Genetic and Physical Map Correlation

Abstract

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 www.soybase.org

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.

close

References

Alves JM, Chikhi L, Amorim A and Lopes AM (2014) The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations. Genome Biology and Evolution 6: 921–930.

Auton A, Fledel‐Alon A, Pfeifer S et al. (2012) A fine‐scale chimpanzee genetic map from population sequencing. Science 336: 193–198.

Bennetzen JL (2007) Patterns in grass genome evolution. Current Opinion in Plant Biology 10: 176–181.

Boyko A and Kovalchuk I (2011) Genome instability and epigenetic modification – heritable responses to environmental stress? Current Opinion in Plant Biology 14: 260–266.

Chester M, Leitch AR, Soltis PS and Soltis DE (2010) Review of the application of modern cytogenetic methods (FISH/GISH) to the study of reticulation (Polyploidy/Hybridization). Genes 1: 166–192.

Cloutier S, Ragupathy R, Miranda E et al. (2012) Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.) Theoretical and Applied Genetics 125: 1783–1795.

Cook DE, Lee TG, Guo X et al. (2012) Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338(6111): 1206–1209.

Dal‐Bianco M, Carneiro MS, Hotta CT et al. (2012) Sugarcane improvement: how far can we go? Current Opinion in Biotechnology 23: 265–270.

Davis CR, Kempainen RR, Srodes MS and McClung CR (1994) Correlation of the physical and genetic maps of the centromeric region of the right arm of linkage group III of N. crassa. Genetics 136: 1297–1306.

Frazer KA, Tao H, Osoegawa K et al. (2004) Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Research 14: 367–372.

Grant D, Nelson RT and Cannon SB (2014) Soybase. The USDA‐ARS Soybean Genetics and Genomics Database. http://soybase.org/

Han Y, Zheng D, Vimolmangkang S et al. (2011) Integration of physical and genetic maps in apple confirms whole‐genome and segmental duplication in the apple genome. Journal of Experimental Botany 62: 5117–5130.

Hardtke CS and Berleth T (1996) Genetic and contig map of a 2222 kb region encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana. Genome 39: 1086–1092.

Hendre PS, Bhat PR, Krishnakumar V and Aggarwal RK (2011) Isolation and characterization of resistance gene analogues from Psilanthus species that represent wild relatives of cultivated coffee endemic to India. Genome 54: 377–390.

Kaback DB, Guacci V, Barber D and Mahon JW (1992) Chromosome size‐dependent control of meiotic recombination. Science 256(5054): 228–232.

Keogh RS, Seoigh C and Wolfe KH (1998) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14: 443–457.

Lee WK, Kim N, Kim J et al. (2013) Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence‐based physical maps. Theoretical and Applied Genetics 126: 1103–1119.

Lewin HA, Larkin DM, Pontius J and O'Brien SJ (2009) Every genome sequence needs a good map. Genome Research 19: 1925–1928.

McHale LK, Haun WJ, Xu WW et al. (2012) Structural variants in the soybean genome localize to clusters of biotic stress response genes. Plant Physiology 159: 1295–1308.

Meyer JL, Silva DCG, Yang C et al. (2009) Identification and analysis of candidate genes for Rpp4‐mediated resistance to Asian soybean rust in soybean. Plant Physiology 150: 295–307.

Mullaney JM, Milles RE, Pittard S and Devine SE (2010) Small insertions and deletions (INDELs) in human genomes. Human Molecular Genetics 19(2): R131–R136.

Ooi A, Takehana T, Li X et al. (2004) Protein overexpression and gene amplification of HER‐2 and EGFR in colorectal cancers: an immunohistochemical and fluorescent in situ hybridization study. Modern Pathology 17: 895–904.

Schmutz J, Cannon SB, Schlueter J et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178–183.

The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.

The Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69–87.

Varshney RK, Mir RR, Bhatia S et al. (2014) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.) Functional Integrated Genomics 14: 59–73.

Yu A, Zhao C, Fan Y et al. (2001) Comparison of human genetic and sequence‐based physical maps. Nature 409: 951–953.

Further Reading

Botstein D and Fink GR (2011) Yeast: an experimental organism for 21st century biology. Genetics 189(3): 695–704.

Brown JR (ed.) (2008) Comparative Genomics: Basic and Applied Research. Boca Raton, FL: CRC Press.

Brown TA (2006) Genomes 3. New York, NY: Garland Science.

Frazer KA (2012) Decoding the human genome. Genome Research 22(9): 1599–1601.

Mefford HC and EE Eichler (2009) Duplication hotspots, rare genomic disorders, and common disease. Current Opinion in Genetics and Development 19(3): 196–204.

Meksem K and Kahl G (eds) (2005) The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Weinheim: Wiley‐VCH.

Meyers BC, Scalabrin S and Morgante M (2004) Mapping and sequencing complex genomes: let's get physical! Nature Reviews Genetics 5: 578–588.

Rahman M and Patterson AH (2010) Comparative genomics in crop plants. In: Jain SM and Brar DS (eds) Molecular Techniques in Crop Improvement, 2nd edn, pp. 23–61. New York, NY: Springer, Netherlands.

Zickler D (2009) Observing meiosis in filamentous fungi: Sordaria and Neurospora. Methods in Molecular Biology 558: 91–114.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

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