is used, but these have such low sensitivity that lengthy exposures are needed, leading to a high background and difficulties in discerning the genuine signal.

These problems were solved in the late 1980s by the development of non-radioactive fluorescent DNA labels. These labels combine high sensitivity with high resolution and are ideal for in situ hybridization. Fluorolabels with different colored emissions have been designed, making it possible to hybridize a number of different probes to a single chromosome and distinguish their individual hybridization signals, thus enabling the relative positions of the probe sequences to be mapped. To maximize sensitivity, the probes must be labeled as heavily as possible, which in the past has meant that they must be quite lengthy DNA molecules - usually cloned DNA fragments of at least 40 kb. This requirement is less important now that techniques for achieving heavy labeling with shorter molecules have been developed. As far as the construction of a physical map is concerned, a cloned DNA fragment can be looked upon as simply another type of marker, although in practice the use of clones as markers adds a second dimension because the cloned DNA is the material from which the DNA sequence is determined. Mapping the positions of clones therefore provides a direct link between a genome map and its DNA sequence.

If the probe is a long fragment of DNA then one potential problem, at least with higher eukaryotes, is that it is likely to contain examples of repetitive DNA sequences (Section 2.4) and so may hybridize to many chromosomal positions, not just the specific point to which it is perfectly matched. To reduce this non-specific hybridization, the probe, before use, is mixed with unlabeled DNA from the organism being studied. This DNA can simply be total nuclear DNA (i.e. representing the entire genome) but it is better if a fraction enriched for repeat sequences is used. The idea is that the unlabeled DNA hybridizes to the repetitive DNA sequences in the probe, blocking these so that the subsequent in situ hybridization is driven wholly by the unique sequences (Lichter et al., 1990). Non-specific hybridization is therefore reduced or eliminated entirely (Figure 5.30).

Figure 5.30. A method for blocking repetitive DNA sequences in a hybridization probe.

Figure 5.30

A method for blocking repetitive DNA sequences in a hybridization probe. In this example the probe molecule contains two genome-wide repeat sequences (shown in green). If these sequences are not blocked then the probe will hybridize non-specifically to (more...)

FISH in action

FISH was originally used with metaphase chromosomes (Section 2.2.1). These chromosomes, prepared from nuclei that are undergoing division, are highly condensed and each chromosome in a set takes up a recognizable appearance, characterized by the position of its centromere and the banding pattern that emerges after the chromosome preparation is stained (see Figure 2.8). With metaphase chromosomes, a fluorescent signal obtained by FISH is mapped by measuring its position relative to the end of the short arm of the chromosome (the FLpter value). A disadvantage is that the highly condensed nature of metaphase chromosomes means that only low-resolution mapping is possible, two markers having to be at least 1 Mb apart to be resolved as separate hybridization signals (Trask et al., 1991). This degree of resolution is insufficient for the construction of useful chromosome maps, and the main application of metaphase FISH has been in determining the chromosome on which a new marker is located, and providing a rough idea of its map position, as a preliminary to finer scale mapping by other methods.

For several years these ‘other methods’ did not involve any form of FISH, but since 1995 a range of higher resolution FISH techniques has been developed. With these techniques, higher resolution is achieved by changing the nature of the chromosomal preparation being studied. If metaphase chromosomes are too condensed for fine-scale mapping then we must use chromosomes that are more extended. There are two ways of doing this (Heiskanen et al., 1996):

  • Mechanically stretched chromosomes can be obtained by modifying the preparative method used to isolate chromosomes from metaphase nuclei. The inclusion of a centrifugation step generates shear forces which can result in the chromosomes becoming stretched to up to 20 times their normal length. Individual chromosomes are still recognizable and FISH signals can be mapped in the same way as with normal metaphase chromosomes. The resolution is significantly improved and markers that are 200–300 kb apart can be distinguished.
  • Non-metaphase chromosomes can be used because it is only during metaphase that chromosomes are highly condensed: at other stages of the cell cycle the chromosomes are naturally unpacked. Attempts have been made to use prophase nuclei (see Figure 5.14) because in these the chromosomes are still sufficiently condensed for individual ones to be identified. In practice, however, these preparations provide no advantage over mechanically stretched chromosomes. Interphase chromosomes are more useful because this stage of the cell cycle (between nuclear divisions) is when the chromosomes are most unpacked. Resolution down to 25 kb is possible, but chromosome morphology is lost so there are no external reference points against which to map the position of the probe. This technique is therefore used after preliminary map information has been obtained, usually as a means of determining the order of a series of markers in a small region of a chromosome.

