Genetic mapping

Genetic mapping

The aim of genetic mapping is to determine the linear sequence of genes in genetic material. The mapping can be performed at several levels of detail (resolution) that fall into two broad types: traditional genetic or linkage mapping and more detailed, physical mapping.

Linkage mapping shows the relative rather than absolute positions of genes along a chromosome and is a technique that has been used since the early 1900s. Early geneticists determined that genes were found on chromosomes. They also reasoned that because the various forms of genes, or alleles, could be precisely exchanged during meiosis through crossovers between homologous chromosomes, the genes for specific characteristics must lie at precise points along each chromosome. It followed that the mapping of chromosomes could, therefore, be made from the observation of crossovers. Between 1912 and 1915, the American scientist Thomas Hunt Morgan (1866–1945) hypothesized that if genes were arranged linearly along chromosomes, then those genes lying closer together would be separated by crossovers less often than those lying further apart. Genes lying closer together would thus have a greater probability of being passed along as a unit. It follows that the percentage of crossovers would be proportional to the distance between two genes on a chromosome. The percentage crossover can be expressed as the number of crossovers between two genes in meiosis. One genetic map unit (m.u.) is defined as the distance between gene pairs for which one product out of 100 is recombinant (a product of crossover). S recombinant frequency (R.F.) of 0.01 (1%) is defined as 1 m.u., and a map unit is sometimes referred to as a centimorgan (cM) in honor of Thomas Hunt Morgan.

As an example of how linkage mapping might work, suppose two characteristics, A and B, show a 26% crossover. Assign 26 crossover units to the distance between these two genes. If a characteristic C turns out in breeding experiments to have 9% crossover with B and 17% crossover with A, it would then be located between A and B at a point 9 units from B and 17 units from A. Compiling the information from many such breeding experiments creates a chromosome map that indicates the relative positions of the genes that code for certain characteristics. Accordingly, the further apart any two genes are on the same chromosome, the greater the incidence of crossing over between them.

A linkage map is limited because recombination frequencies can be distorted relative to the physical distance between sites. As a result, the linkage map is not always the best possible representation of genetic material.

While linkage maps only indicate relative positions of genes, physical maps are more accurate and aim to show the actual number of nucleotides between each gene. Restriction maps are constructed by cleaving DNA into fragments with restriction enzymes. These enzymes recognize specific short DNA sequences and cut the duplex. The distances between the sites of cleavage are then measured. The positions of the target restriction sites for these enzymes along the chromosome can be used as DNA markers. Restriction sites generally exist in the same positions on homologous chromosomes so the positions of these target sites can be used rather like milestones along a road and can act as reference points for locating significant features in the chromosome.

A map of the positions of restriction sites can be made for a localized region of a chromosome. It is made by comparing the sizes of single enzyme breakages (digests) of the region of interest with double digests of the same region. This means that two different restriction enzymes are applied, one to each of two separate chromosome extracts of the region of interest, and subsequently the two enzymes are used together in a third digestion with the chromosome extract. The chromosome fragments resulting from the three digestions are then subjected to a biochemical procedure known as gel electrophoresis, which separates them and gives an estimation of their size. Comparison of the sizes of the chromosome fragments resulting from single and double restriction enzyme digestions allows for an approximate location of the target restriction sites. Thus, such maps represent linear sequences of restriction sites. As this procedure determines the sizes of digested chromosome fragments, the distances between sites in terms of the length of DNA can be calculated, because the size of a fragment estimated from an electrophoresis experiment is proportional to the number of base pairs in that fragment.

A restriction map does not intrinsically identify sites of genetic interest. For it to be of practical use, mutations have to be characterized in terms of their effects upon the restriction sites. In the 1980s, it was shown how restriction fragment length polymorphisms (RFLPs) could be used to map human disease genes. RFLPs are inherited by Mendelian segregation and are distributed in populations as classical examples of common genetic polymorphisms. If such a DNA variant is located close to a defective gene (which cannot be tested directly), the DNA variant can be used as a marker to detect the presence of the disease-causing gene. The prenatal examination of DNA for particular enzyme sites associated with certain hereditary diseases has proved to be an important method of diagnosis. Clinically useful polymorphic restriction enzyme sites have been detected within the Beta-like globin gene cluster. For example, the absence of a recognition site for the restriction enzyme HpaI is frequently associated with the allele for sickle-cell anemia, and this association has been useful in prenatal diagnosis of this disease.

The ultimate genetic map is the complete nucleotide sequence of the DNA in the whole chromosome complement, or genome, of an organism. Today, several completed genome maps already exist. Simple prokaryotic organisms, e.g., bacteria, with their relatively small chromosomes of one to two million base pairs were the first to be mapped. Later, eukaryotic organisms such as the yeast, Saccharomyces cerevisiae, and the nematode worm, Caenorhabditis elegans, were mapped. In 2000, the Human Genome Project produced the first draft of the human genome. The project adopted two methods for mapping the three billion nucleotides. The earlier approach was a "clone by clone" method. In this, the entire genome was cut into fragments up to several thousand base pairs long, and inserted into synthetic chromosomes known as bacterial artificial chromosomes (BACs). The subsequent mapping step involved positioning the BACs on the genome's chromosomes by looking for distinctive marker sequences called sequence tagged sites (STSs), whose location had already been pinpointed. Clones of the BACs are then broken into smaller fragments in a process known as shotgun cloning. Each small fragment was then sequenced and computer algorithms, that recognize matching sequence information from overlapping fragments, were used to reconstruct the complete sequence inserted into each BAC. It was later argued that the first mapping step was unnecessary and that the algorithms used to reassemble the shotgunned DNA fragments could be applied to cloned random fragments taken directly from the whole genome. In this whole genome shotgun strategy, fragments were first assembled by algorithms into larger scaffolds and the correct position of these scaffolds on the genome was worked out by STSs. The latter method speeded up the whole procedure considerably and is currently being used to sequence genomes from other organisms.

Judyth Sassoon, ARCS, PhD