Efficient multipoint mapping: Making use of dominant repulsion-phase markers

Theoretical and Applied Genetics

Volumn 107, Issue 6, 2003, Pages 1102-1112

  Mester, D I ^a   Ronin, Y I ^a   Hu, Y ^a   Peng, J ^a   Nevo, E ^a   Korol, A B ^a  

^a UNIVERSITY OF HAIFA   (Israel)

Author keywords

Bootstrap; Dominant marker; Multilocus ordering; Repulsion phase; Synchronized optimization algorithm

Indexed keywords

ALGORITHMS; DATA PROCESSING; TRAVELING SALESMAN PROBLEM;

MULTIPOINT MAPPING;

BIOMARKERS;

ALGORITHM; ARTICLE; CHROMOSOME MAP; GENETIC LINKAGE; GENETIC MARKER; MATHEMATICS;

ALGORITHMS; CHROMOSOME MAPPING; GENETIC MARKERS; LINKAGE (GENETICS); MATHEMATICS;

EMBRYOPHYTA;

EID: 0142092457     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-003-1305-1     Document Type: Article

References (52)

1. Bailey NTJ (1961) Introduction to mathematical theory of genetic linkage. Calendon Press, Oxford
2. Bourque G, Pevzner PA (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 12:26-36
3. Boyko E, Kalendar R, Korzun V, Fellers J, Korol AB, Schulman AH, Gill BS (2002) A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. Plant Mol Biol 48:767-790
4. Buetow KN, Chakravarti A (1987) Multipoint gene mapping using seriation. Am J Hum Genet 41:189-201
5. Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH Jr (2002) Genetic, physical, and informatics resources for maize: on the road to an integrated map. Plant Physiol 130:1598-1605
6. Curtis D, Gurling H (1993) A procedure for combining two-point lod scores into a summary multipoint map. Hum Hered 43:173-185
7. Efron B (1979) Bootstrap method: another look at the jackknife. Ann Stat 7:1-26
8. Ellis T (1997) Neighbour mapping as a method for ordering genetic markers. Genet Res 69:35-43
9. Esch E, Weber WE (2002) Investigation of crossover interference in barley (Hordeum vulgare L.) using the coefficient of coincidence. Theor Appl Genet 104:786-796
10. Falk CT (1992) Preliminary ordering of multiple linked loci using pairwise linkage data. Genet Epidemiology 9:367-375
11. Fogel D (1992) Evolving artificial intelligence. PhD thesis, University of California, San-Diego
12. Hall D, Bhandarkar SH, Wang J (2001) ODS2: a multiplatform software application for creating integrated physical and genetic maps. Genetics 157:1045-1056
13. 2 population. Genetics 148:479-494
14. Holland J (1975) Adaptation in natural and artificial systems. MIT PRESS, Cambridge, USA
15. Homberger J, Gehring H (1999) Two evolutionary metaheuristics for a vehicle routing problem with time windows. INFOR 37:297-318
16. Jansen J, de Jong AC, van Ooijen JW (2001) Constructing dense genetic linkage maps. Theor Appl Genet 102:1113-1122
17. Kirkpatrick S, Gellatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220:671-680
18. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE (2000) A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res 10:789-807
19. 2 mating. Theor Appl Genet 91:74-81
20. Lathrop GM, Llouel JM (1984) Easy calculation of lod scores and genetic risks on small computers. Am J Hum Genet 36:469-465
21. Lathrop GM, Llouel JM, Julier C, Ott J (1985) Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am J Hum Genet 37:482-498
22. Lander ES, Green P (1987) Construction of multilocus linkage maps in human. Proc Natl Acad Sci USA 84:2363-2367
23. Lin S, Kernighan B (1973) An effective heuristic algorithm for the TSP. Operation Res 21:498-516
24. Liu BH (1998) Statistical genomics: linkage, mapping, and QTL analysis. CRC Press, New York
25. Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE (2002) A high-density genetic map of Sorghum bicolor (L.) Moench based on 2,926 AFLP, RFLP and SSR markers. Plant Mol Biol 48:483-499
