Genetic and Physical Map Correlation


Genetic and physical maps illustrate the arrangement of genes and DNA markers on a chromosome. The relative distances between positions on a genetic map are calculated using recombination frequencies, whereas a physical map is based on the actual number of nucleotide pairs between loci. These maps are a key resource for understanding genome organisation. They are the basis for map‐based cloning and marker‐assisted selection, serving as a bridge between breeding and sequencing research. A comparison of marker position and order may provide interesting insight into the evolutionary history of even distantly related species. Physical and genetic maps can unravel the complexities of large duplicated genomes intractable to sequencing efforts; whereas in species more amenable to genetic studies high‐resolution maps provide the scaffold on which whole genome sequences are assembled. A complete genome sequence is a physical map at its highest resolution.

Key Concepts:

  • Genetic maps are based on the recombination frequency between molecular markers. These maps are population specific.

  • Physical maps are an alignment of DNA sequences, with distance between markers measured in base pairs.

  • Unique DNA sequences called molecular markers are compared to each other to determine correct marker order (genetic map) and used to identify overlapping segments of larger DNA pieces (physical map).

  • Genetic mapping is based on recombination, the exchange of DNA sequence between sister chromatids during meiosis.

  • High‐resolution genetic and physical maps serve as the scaffold for genome sequence assembly.

  • Tightly correlated marker order between species can identify conserved syntenic regions.

Keywords: recombination; genome; molecular marker; synteny; genetic map; physical map

Figure 1.

Soybean chromosome 5. (A) BAC contig alignment illustrating the overlapping segments identified with molecular markers (SSRs and RFLPs). (B) Physical map of soybean chromosome 5 constructed from BAC contig alignment. Distance between markers is measured in base pairs. (C) Genetic map of soybean chromosome 5 constructed from measuring recombination frequencies between markers. Distances between markers are measured in centiMorgans. SSR markers are represented by Sat or Satt IDs, SNPs are represented by BARC IDs. All other marker IDs represent RFLP markers. Blue lines illustrate the correlation of marker order between the physical and genetic maps. Figure adapted from data freely available at

Figure 2.

Aligned maps showing chromosomal locations of conserved DNA sequences in two species (A and B). Lines connect analogous DNA markers (m) between species. Changes in the positions of the m markers in species B could be due to chromosomal rearrangements during divergent evolutionary processes. There is a strong possibility that a gene from a conserved block of DNA (e.g. gene 1 of species A, located between m4 and m5) is present in the syntenic region in species B.



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O'Rourke, Jamie A(Nov 2014) Genetic and Physical Map Correlation. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000819.pub3]