Detection of quantitative trait loci in outbred populations with incomplete marker data

Genetics

Volumn 151, Issue 1, 1999, Pages 409-420

  Bink, Marco C A M ^a   Van Arendonk, Johan A M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE LOCUS; GENETIC MODEL; HETEROZYGOSITY; MARKER GENE; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE TRAIT;

ANIMALS; BAYES THEOREM; CHROMOSOME MAPPING; FEMALE; GENETIC MARKERS; MALE; MARKOV CHAINS; MODELS, GENETIC; QUANTITATIVE TRAIT, HERITABLE;

EID: 0032896377     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (49)

1. ANDERSSON, L., C. S. HALEY, H. ELLEGREN, S. A. KNOTT, M. JOHANSSON et al., 1994 Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263: 1771-1774.
2. BARENDSE, W., S. M. ARMITAGE, L. M. KOSSAREK, A. SHALOM and B. W. KIRKPATRICK, 1994 A genetic linkage map of the bovine genome. Nat. Genet. 6: 227-235.
3. BINK, M. C. A. M., J. A. M. VAN ARENDONK and R. L. QUAAS, 1998a Breeding value estimation with incomplete marker data. Genet. Sel. Evol. 30: 45-58.
4. BINK, M. C. A. M., R. L. QUAAS and J. A. M. VAN ARENDONK, 1998b Bayesian estimation of dispersion parameters with a reduced animal model including polygenic and QTL effects. Genet. Sel. Evol. 30: 103-125.
5. BINK, M. C. A. M., L. L. G. JANSS and R. L. QUAAS, 1998c Mapping a polyallelic quantitative trait locus using simulated tempering. Proc. 6th World Congr. Genet. Appl. Livest. Prod. Sci., Armidale, Australia 26: 277-280.
6. BOVENHUIS, H., J. A. M. VAN ARENDONK, G. DAVIS, J.-M. ELSEN, C. S. HALEY et al., 1997 Detection and mapping of quantitative trait loci in farm animals. Livest. Prod. Sci. 52: 135-144.
7. CHIB, S., and E. GREENBERG, 1995 Understanding the Metropolis Hastings algorithm. Am. Stat. 49: 327-335.
8. FERNANDO, R. L., and M. GROSSMAN, 1989 Marker-assisted selection using best linear unbiased prediction. Genet. Sel. Evol. 21: 467-477.
9. GARCIA-CORTES, L. A., and D. SORENSEN, 1996 On a multivariate implementation of the Gibbs sampler. Genet. Sel. Evol. 28: 121-126.
10. GEMAN, S., and D. GEMAN, 1984 Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. IEEE Trans Pattern Anal. Machine Intelligence 6: 721-741.
11. GELFAND, A. E., 1994 Gibbs sampling (A contribution to the Encyclopedia of Statistical Sciences). Technical Report, Department of Statistics, University of Connecticut.
12. GELMAN, A., J. B. CARLIN, H. S. STERN and D. B. RUBIN, 1995 Bayesian Data Analysis. Chapman & Hall, London, UK.
13. GEORGE, A. W., K. L. MENGERSEN and G. P. DAVIS, 1998 A Bayesian analysis of a QTI, under a half-sib design. Proc. 6th World Congr. Genet. Appl. Livest. Prod. Sci., Armidale, Australia 26: 225-228.
14. GEORGES, M., D. NIELSEN, M. MACKINNON, A. MISHRA, R. OKIMOTO et al., 1995 Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139: 907-920.
15. GEYER, C. J., and E. A. THOMPSON, 1995 Annealing Markov chain Monte Carlo with applications to ancestral inference. J. Am. Stat. Assoc. 90: 909-920.
16. GREEN, P. J., 1995 Reversible jump Markov chain Monte Carlo computation and Baysian model determination. Biometrika 82: 711-732.
17. GRIGNOLA, F. E., I. HOESCHELE and B. TIER, 1996a Mapping quantitative trait loci via Residual Maximum Likelihood: I. Methodology. Genet. Sel. Evol. 28: 479-490.
18. GRIGNOLA, F. E., I. HOESCHELE, Q. ZHANG and G. THALLER, 1996b Mapping quantitative trait loci via Residual Maximum Likelihood: II. A simulation study. Genet. Sel. Evol. 28: 491-504.
19. GUO, S. W., and E. A. THOMPSON, 1992 A Monte Carlo method for combined segregation and linkage analysis. Am. J. Hum. Genet. 51: 1111-1126.
20. HASTINGS, W. K., 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
21. HEATH, S. C., 1997a Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am. J. Hum. Genet. 61: 748-760.
22. HEATH, S. C., 1997b Markov chain Monte Carlo methods for radiation hybrid mapping. J. Comp. Biol. 4: 505-515.
23. HENDERSON, C. R., 1988 Theoretical basis and computational methods for a number of different animal models. J. Dairy Sci. 71 (Suppl 2): 1-16.