Interphase chromosomes contain the most unpacked of all cellular DNA molecules. To improve the resolution of FISH to better than 25 kb it is therefore necessary to abandon intact chromosomes and instead use purified DNA. This approach, called fiber-FISH, makes use of DNA prepared by gel stretching or molecular combing (see Figure 5.28) and can distinguish markers that are less than 10 kb apart.

5.3.3. Sequence tagged site (STS) mapping

To generate a detailed physical map of a large genome we need, ideally, a high-resolution mapping procedure that is rapid and not technically demanding. Neither of the two techniques that we have considered so far - restriction mapping and FISH - meets these requirements. Restriction mapping is rapid, easy, and provides detailed information, but it cannot be applied to large genomes. FISH can be applied to large genomes, and modified versions such as fiber-FISH can give high-resolution data, but FISH is difficult to carry out and data accumulation is slow, map positions for no more than three or four markers being obtained in a single experiment. If detailed physical maps are to become a reality then we need a more powerful technique.

At present the most powerful physical mapping technique, and the one that has been responsible for generation of the most detailed maps of large genomes, is STS mapping. A sequence tagged site or STS is simply a short DNA sequence, generally between 100 and 500 bp in length, that is easily recognizable and occurs only once in the chromosome or genome being studied. To map a set of STSs, a collection of overlapping DNA fragments from a single chromosome or from the entire genome is needed. In the example shown in Figure 5.31 a fragment collection has been prepared from a single chromosome, with each point along the chromosome represented on average five times in the collection. The data from which the map will be derived are obtained by determining which fragments contain which STSs. This can be done by hybridization analysis but PCR is generally used because it is quicker and has proven to be more amenable to automation. The chances of two STSs being present on the same fragment will, of course, depend on how close together they are in the genome. If they are very close then there is a good chance that they will always be on the same fragment; if they are further apart then sometimes they will be on the same fragment and sometimes they will not (Figure 5.31). The data can therefore be used to calculate the distance between two markers, in a manner analogous to the way in which map distances are determined by linkage analysis (Section 5.2.3). Remember that in linkage analysis a map distance is calculated from the frequency at which crossovers occur between two markers. STS mapping is essentially the same, except that each map distance is based on the frequency at which breaks occur between two markers.

Figure 5.31. A fragment collection suitable for STS mapping.

Figure 5.31

A fragment collection suitable for STS mapping. The fragments span the entire length of a chromosome, with each point on the chromosome present in an average of five fragments. The two blue markers are close together on the chromosome map and there is (more...)

The description of STS mapping given above leaves out some critical questions: What exactly is an STS? How is the DNA fragment collection obtained?

Any unique DNA sequence can be used as an STS

To qualify as an STS, a DNA sequence must satisfy two criteria. The first is that its sequence must be known, so that a PCR assay can be set up to test for the presence or absence of the STS on different DNA fragments. The second requirement is that the STS must have a unique location in the chromosome being studied, or in the genome as a whole if the DNA fragment set covers the entire genome. If the STS sequence occurs at more than one position then the mapping data will be ambiguous. Care must therefore be taken to ensure that STSs do not include sequences found in repetitive DNA.

These are easy criteria to satisfy and STSs can be obtained in many ways, the most common sources being expressed sequence tags (ESTs), SSLPs, and random genomic sequences.

