Evaluation of algorithms used to order markers on genetic maps

Heredity

Volumn 103, Issue 6, 2009, Pages 494-502

  Mollinari, M ^a   Margarido, G R A ^a   Vencovsky, R ^a   Garcia, A A F ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Multipoint estimates; Rapid chain delineation; Recombination counting and ordering; Seriation; Unidirectional growth

Indexed keywords

ALGORITHM; DATA SET; ERROR ANALYSIS; GENETIC ANALYSIS; GENETIC MARKER; GROWTH RATE; POPULATION SIZE; RECOMBINATION;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; EVALUATION; GENETIC LINKAGE; GENETIC MARKER; GENETICS; METHODOLOGY; PLANT;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC MARKERS; LINKAGE (GENETICS); MODELS, GENETIC; PLANTS; SOFTWARE;

EID: 70549083922     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2009.96     Document Type: Article

References (39)

1. Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang S et al. (2006). Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113: 1409-1420.
2. Ahn S, Tanksley SD (1993). Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980-7984.
3. Basten CJ, Weir BS, Zeng ZB (2003). QTL Cartographer: Version 1.17. Department of Statistics, North Carolina State University, North Carolina: Raleigh.
4. Botstein D, White RL, Skolnick M, Davis RW (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
5. Bowers JE, Abbey C, Anderson S, Chang C, Draye X, Hoppe AH et al. (2003). A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165: 367-386.
6. Broman KW, Wu H, Churchill G, Sen S, Yandell B (2008). qtl: Tools for analyzing QTL experiments. R package version 1.08-56. http://www.rqtl.org.
7. Buetow KH, Chakravarti A (1987). Multipoint gene mapping using seriation. I. General methods. Am J Hum Genet 41: 180-188.
8. Dempster AP, Laird NM, Rubin DB (1977). Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc 39: 1-38.
9. Doerge RW (1996). Constructing genetic maps by rapid chain delineation. J Quant Trait Loci 2.Electronic publication available at http://wheat.pw.usda. gov/jag/papers96/paper696/doerge2.htm.
10. Electronic publication available at http://wheat.pw.usda.gov/jag/ papers96/ paper696/doerge2.htm. Edwards JH (1971). The analysis of X-linkage. Ann Hum Genet 34: 229-250.
11. Falk CT (1989). A simple scheme for preliminary ordering of multiple loci: Application to 45 CF families. In: Elston RC, Spence MA, Hodge SE, MacCluer JW (eds). Multipoint Mapping and Linkage based upon Affected Pedigree Members. Genetic Workshop 6, Liss: New York. pp 17-22.
12. 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: 33-38.
13. Haldane JBS (1919). The combination of linkage values, and the calculation of distance between linked factors. J Genet 8: 299-309.
14. Hansen M, Kraft T, Chistiansson M, Nilsson ON (1999). Evaluation of AFLP in Beta. Theor Appl Genet 98: 845-852.
15. Jiang C, Zeng Z-B (1997). Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
16. Lander ES, Green P (1987). Construction of multilocus genetic linkage maps in human. Proc Natl Acad Sci 84: 2363-2367. (Pubitemid 17075870)
17. Lander ES, Green P, Abrahanson J, Barlow A, Daly MJ, Lincon SE et al. (1987). MAPMAKER: An interactive computing package for constructing primary genetic linkages of experimental and natural populations. Genomics 1: 174-181.
18. Lander ES, Botstein D (1989). Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
19. Lange K (2002). Mathematical and Statistical Methods for Genetic Analysis, 2nd edn. Springer: New York.
20. Lathrop GM, Lalouel JM, Julier C, Ott J (1984). Strategies for multilocus linkage analysis in human. Proc Natl Acad Sci 81: 3443-3446.
21. Lathrop GM, Lalouel 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. Liu BH (1998). Statistical Genomics: Linkage, Mapping, and QTL Analysis, 2nd edn. CRC Press: Boca Raton.
23. Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Huttner E et al. (2008). DArT markers: Diversity analyses and mapping in Sorghum bicolor. BMC Genomics 9: 26.
24. Manly B (1997). Randomization, Bootstrap and Monte Carlo Methods in Biology, 2nd edn. Chapman & Hall/CRC: London.
25. Margarido GRA, Souza AP, Garcia AAF (2007). OneMap: software for genetic mapping in outcrossing species. Hereditas 144: 78-79.
26. Mester D, Ronin Y, Minkov D, Nevo E, Korol A (2003). Constructing large-scale genetic maps using an evolutionary strategy algorithm. Genetics 165: 2269-2282.
27. Olson JM, Boehnke M (1990). Monte Carlo comparison of preliminary methods for ordering multiple genetic loci. Am J Hum Genet 47: 470-482.
28. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX et al. (2000). Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1540.
29. R Development Core Team (2008). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.
30. Spearman C (1904). The proof and measurement of association between two things. Am J Psychol 15: 72-101.
31. Stam P (1993). Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3: 739-744.
32. Tan Y, Fu Y (2006). A novel method for estimating linkage maps. Genetics 173: 2383-2390.
33. Thompson EA (1984). Information gain in joint linkage analysis. IMA J Math Appl Med Biol 1: 31-49.
34. Van Os H, Stam P, Visser RGF, Van Eck HJ (2005). RECORD: A novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112: 30-40.
35. Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW et al. (1999). Two high-density AFLP linkage maps of Zea mays L.: Analysis of distribution of AFLP markers. Theor Appl Genet 99: 921-925.
36. Weeks D, Lange K (1987). Preliminary ranking procedure for multilocus ordering. Genomics 1: 236-242.
37. Wilson SR (1988). A major simplification in the preliminary ordering of liked loci. Genet Epidemiol 5: 75-80.
38. Wu J, Jenkins J, Zhu J, Mccarty J, Watson C (2003). Monte Carlo simulations on marker grouping and ordering. Theor Appl Genet 107: 568-573.
39. Zeng Z-B (1993). Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. Proc Natl Acad Sci USA 90: 10972-10976.