Genetic Linkage Mapping


Random occurrences of crossovers along a chromosome permit definition of a genetic distance. Such distances are used to create genetic maps and localise disease genes on these maps. Human genetic maps consist of dense sets of DNA polymorphisms, notably single‚Äźnucleotide polymorphisms (SNPs) and, resulting from DNA sequencing, single‚Äźnucleotide variants (SNVs). The main application of linkage mapping is to localise hypothesised disease genes on the human marker maps, which in turn represents the first step towards understanding of disease aetiology. While linkage analysis represents the mainstay for genetic mapping, newer approaches have been developed, for example, methods allowing the use of a single affected individual in conjunction with a number of control individuals, a situation not tractable by standard linkage and genetic association analyses.

Key Concepts

  • Genetic distances are based on the random occurrence of crossovers along a chromosome, and a crossover will lead to a recombination in half of the gametes.
  • Genetic loci in close proximity will rarely experience a recombination between them, so the recombination fraction will be small.
  • For short distances, the recombination fraction represents genetic distance in units of Morgans.
  • DNA sequencing has established the order of variants on a chromosome, so genetic linkage mapping essentially aims to measure distances in each interval (between two adjacent variants) on a chromosome.
  • Disease gene mapping hypothesises the presence of a disease locus, for which genetic distances to one after another genetic variant are estimated. A significantly small such distance (recombination fraction significantly smaller than 50%) establishes genetic linkage between the disease locus and a given variant.

Keywords: recombination; crossover; chiasma; genetic marker; statistical genetics; disease gene

Figure 1. Effects of a crossover between two loci on the resulting gametes (b) and corresponding genetic phenotypes (a), where R = recombinant and N = nonrecombinant gamete (child).


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Imai‐Okazaki, Atsuko, and Ott, Jurg(Jan 2018) Genetic Linkage Mapping. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005360.pub2]