  • Expressed sequence tags (ESTs). These are short sequences obtained by analysis of cDNA clones (Marra et al., 1998). Complementary DNA is prepared by converting an mRNA preparation into double-stranded DNA (Figure 5.32). Because the mRNA in a cell is derived from protein-coding genes, cDNAs and the ESTs obtained from them represent the genes that were being expressed in the cell from which the mRNA was prepared. ESTs are looked upon as a rapid means of gaining access to the sequences of important genes, and they are valuable even if their sequences are incomplete. An EST can also be used as an STS, assuming that it comes from a unique gene and not from a member of a gene family in which all the genes have the same or very similar sequences.
  • SSLPs . In Section 5.2.2 we examined the use of microsatellites and other SSLPs in genetic mapping. SSLPs can also be used as STSs in physical mapping. SSLPs that are polymorphic and have already been mapped by linkage analysis are particularly valuable as they provide a direct connection between the genetic and physical maps.
  • Random genomic sequences . These are obtained by sequencing random pieces of cloned genomic DNA, or simply by downloading sequences that have been deposited in the databases.
Figure 5.32. One method for preparing cDNA.

Figure 5.32

One method for preparing cDNA. Most eukaryotic mRNAs have a poly(A) tail at their 3′ end (Section 10.1.2). This series of A nucleotides is used as the priming site for the first stage of cDNA synthesis, carried out by reverse transcriptase - a (more...)

Fragments of DNA for STS mapping

The second component of an STS mapping procedure is the collection of DNA fragments spanning the chromosome or genome being studied. This collection is sometimes called the mapping reagent and at present there are two ways in which it can be assembled: as a clone library and as a panel of radiation hybrids. We will consider radiation hybrids first.

A radiation hybrid is a rodent cell that contains fragments of chromosomes from a second organism (McCarthy, 1996). The technology was first developed in the 1970s when it was discovered that exposure of human cells to X-ray doses of 3000–8000 rads causes the chromosomes to break up randomly into fragments, larger X-ray doses producing smaller fragments (Figure 5.33A). This treatment is of course lethal for the human cells, but the chromosome fragments can be propagated if the irradiated cells are subsequently fused with non-irradiated hamster or other rodent cells. Fusion is stimulated either chemically with polyethylene glycol or by exposure to Sendai virus (Figure 5.33B). Not all of the hamster cells take up chromosome fragments so a means of identifying the hybrids is needed. The routine selection process is to use a hamster cell line that is unable to make either thymidine kinase (TK) or hypoxanthine phosphoribosyl transferase (HPRT), deficiencies in either of these two enzymes being lethal when the cells are grown in a medium containing a mixture of hypoxanthine, aminopterin and thymidine (HAT medium). After fusion, the cells are placed in HAT medium. Those that grow are hybrid hamster cells that have acquired human DNA fragments that include genes for the human TK and HPRT enzymes, which are synthesized inside the hybrids, enabling these cells to grow in the selective medium. The treatment results in hybrid cells that contain a random selection of human DNA fragments inserted into the hamster chromosomes. Typically the fragments are 5–10 Mb in size, with each cell containing fragments equivalent to 15–35% of the human genome. The collection of cells is called a radiation hybrid panel and can be used as a mapping reagent in STS mapping, provided that the PCR assay used to identify the STS does not amplify the equivalent region of DNA from the hamster genome.

Figure 5.33. Radiation hybrids.

Figure 5.33

Radiation hybrids. (A) The result of irradiation of human cells: the chromosomes break into fragments, smaller fragments generated by higher X-ray doses. In (B), a radiation hybrid is produced by fusing an irradiated human cell with an untreated hamster (more...)

Box Icon

Box 5.1

The radiation hybrid map of the mouse genome. Physical mapping is a prelude to sequencing of the mouse genome and enables comparisons to be made between mouse and human chromosomes. Completion of the human genome sequence is not the only objective of (more...)

