Determination of recombination rates across the human genome has been constrained by the limited resolution and accuracy of existing genetic maps and the draft genome sequence. We have genotyped 5,136 microsatellite markers for 146 families, with a total of 1,257 meiotic events, to build a high-resolution genetic map meant to: (i) improve the genetic order of polymorphic markers; (ii) improve the precision of estimates of genetic distances; (iii) correct portions of the sequence assembly and SNP map of the human genome; and (iv) build a map of recombination rates. Recombination rates are significantly correlated with both cytogenetic structures (staining intensity of G bands) and sequence (GC content, CpG motifs and poly(A)/poly(T) stretches). Maternal and paternal chromosomes show many differences in locations of recombination maxima. We detected systematic differences in recombination rates between mothers and between gametes from the same mother, suggesting that there is some underlying component determined by both genetic and environmental factors that affects maternal recombination rates.
This is a preview of subscription content
Subscribe to Journal
Get full journal access for 1 year
only $4.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Dib, C. et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380, 152–154 (1996).
Murray, J.C. et al. A comprehensive human linkage map with centimorgan density. Science 265, 2049–2054 (1994).
Broman, K.W., Murray, J.C., Sheffield, V.C., White, R.L. & Weber, J.L. Comprehensive human genetic map: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63, 861–869 (1998).
Sheffield, V.C. et al. A collection of tri- and tetranucleotide repeat markers used to generate high quality, high resolution human genome-wide linkage maps. Hum. Mol. Genet. 4, 1837–1844 (1995).
Sunden, S.L. et al. Chromosomal assignment of 2900 tri- and tetranucleotide repeat markers using NIGMS somatic cell hybrid panel 2. Genomics 32, 15–20 (1996).
Utah Marker Development Group. A collection of ordered tetranucleotide-repeat markers from the human genome. Am. J. Hum. Genet. 57, 619–628 (1995).
Rosenberg, M. et al. Characterization of short tandem repeats from thirty-one human telomeres. Genome Res. 7, 917–923 (1996).
DeWan, A.T., Parrado, A.R., Matise, T.C. & Leal, S.M. The map problem: a comparison of genetic and sequence-based physical maps. Am. J. Hum. Genet. 70, 101–107 (2002).
Gudbjartsson, D.F., Jonasson, K., Frigge, M.L. & Kong, A. Allegro, a new computer program for multipoint linkage analysis. Nature Genet. 25, 12–14 (2000).
Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. R. Statist. Soc. B39, 1–38 (1997).
Giglio, S. et al. Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am. J. Hum. Genet. 68, 874–883 (2001).
Yu, A. et al. Comparison of human genetic and sequence-based physical maps. Nature 409, 951–953 (2001).
The BAC Resource Consortium. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409, 953–958 (2001).
Halpern, J. & Whittemore, A.S. Multipoint linkage analysis. A cautionary note. Hum. Hered. 49, 194–196 (1999).
Gretarsdottir, S. et al. Localization of a susceptibility gene for common forms of stroke to chromosome 5q12. Am. J. Hum. Genet. 70, 593–603 (2002).
Daw, E.W., Thompson, E.A. & Wijsman, E.M. Bias in multipoint linkage analysis arising from map misspecification. Genet. Epidemiol. 19, 366–380 (2000).
Thompson, E.A. Crossover counts and likelihood in multipoint linkage analysis. IMA J. Math. Appl. Med. Biol. 4, 93–108 (1987).
The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).
Mohrenweiser, H.W., Tsujimoto, S., Gordon, L. & Olsen, A. Regions of sex-specific hypo- and hyper-recombination identified through integration of 180 genetic markers into the metric physical map of the human chromosome 19. Genomics 47, 153–162 (1998).
Laurie, D.A. & Hulten, M.A. Further studies on bivalent chiasma frequency in human males with normal karyotypes. Ann. Hum. Genet. 49, 189–201 (1985).
Ji, Y., Stelly, D.M., DeDonato, M., Goodman, M.M. & Williams, C.G. A candidate recombination modifier gene for Zea mays L. Genetics 151, 821–830 (1999).
Jeffreys, A.J., Kauppi, L. & Neuman, R. Intensely punctuate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genet. 29, 217–222 (2001).
Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J. & Lander, E.S. High-resolution haplotype structure in the human genome. Nature Genet. 29, 229–232 (2001).
Gulcher, J.R., Kristjansson, K., Gudbjartsson, H. & Stefansson, K. Protection of privacy by third-party encryption in genetic research in Iceland. Eur. J. Hum. Genet. 8, 739–742 (2000).
Venables, W.N. & and Ripley, B.D. Modern Applied Statistics with S-plus (Springer, New York, 1994).
The authors wish to extend their gratitude to the 869 individuals providing DNA to this study, the Human Genome Project for providing the draft human genome sequence, and J.L. Weber and his colleagues for constructing the Marshfield genetic map.
The authors are employed by deCODE genetics, and some of them own stock or stock options in the company.
Technical Note: How to download this Excel file to your computer PC Users: Right-mouse click on the link. Choose "Save Target As," then choose where you want the file to be saved. Mac Users: Most Macs are configured to download files automatically. Otherwise, hold down the OPTION key while clicking the link.
Technical Note: This is a compressed .ZIP file containing 23 individual text files (60MB total). These files can be viewed in any text editor, but are best viewed in Word or WordPad. Simply click on the link to download the compressed file. Then ... PC Users: You can open this file using WinZip software (if you don't already have WinZip, click on the "Download Plugins" link on the left nav bar). Once you have unzipped the compressed file, you can choose to extract the individual chromosomes that you are interested in. Mac Users: You can open this file using StuffIt software (if you don't already have StuffIt, click on the "Download Plugins" link on the left nav bar). Once you have unzipped the compressed file, you can choose to extract the individual chromosomes that you are interested in.
About this article
Cite this article
Kong, A., Gudbjartsson, D., Sainz, J. et al. A high-resolution recombination map of the human genome. Nat Genet 31, 241–247 (2002). https://doi.org/10.1038/ng917
Genome Biology (2022)
Genome Biology (2021)
FISH landmarks reflecting meiotic recombination and structural alterations of chromosomes in wheat (Triticum aestivum L.)
BMC Plant Biology (2021)
Genetics Selection Evolution (2021)
BMC Medical Genomics (2021)