24. HOESCHELE, L, P. UIMARI, F. E. GRIGNOLA, Q. ZHANG and K. M. GAGE, 1997 Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics 147: 1445-1457.
25. JANSEN, R. C., D. L. JOHNSON and J. A. M. VAN ARENDONK, 1998 A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families. Genetics 148: 391-399.
26. JANSS, L. L. G., R. THOMPSON and J. A. M. VAN ARENDONK, 1995 Application of Gibbs sampling in a mixed major gene - polygenic inheritance model in animal populations. Theor. Appl. Genet. 91: 1137-1147.
27. LIU, J. S., W. H. WONG and A. KONG, 1994 Covariance structure of the Gibbs sampler with applications to the comparisons of estimators and augmentation schemes. Biometrika 81: 27-40.
28. METROPOLIS, N., A. W. ROSENBLUTH, M. N. ROSENBLUTH, H. TELLER and E. TELLER, 1953 Equations of state calculations by fast computing machines. J. Chem. Physics 21: 1087-1091.
29. PATERSON, A. H., E. S. LANDER, J. D. HEWITT, S. PETERSON, S. E. LINCOLN et al., 1988 Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment polymorphisms. Nature 335: 721-726.
30. QUAAS, R. L., and E. J. POLLAK, 1980 Mixed model methodology for farm and ranch beef cattle testing programs. J. Anim. Sci. 51: 1277-1287.
31. 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.
32. SEARLE, S. R., 1982 Matrix Algebra Useful for Statistics. John Wiley & Sons, New York.
33. SHEEHAN, N., and A. THOMAS, 1993 On the irreducibility of a Markov chain defined on a space of genotype configurations by a sampling scheme. Biometrics 49: 163-175.
34. SILLANPÄÄ, M. J., and E. ARJAS, 1998 Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
35. SMITH, A. F. M., and G. O. ROBERTS, 1993 Bayesian computation via the Gibbs sampler and related Markov chain Monte Carlo methods. J. R. Stat. Soc. B 55: 3-23.
36. SORENSEN, D. A., S. ANDERSEN, D. GIANOLA and I. KORSGAARD, 1995 Bayesian inference in threshold models using Gibbs sampling. Genet. Sel. Evol. 27: 229-249.
37. SPELMAN, R. J., W. COPPIETERS, L. KARIM, J. A. M. VAN ARENDONK and H. BOVENHUIS, 1996 Quantitative trait loci analysis for five milk production traits on chromosome six in the Dutch Holstein-Friesian population. Genetics 144: 1799-1808.
38. STUBER, C. W., S. E. LINCOLN, D. W. WOLFF, T. HELENTJARIS and E. S. LANDER, 1992 Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132: 823-839.
39. TANNER, M. A., 1993 Tools for Statistical Inference: Methods for the Exploration of Posterior Distributions and Likelihood Functions, Ed. 2. Springer-Verlag, Berlin.
40. THALLER, G., and I. HOESCHELE, 1996a A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci: I. Methodology. Theor. Appl. Genet. 93: 1161-1166.
41. THALLER, G., and I. HOESCHELE, 1996b A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci: II. A simulation study. Theor. Appl. Genet. 93: 1167-1174.
42. THOMAS, D., and C. CORTESSIS, 1992 A Gibbs sampling approach to linkage analysis. Hum. Hered. 42: 63-76.
43. UIMARI, P., G. THALLER and I. HOESCHELE, 1996 The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics 143: 1831-1842.
44. UIMARI, P., and I. HOESCHELE, 1997 Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics 146: 735-743.
45. VAN ARENDONK, J. A. M., B. TIER and B. P. KINGHORN, 1994 Use of multiple genetic markers in prediction of breeding values. Genetics 137: 319-329.
46. VAN ARENDONK, J. A. M., B. TIER, M. C. A. M. BINK and H. BOVENHUIS, 1998 Restricted maximum likelihood analysis of linkage between genetic markers and quantitative trait loci for a granddaughter design. J. Dairy Sci. 81(2): 76-84.
47. WANG, C. S., 1998 Implementation issues in Bayesian analysis in animal breeding. Proc. 6th World Congr. Genet. Appl. Livest. Prod. Sci., Armidale, Australia 25: 481-488.
48. WANG, T., R. L. FERNANDO, S. VAN DER BEEK, M. GROSSMAN and J. A. M. VAN ARENDONK, 1995 Covariance between relatives for a marked quantitative trait locus. Genet. Sel. Evol. 27: 251-272.
49. WELLER, J. I., Y. KASHI and M. SOLLER, 1990 Power of daughter and granddaughter designs for determining linkage between marker loci and quantitative trait loci in dairy cattle. J. Dairy Sci. 73: 2525-2537.