A second type of radiation hybrid panel, containing DNA from just one human chromosome, can be constructed if the cell line that is irradiated is not a human one but a second type of rodent hybrid. Cytogeneticists have developed a number of rodent cell lines in which a single human chromosome is stably propagated in the rodent nucleus. If a cell line of this type is irradiated and fused with hamster cells, then the hybrid hamster cells obtained after selection will contain either human or mouse chromosome fragments, or a mixture of both. The ones containing human DNA can be identified by probing with a human-specific genome-wide repeat sequence, such as the short interspersed nuclear element (SINE) called Alu (Section 2.4.2), which has a copy number of just over 1 million (see Table 1.2) and so occurs on average once every 4 kb in the human genome. Only cells containing human DNA will hybridize to Alu probes, enabling the uninteresting mouse hybrids to be discarded and STS mapping to be directed at the cells containing human chromosome fragments.

Radiation hybrid mapping of the human genome was initially carried out with chromosome-specific rather than whole-genome panels because it was thought that fewer hybrids would be needed to map a single chromosome than would be needed to map the entire genome. It turns out that a high-resolution map of a single human chromosome requires a panel of 100–200 hybrids, which is about the most that can be handled conveniently in a PCR screening program. But whole-genome and single-chromosome panels are constructed differently, the former involving irradiation of just human DNA, and the latter requiring irradiation of a mouse cell containing much mouse DNA and relatively little human DNA. This means that the human DNA content per hybrid is much lower in a single-chromosome panel than in a whole-genome panel. It transpires that detailed mapping of the entire human genome is possible with fewer than 100 whole-genome radiation hybrids, so whole-genome mapping is no more difficult than single-chromosome mapping. Once this was realized, whole-genome radiation hybrids became a central component of the mapping phase of the Human Genome Project (Section 6.3.1). Whole-genome libraries are also being used for STS mapping of other mammalian genomes and for those of the zebra fish and the chicken (McCarthy, 1996).

A clone library can also be used as the mapping reagent for STS analysis

A preliminary to the sequencing phase of a genome project is to break the genome or isolated chromosomes into fragments and to clone each one in a high-capacity vector, one able to handle large fragments of DNA (Section 4.2.1). This results in a clone library, a collection of DNA fragments, which, in this case, have an average size of several hundred kb. As well as supporting the sequencing work, this type of clone library can also be used as a mapping reagent in STS analysis.

As with radiation hybrid panels, a clone library can be prepared from genomic DNA, and so represents the entire genome, or a chromosome-specific library can be made if the starting DNA comes from just one type of chromosome. The latter is possible because individual chromosomes can be separated by flow cytometry. To carry out this technique, dividing cells (ones with condensed chromosomes) are carefully broken open so that a mixture of intact chromosomes is obtained. The chromosomes are then stained with a fluorescent dye. The amount of dye that a chromosome binds depends on its size, so larger chromosomes bind more dye and fluoresce more brightly than smaller ones. The chromosome preparation is diluted and passed through a fine aperture, producing a stream of droplets, each one containing a single chromosome. The droplets pass through a detector that measures the amount of fluorescence, and hence identifies which droplets contain the particular chromosome being sought. An electric charge is applied to these drops, and no others (Figure 5.34), enabling the droplets containing the desired chromosome to be deflected and separated from the rest. What if two different chromosomes have similar sizes, as is the case with human chromosomes 21 and 22? These can usually be separated if the dye that is used is not one that binds non-specifically to DNA, but instead has a preference for AT- or GC-rich regions. Examples of such dyes are Hoechst 33258 and chromomycin A3, respectively. Two chromosomes that are the same size rarely have identical GC contents, and so can be distinguished by the amounts of AT- or GC-specific dye that they bind.

Figure 5.34. Separating chromosomes by flow cytometry.

Figure 5.34

Separating chromosomes by flow cytometry. A mixture of fluorescently stained chromosomes is passed through a small aperture so that each drop that emerges contains just one chromosome. The fluorescence detector identifies the signal from drops containing (more...)

Compared with radiation hybrid panels, clone libraries have one important advantage for STS mapping. This is the fact that the individual clones can subsequently provide the DNA that is actually sequenced. The data resulting from STS analysis, from which the physical map is generated, can equally well be used to determine which clones contain overlapping DNA fragments, enabling a clone contig to be built up (Figure 5.35; for other methods for assembling clone contigs see Section 6.2.2). This assembly of overlapping clones can be used as the base material for a lengthy, continuous DNA sequence, and the STS data can later be used to anchor this sequence precisely onto the physical map. If the STSs also include SSLPs that have been mapped by genetic linkage analysis then the DNA sequence, physical map and genetic map can all be integrated.