26. Mester D (1999) The parallel algorithm for vehicle routing problem with time window restrictions. Scientific report, Minerva Optimization Center, Technion, Haifa, Israel
27. Mester D (2003) Evolutionary strategies algorithm for a large-scale vehicle routing problem with capacitate and time-windows restrictions. J Heuristics (revised)
28. Mester D, Ronin Y, Minkov D, Nevo E, Korol A (2003) Constructing large scale genetic maps using evolutionary strategy algorithm. Genetics (revised)
29. Muhlenbein H, Gorges-Scheuter MO, Kramer O (1998) Evolution algorithm in combinatorial optimization. Parallel Computing 7:65-85
30. Newell RW, Mott R, Beck S, Lehrach H (1995) Construction of genetic maps using distance geometry. Genomics 30:59-70
31. Nissen V (1994) Evolutionare algorithmen. Deutscher Universitats-Verlag, Wiesbaden
32. Olson JM, Boehnke M (1990) Monte Carlo comparison of preliminary methods of ordering multiple genetic loci. Am J Hum Genet 47:470-482
33. Or I (1976) Traveling salesman - type combinatorial problems and their relations to the logistics of regional blood banking. PhD thesis, Dept Industrial Engendering and Management Science, Northwestern University
34. Osman I (1993) Metastrategy simulated annealing and Tabu Search algorithm for VRP. Ann Operation Res 41:421-451
35. Parsons YM, Shaw KL (2002) Mapping unexplored genomes. A genetic linkage map of the Hawaiian cricket laupala. Genetics 162:1275-1282
36. Peng J, Korol A, Fahima T, Roder M, Ronin Y, Li Y, Nevo E (2000) Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage. Genome Res 10:1509-1531
37. Peng J, Ronin Y, Fahima T, Röder MS, Li Y, Nevo E, Korol A (2003) Domestication QTLs in Triticum dicoccoides, the progenitor of wheat. Proc Natl Acad Sci USA 100:2489-2494
38. Pérez-Enciso M, Roussot O (2002) A method for computing identity by descent probabilities and quantitative trait loci mapping with dominant (AFLP) markers. Genetical Res 79:247-258
39. Press WT, Hannery BP, Teucolsky SA, Veterling WT (1986) Numerical recipes: the art of scientific computing. Cambridge University Press, London
40. Rechenberg I (1973) Evolutionstrategie. Fromman-Holzboog, Stutgart
41. Sall T, Nilsson NO (1994) The robustness of recombination frequency estimates in intercrosses with dominant markers. Genetics 137:589-596
42. Schwefel H-P (1977) Numeriche Optimierung von Computer-Modelen Mittels der Evolutions-Strategie. Birkauser, Basel
43. Schwefel H-P (1987) Collective phenomena in evolutionary systems. Interne Berichte und Skripten, Fachbereich Informatic, University Dortmund
44. Schinex T, Gaspin C (1997) Carthagene: constructing and joining maximum-likelihood genetic maps. ISMB 5:258-267
45. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739-744
46. Thompson EA (1984) Information gain in joint linkage analysis. IMA J Math Appl Med Biol 1:31-49
47. VanOoijen JW (2002) JoinMap 3.0: advanced computer software for the calculation of genetic linkage maps in experimental populations. j.w.vanooijen@plant.wag-ur.nl
48. Wang Y, Prade R, Griffith J, Timberlake W, Arnold J (1994) ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap re-sampling. CABIOS 10:625-634
49. Weeks D, Lange K (1987) Preliminary ranking procedures for multilocus ordering. Genomics 1:236-242
50. Wilson S (1988) A major simplification in the preliminary ordering of linked loci. Genet Epidemiology 5:75-80
51. Whitaker D, Williams ER (2001) OutMap version 1.0. http:// www.ffp.csiro.au/tigr/software/outmap/outmap.htm
52. Yang YP, Womack JE (1998) Parallel radiation hybrid mapping: a powerful tool for high-resolution genomic comparison. Genome Res 8:731-736