Theoretical and Applied Genetics

, Volume 112, Issue 1, pp 30–40 | Cite as

RECORD: a novel method for ordering loci on a genetic linkage map

  • Hans Van Os
  • Piet Stam
  • Richard G. F. Visser
  • Herman J. Van Eck
Original Paper


A new method, REcombination Counting and ORDering (RECORD) is presented for the ordering of loci on genetic linkage maps. The method minimizes the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local reshuffling. Since the criterion we propose does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. A simulation study was performed to compare the performance of RECORD and JoinMap. RECORD is much faster and less sensitive to missing observations and scoring errors, since the optimisation criterion is less dependent on the position of the erroneous markers. In particular, RECORD performs better in regions of the map with high marker density. The implications of high marker densities on linkage map construction are discussed.


Linkage Group Mapping Population Recombination Event Target Function Marker Order 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We are very grateful to Dr. Hans Jansen and Dr. Johan van Ooijen for providing valuable comments. This work was carried out under the European Union framework 5 program grant: FAIR5-PL97-3565.


  1. Buetow KH (1991) Influence of aberrant observations on high-resolution linkage analysis outcomes. Am J Hum Genet 49:985–994PubMedPubMedCentralGoogle Scholar
  2. Buetow KH, Chakravarti A (1987) Multipoint gene mapping using seriation. I General methods. Am J Hum Genet 41:180–188PubMedPubMedCentralGoogle Scholar
  3. Buntjer JB, Van Os H, Van Eck HJ (2000a) ComBin: software for ultra-dense mapping plant and animal genome conference VIII, San Diego, CA;
  4. Buntjer JB, Van Os H, Van Eck HJ (2000b) Construction of ultra-dense maps using novel software plant and animal genome conference VIII, San Diego, CA;
  5. Büschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Topsch S, Vos P, Salamini F, Schulze-Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695–705CrossRefPubMedGoogle Scholar
  6. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedPubMedCentralGoogle Scholar
  7. Hackett CA, Broadfoot LB (2003) Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 90:33–38CrossRefPubMedGoogle Scholar
  8. Hackett CA, Pande B, Bryan GJ (2003) Constructing linkage maps in autotetraploid species using simulated annealing. Theor Appl Genet 106:1107–115PubMedGoogle Scholar
  9. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494PubMedPubMedCentralGoogle Scholar
  10. Isidore E, Van Os H, Andrzejewski S, Bakker J, Barrena I, Bryan G, Buntjer J, Caromel B, Van Eck HJ, Ghareeb B, Jong W de, Koert P van, Lefebvre V, Milbourne D, Ritter E, Rouppe van der Voort J, Rousselle-Bourgeois F, Vliet J van, Waugh R (2003) Towards a marker-dense meiotic map of the potato genome: lessons from linkage group I. Genetics 165:2107–2116PubMedPubMedCentralGoogle Scholar
  11. Jansen J, De Jong AG, Van Ooijen JW (2001) Constructing dense genetic linkage maps. Theor Appl Genet 102:1113–1122CrossRefGoogle Scholar
  12. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671–680CrossRefPubMedGoogle Scholar
  13. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K (2002) A high-resolution recombination map of the human genome. Nat Genet 31:241–247PubMedGoogle Scholar
  14. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  15. Liu BH, Knapp SJ (1990) GMENDEL: a program for Mendelian segregation and linkage analysis of individual or multiple progeny populations using log-likelihood ratio’s. J Hered 81:407Google Scholar
  16. Lu YY, Liu BH (1995) A new computer package for genomic research: PGRI (Plant Genome Research Initiative), plant genome conference III, San Diego, CA;
  17. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744CrossRefGoogle Scholar
  18. Stam P, Van Ooijen JW (1995) JoinMap™ Version 2.0: software for the calculation of genetic linkage maps, CPRO-DLO, WageningenGoogle Scholar
  19. Steen RG, Kwitek-Black AE, Glenn C, Gullings-Handley J, Van Etten W, Atkinson OS, Appel D, Twigger S, Muir M, Mull T, Granados M, Kissebah M, Russo K, Crane R, Popp M, Peden M, Matise T, Brown DM, Lu J, Kingsmore S, Tonellato PJ, Rozen S, Slonim D, Young P, Knoblauch M, Provoost A, Ganten D, Colman SD, Rothberg J, Lander ES, Jacob HJ (1999) A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat. Genome Res 9:AP1–AP8PubMedGoogle Scholar
  20. Sturtevant AH (1913) The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of a association. J Exp Zool 14:43–59CrossRefGoogle Scholar
  21. Thompson EA (1987) Crossover counts and likelihood in multipoint linkage analysis. IMA J Math Appl Med Biol 4:93–108CrossRefPubMedGoogle Scholar
  22. Van Ooijen JW, Voorrips RE (2001) JoinMap® Version 3.0, software for the calculation of genetic linkage maps. Plant research international, WageningenGoogle Scholar
  23. Zhong XB, Bodeau J, Fransz PF, Williamson VM, Van Kammen A, De Jong HJ, Zabel P (1999) FISH to meiotic pachytene chromosomes of tomato locates the root-knot nematode resistance gene Mi-1 and the acid phosphatase gene Aps-1 near the junction of euchromatin and pericentromeric heterochromatin of chromosome arms 6S and 6L, respectively. Theor Appl Genet 98:365–370CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Hans Van Os
    • 1
  • Piet Stam
    • 1
  • Richard G. F. Visser
    • 1
  • Herman J. Van Eck
    • 1
  1. 1.Laboratory of Plant BreedingWageningen University WageningenThe Netherlands

Personalised recommendations