Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data

Genetics

Volumn 148, Issue 3, 1998, Pages 1373-1388

  Sillanpää, Mikko J ^a   Arjas, Elja ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CHROMOSOMAL LOCALIZATION; COMPUTER PROGRAM; CONTROLLED STUDY; CROSS BREEDING; GENE LOCUS; GENE MAPPING; GENOTYPE; INBRED STRAIN; PHENOTYPE; PRIORITY JOURNAL; PROGENY; QUANTITATIVE TRAIT;

BAYES THEOREM; CHROMOSOME MAPPING; CHROMOSOMES; COMPUTER SIMULATION; CROSSES, GENETIC; GENETIC MARKERS; INBREEDING; MODELS, GENETIC; QUANTITATIVE TRAIT, HERITABLE;

EMBRYOPHYTA;

EID: 0031961421     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (48)

1. ARJAS, E., and D. GASBARRA, 1994 Nonparametric Bayesian inference from right censored survival data using the Gibbs sampler. Statist. Sinica 4: 505-524.
2. BASTEN, C. J., B. S. WEIR and Z.-B. ZENG, 1996 QTL Cartografer, the reference manual and tutorial for QTL mapping, (available at http://statgen.ncsu.edu.)
3. BESAG, J., P. GREEN, D. HIGDON and K. MENGERSEN, 1995 Bayesian computation and stochastic systems. Statist. Sci. 10: 3-66.
4. BEST, N. G., M. K. COWLES and S. K. VINES, 1995 CODA: Convergence Diagnosis and Output Analysis software for Gibbs Sampler output: Version 0.3. Cambridge: Medical Research Council Biostatistic Unit.
5. CASELLA, G., and E. I. GEORGE, 1992 Explaining the Gibbs sampler. American Statistician 46: 167-174.
6. CHIB, S., and E. GREENBERG, 1995 Understanding the Metropolis-Hastings algorithm. American Statistician 49: 327-335.
7. CHURCHILL, G. A., and R. W. DOERGE, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
8. DEMPSTER, A. P., N. M. LAIRD and D. B. RUBIN, 1977 Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Statist. Soc., Ser. B. 39: 1-38.
9. GEMAN, S., and D. GEMAN, 1984 Stochastic relaxation, gibbs distribution, and the Bayesian restoration of images. IEEE Trans. Pattn. Anal. Mach. Intell. 6: 721-741.
10. GEYER, C. J., 1992 Practical Markov Chain Monte Carlo. Statist. Sci. 7: 473-511.
11. GEYER, C. J., 1996 Likelihood inference for spatial point processes, (available at http://www.stats.bris.ac.uk/MCMC/)
12. GREEN, P. J., 1995 Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
13. Guo, S. W., and E. A. THOMPSON, 1992 Monte Carlo method for combined segregation and linkage analysis. Am. J. Hum. Genet. 51: 1111-1126.
14. HACKETT, C. A., and J. I. WELLER, 1995 Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 51: 1252-1263.
15. HALEY, C. S., and S. A. KNOTT, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
16. HALEY, C. S., S. A. KNOTT, and J.-M. ELSEN, 1994 Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195-1207.
17. HASTINGS, W. K., 1979 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
18. JANSEN, R. C., 1993 Interval mapping of multiple quantitative trait loci. Genetics 135: 205-211,
19. JANSEN, R. C., 1996 A General Monte Carlo method for mapping multiple quantitative trait loci. Genetics 142: 305-311.
20. JANSEN, R. C., and P. STAM, 1994 High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455.
21. KRUGLYAK, L., and E. S. LANDER, 1995 A Nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421-1428.
22. KUITTINEN, H., M. J. SILLANPÄÄ, and O. SAVOLAINEN, 1997 Genetic basis of adaptation: flowering time in Arabidopsis Thaliana. Theor. Appl. Genel. 95: 573-583.
23. LANDER, E. S., and D. BOTSTEIN, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
24. LINCOLN, S., M. DALY, and E. S. LANDER, 1992 Mapping genes controlling quantitative traits with MAPMAKER/QTL 1.1 Whitehead Institute Technical Report. 2nd edition.
25. METROPOLIS, N., A. W. ROSENBLUTH, M. N. ROSENBLUTH, A. H. TELLER, and E. TELLER, 1953 Equation of stale calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
26. OTT, J., 1991 Analysis of Human Genetic Linkage. Revised edition. The John Hopkins University Press, Baltimore.
27. RICHARDSON, S., and P. J. GREEN, 1997 On Bayesian analysis of mixtures with an unknown number oF components. J. Roy. Statist. Soc., Ser. B, 59: 731-792.
28. SATAGOPAN, J. M., and B. S. YANDELL, 1996 Estimating the number of quantitative trait loci via Bayesian model determination. Special Contributed Paper Session on Genetic Analysis of Quantitative Traits and Complex Diseases. BiometriC Section. Joint Statistical Meetings, Chicago, IL. (available at ftp://ftp.stat.wisc.edu/pnb/ yandell/revjump.html)
29. SATAGOPAN, J. M., B. S. YANDELL, M. A. NEWTON, and T. C. OSBORN, 1996 A Bayesian approach to detect quantitative trait loci using Markov Chain Monte Carlo. Genetics 144: 805-816.
30. SMITH, A. F. M., 1996 Bayesian curves and CARTs. First European Conference on Highly Structured Stochastic Systems, Rebild, May 1996.
31. SMITH, A. F. M., and G. O. ROBERTS, 1993 Bayesian compulation via the Gibbs sampler and related Markov Chain Monte Carlo methods. J. Roy. Statist. Soc., Ser. B, 55: 3-23.
32. STEPHENS, D. A., and R. D. FISCH, 1996 Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Technical report, (available at http://www.ma.ic.ac.uk/ statistics/techrep.html)
33. STEPHENS, D. A., and A. F. M. SMITH, 1993 Bayesian inference in multipoint gene mapping. Ann. Human Genet. 57: 65-82.
34. TAI, J. J., 1989 Application of Bayesian decision procedure to the inference of genetic linkage. J. Am. Statist. Assoc. 84: 669-673.
35. TANKSLEY, S. D., 1993 Mapping polygones. Annu. Rev. Genet. 27: 205-233.
36. THOMAS, D. C., and V. CORTESSIS, 1992 A Gibbs sampling approach in linkage analysis. Hum. Hered. 42: 63-76.
37. THOMAS, D. C., and W. J. GAUDERMAN, 1995 Gibbs sampling methods in genetics, pp. 419-440 in Markov Chain Monte Carlo in Practice, edited by W. R. GILKS, S. RICHARDSON and D. J. SPIEGEL-HALTER. Chapman & Hall, London.
38. THOMPSON, E. A., 1994 Monte Carlo likelihood in genetic mapping. Statist. Sci. 9: 355-366.
39. UIMARI, P., and I. HOESCHELE, 1997 Mapping linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics 146: 735-743.
40. UIMARI, P., G. THALLER, and I. HOESCHELE, 1996a The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics 143: 1831-1842.
41. UIMARI, P., Q. ZHANG, F. GRIGNOLA, I. HOESCHELE, and G. THALLER, 1996b Analysis of QTL workshop I Granddaughter design data using least-squares, residual maximum likelihood and Bayesian methods. J. QTL 1996: 2, art. 7.
42. UTZ, H. F., and A. E. MELCHINGER 1996 PLABQTL: A program for composite interval mapping of QTL. J. Quant. Trait Loci 2: 7.
43. VAN OOIJEN J. W., and C. MALIEPAARD, 1996 Plant Genome IV. Abstract at: http://probe.nalusda.gov:8000/otherdocs/pg/pg4/ abstracts/p316.html.
44. VISSCHER, P. M., C. S. HALEY, and S. A. KNOTT, 1996a Mapping QTLs for binary traits in backcross and F2 populations. Genet. Res., Camb. 68: 55-63.
45. VISSCHER, P. M., R. THOMPSON, and C. S. HALEY, 1996b Confidence intervals in QTL mapping by bootstrapping. Genetics 143: 1013-1020.
46. XU, S., and W. R. ATCHLEY, 1996 Mapping quantitative trail loci for complex binary diseases using line crosses. Genetic 143: 1417-1424.
47. ZENG, Z.-B., 1993 Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc. Natl. Acad. Sci. USA. 90: 10972-10976.
48. ZENG, Z.-B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.