Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 2000 May;155(1):407–420. doi: 10.1093/genetics/155.1.407

Selective mapping: a strategy for optimizing the construction of high-density linkage maps.

T J Vision 1, D G Brown 1, D B Shmoys 1, R T Durrett 1, S D Tanksley 1
PMCID: PMC1461083  PMID: 10790413

Abstract

Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.

Full Text

The Full Text of this article is available as a PDF (184.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ben-Dor A., Chor B. On constructing radiation hybrid maps. J Comput Biol. 1997 Winter;4(4):517–533. doi: 10.1089/cmb.1997.4.517. [DOI] [PubMed] [Google Scholar]
  2. Blake J. A., Richardson J. E., Davisson M. T., Eppig J. T. The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group. Nucleic Acids Res. 1999 Jan 1;27(1):95–98. doi: 10.1093/nar/27.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Crippen G. M. Prediction of protein folding from amino acid sequence over discrete conformation spaces. Biochemistry. 1991 Apr 30;30(17):4232–4237. doi: 10.1021/bi00231a018. [DOI] [PubMed] [Google Scholar]
  4. Darvasi A. Interval-specific congenic strains (ISCS): an experimental design for mapping a QTL into a 1-centimorgan interval. Mamm Genome. 1997 Mar;8(3):163–167. doi: 10.1007/s003359900382. [DOI] [PubMed] [Google Scholar]
  5. Fain P. R., Kort E. N., Yousry C., James M. R., Litt M. A high resolution CEPH crossover mapping panel and integrated map of chromosome 11. Hum Mol Genet. 1996 Oct;5(10):1631–1636. doi: 10.1093/hmg/5.10.1631. [DOI] [PubMed] [Google Scholar]
  6. Griffin T. J., Tang W., Smith L. M. Genetic analysis by peptide nucleic acid affinity MALDI-TOF mass spectrometry. Nat Biotechnol. 1997 Dec;15(13):1368–1372. doi: 10.1038/nbt1297-1368. [DOI] [PubMed] [Google Scholar]
  7. Gyapay G., Schmitt K., Fizames C., Jones H., Vega-Czarny N., Spillett D., Muselet D., Prud'homme J. F., Dib C., Auffray C. A radiation hybrid map of the human genome. Hum Mol Genet. 1996 Mar;5(3):339–346. doi: 10.1093/hmg/5.3.339. [DOI] [PubMed] [Google Scholar]
  8. Haldane J B, Waddington C H. Inbreeding and Linkage. Genetics. 1931 Jul;16(4):357–374. doi: 10.1093/genetics/16.4.357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Keats B. J., Sherman S. L., Morton N. E., Robson E. B., Buetow K. H., Cartwright P. E., Chakravarti A., Francke U., Green P. P., Ott J. Guidelines for human linkage maps: an international system for human linkage maps (ISLM, 1990). Genomics. 1991 Mar;9(3):557–560. doi: 10.1016/0888-7543(91)90426-f. [DOI] [PubMed] [Google Scholar]
  10. Lincoln S. E., Lander E. S. Systematic detection of errors in genetic linkage data. Genomics. 1992 Nov;14(3):604–610. doi: 10.1016/s0888-7543(05)80158-2. [DOI] [PubMed] [Google Scholar]
  11. Paterson A. H., DeVerna J. W., Lanini B., Tanksley S. D. Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics. 1990 Mar;124(3):735–742. doi: 10.1093/genetics/124.3.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Postlethwait J. H., Yan Y. L., Gates M. A., Horne S., Amores A., Brownlie A., Donovan A., Egan E. S., Force A., Gong Z. Vertebrate genome evolution and the zebrafish gene map. Nat Genet. 1998 Apr;18(4):345–349. doi: 10.1038/ng0498-345. [DOI] [PubMed] [Google Scholar]
  13. Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 1979 Jun 11;6(7):2601–2610. doi: 10.1093/nar/6.7.2601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Tanksley S. D., Ganal M. W., Prince J. P., de Vicente M. C., Bonierbale M. W., Broun P., Fulton T. M., Giovannoni J. J., Grandillo S., Martin G. B. High density molecular linkage maps of the tomato and potato genomes. Genetics. 1992 Dec;132(4):1141–1160. doi: 10.1093/genetics/132.4.1141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Tanksley S. D. Mapping polygenes. Annu Rev Genet. 1993;27:205–233. doi: 10.1146/annurev.ge.27.120193.001225. [DOI] [PubMed] [Google Scholar]
  16. Underhill P. A., Jin L., Lin A. A., Mehdi S. Q., Jenkins T., Vollrath D., Davis R. W., Cavalli-Sforza L. L., Oefner P. J. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 1997 Oct;7(10):996–1005. doi: 10.1101/gr.7.10.996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Wang D. G., Fan J. B., Siao C. J., Berno A., Young P., Sapolsky R., Ghandour G., Perkins N., Winchester E., Spencer J. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science. 1998 May 15;280(5366):1077–1082. doi: 10.1126/science.280.5366.1077. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES