In genetic mapping, different polymorphic markers are assayed in all members of a variety of multigeneration families. The resulting genotypes are then analyzed using genetic linkage programs to work out how alleles of the different markers segregate at each meiotic event connecting parents to their offspring, and to identify markers where specific alleles co-segregate. The discovery of apparently random DNA polymorphisms in the human genome prompted the idea of constructing a comprehensive, nonclassical human genetic map, one that was predominantly based on anonymous DNA markers rather than on genes.
The first genetic linkage map of the human genome, published in 1987, was based on restriction fragment length polymorphisms (RFLPs), a type of DNA polymorphism that results in creation or destruction of one recognition sequence for a specific restriction nuclease (Figure 1A). Although an outstanding achievement, the map was of limited use: the markers were too few, just one marker per 9 Mb of DNA, and not very polymorphic (having just two alleles—either the restriction site is present or it is absent).
Fig1. Restriction fragment length polymorphism (RFLP) and microsatellite DNA polymorphism. (A) RFLP. The example shows a polymorphic site for the enzyme MboI, which recognizes the sequence GATC. Allele 1 has a GATC sequence that is altered in allele 2 (GACC) so that MboI makes an extra cut in the DNA of allele 1 compared to allele 2 (at the middle GATC sequence shown). In the past, that difference would be detected by a Southern blot assay using a probe such as probe X, which would hybridize to the individual fragments a and b from allele 1 or a long fragment (a + b) from allele 2. The polymorphism is more conveniently detected by PCR using an upstream primer derived from the a sequence and a downstream primer from b, whereupon the amplified DNA can be digested with MboI and size-fractionated to distinguish between the alleles (not shown). (B) Microsatellite DNA polymorphism. Long runs of the (CA)/(TG) dinucleotide are prone to changes in copy number of the dinucleotide. Here the 5′ ends of upstream primer P1 and downstream primer P2 are located 40 bp from the microsatellite array, and so the length of amplified fragment will be 80 + the array length (32, 28, or 22 bp in this example). The different alleles can be separated by polyacrylamide gel electrophoresis.
Second-generation human genetic maps were based on polymorphic microsatellite DNA markers, which are both quite common and often highly polymorphic (multiple alleles can often be distinguished; see Figure 1B). By 1994 an integrated genetic map (mostly based on microsatellites but containing some other markers) had a sufficiently high marker density (close to one marker per Mb), and from now on the major focus would be on developing and refining physical maps leading to the ultimate physical map, the complete DNA sequence of each chromosome. However, genetic mapping of the human genome continued outside the remit of the HGP: high-density single nucleotide polymorphism (SNP) maps were developed by the International HapMap (haplotype mapping) Consortium to help identify DNA variants contributing to common multifactorial diseases.