Figure 5.35. The value of clone libraries in genome projects.

Figure 5.35

The value of clone libraries in genome projects. The small clone library shown in this example contains sufficient information for an STS map to be constructed, and can also be used as the source of the DNA that will be sequenced.

Study Aids For Chapter 5

Self study questions


Explain why a map is a useful aid to genome sequencing.


Distinguish between ‘genetic mapping’ and ‘physical mapping’. What are the strengths and weaknesses of the two techniques?


Why are genes not ideal markers for construction of a genetic map?


Describe the various types of DNA marker that are used in genetic mapping. How is each type of marker scored?


Refer to Figure 5.5A. Draw the appearance of the autoradiograph if the probe hybridized to a region of DNA entirely between restriction sites R1 and R2. Would detection of the RFLP still be unambiguous?


Explain how Mendel's work led eventually to a method for genetic mapping.


Draw diagrams of the key events occurring during (a) mitosis, and (b) meiosis. Annotate your diagrams to highlight the important differences between the two processes.


Define the term ‘partial linkage’ and show how partial linkage is the basis of genetic mapping.


Describe how linkage analysis is carried out with (a) mice, (b) humans, and (c) bacteria.


What factors are responsible for the inaccuracies that sometimes occur in a genetic map?


Explain how a restriction map is obtained. What special procedures can be used to increase the size of DNA molecule for which a restriction map can be obtained?


What is FISH and how is it used to construct a physical map?


Describe the various types of DNA sequence that can be used in STS mapping.


Draw a diagram showing how a double-stranded cDNA is synthesized.


Define the term ‘mapping reagent’ and explain how a panel of radiation hybrids is used as a mapping reagent.


Explain how a clone library is used as a mapping reagent.


Draw a diagram to show how a sample of a single human chromosome can be obtained by flow cytometry.

Problem-based learning


What are the ideal features of a DNA marker that will be used to construct a genetic map. To what extent can RFLPs, SSLPs or SNPs be considered ‘ideal’ DNA markers?


Explore and assess the applications of DNA chip technology in biological research.


Evaluate the relative importance of genetic and physical mapping in the Human Genome Project.


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Further Reading

  1. Fincham JRS, Day PR and Radford A (1979) Fungal Genetics, 4th edition. Blackwell, London. —The bible for gene mapping in microbial eukaryotes.
  2. Griffiths AJF, Miller JH, Suzuki DT, Lewontin RC and Gelbart WM (2000) An Introduction to Genetic Analysis, 7th edition. W. H. Freeman, New York. —Particularly good for gene mapping by experimental crosses and for mapping in bacteria.
  3. Lichter P. Multicolor FISHing: what's the catch? Trends Genet. (1997);13:475–479.An interesting review of some of the applications of FISH. [PubMed: 9433136]
  4. Lodish H, Berk A, Zipursky AL, Matsudaira P, Baltimore D and Darnell J (2000) Molecular Cell Biology, 4th edn. W. H. Freeman, New York. —Contains full details of mitosis and meiosis.
  5. Primrose SB (1995) Principles of Genome Analysis. Blackwell Science, Oxford. —A little out of date but a good description of mapping strategies.
  6. Strachan T and Read AP (1999) Human Molecular Genetics, 2nd edition. BIOS Scientific Publishers, Oxford. —Chapters 10 and 11 cover human physical and genetic mapping.
  7. Sturtevant AH (1965) A History of Genetics. Harper and Row, New York. —Describes the early gene mapping work carried out by Morgan and his colleagues.
  8. Walter MA, Spillett DJ, Thomas P, Weissenbach J, Goodfellow PN. A method for constructing radiation hybrid maps of whole genomes. Nature Genet. (1994);7:22–28.An excellent review of this approach to mapping. [PubMed: 8075634]
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