Mapping Quantitative Trait Loci in F2 Incorporating Phenotypes of F3 Progeny

Genetics

Volumn 166, Issue 4, 2004, Pages 1981-1993

  Zhang, Yuan Ming ^a   Xu, Shizhong ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CATTLE; COMPUTER PROGRAM; COMPUTER SIMULATION; EXPERIMENTAL ANIMAL; FAMILY; GENE MAPPING; GENOTYPE; MARKER GENE; NONHUMAN; PHENOTYPE; PLANT; PLANT GENETICS; PRIORITY JOURNAL; PROGENY; QUANTITATIVE TRAIT LOCUS; STATISTICAL ANALYSIS;

ALGORITHMS; BAYES THEOREM; COMPUTER SIMULATION; CROSSES, GENETIC; GENOTYPE; MODELS, GENETIC; PHENOTYPE; PLANTS; QUANTITATIVE TRAIT LOCI;

ANIMALIA; BOS TAURUS;

EID: 2442588741     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.166.4.1981     Document Type: Article

References (39)

1. 6.7 generations of quantitative trait loci for grain yield and yield component in maize. Theor. Appl. Genet. 92: 817-826.
2. BOVENHUIS, H., and J. I. WELLER, 1994 Mapping and analysis of dairy cattle quantitative traits loci by maximum likelihood methodology using milk protein genes as genetic markers. Genetics 136: 267-280.
3. 4:6 soybean population. Euphytica 129: 387-393.
4. DEMPSTER, A. P., N. M. LAID and D. B. RUBIN, 1977 Maximum likelihood from incomplete data via EM algorithm (with discussion). J. R. Stat. Soc. B 39: 1-38.
5. FISCH, R. D., M. RAGOT and G. GAY, 1996 A generalization of the mixture model in the mapping of quantitative trait loci for progeny from a biparental cross of inbred lines. Genetics 143: 571-577.
6. GAI, J. Y., Y. M. ZHANG and J. K. WANG, 2003 The Genetic System of Quantitative Traits in Plants. Chinese Science Press, Beijing.
7. GEMAN, S., and D. GEMAN, 1984 Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. IEEE Trans. Patt. Anal. Machine Intell. 6: 721-741.
8. GREEN, P. J., 1995 Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
9. HASTINGS, W. K., 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
10. HOESCHELE, L, and P. M. VANRADEN, 1993 Bayesian analysis of linkage between genetic markers and quantitative trait loci. II. Combining prior knowledge with experimental evidence. Theor. Appl. Genet. 85: 946-952.
11. JANSEN, R. C., D. L. JOHNSON and J. A. M. V. 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.
12. JIANG, C. J., and Z-B. ZENG, 1997 Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
13. KAO, C. H., Z-B. ZENG and R. D. TEASDALE, 1999 Multiple interval mapping for quantitative trait loci. Genetics 152: 1203-1216.
14. KNAPP, S. J., 1991 Using molecular markers to map multiple quantitative trait loci: models for backcross, recombinant inbred, and doubled haploid progeny. Theor. Appl. Genet. 81: 333-338.
15. LANDER, E. S., and D. BOTSTEIN, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
16. MACKINNON, M. J., and J. I. WELLER, 1995 Methodology and accuracy of estimation of quantitative trait loci parameters in a half-sib design using maximum likelihood. Genetics 141: 755-770.
17. MATHER, K., and J. L. JINKS, 1982 Biometrical Genetics, Ed. 2. Chapman & Hall, London.
18. PIEPHO, H. P., 2001 A quick method for computing approximate thresholds for quantitative trait loci detection. Genetics 157: 425-432.
19. RAO, S., and S. XU, 1998 Mapping quantitative trait loci for ordered categorical traits in four-way crosses. Heredity 81: 214-224.
20. RON, M., D. KLIGER, E. FELDMESSER, E. SEROUSSI, F. RZRA et al., 2001 Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics 159: 727-735.
21. 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.
22. SILLANPAA, M. J., and E. ARJAS, 1998 Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
23. SILLANPAA, M. J., and E. ARJAS, 1999 Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics 151: 1605-1619.
24. SORENSEN, D., and D. GIANOLA, 2002 Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer-Verlag, New York.
25. STEPHENS, D. A., and R. D. FISCH, 1998 Bayesian analysis of quantitative trait locus data using reversible jump Markov chain Monte Carlo. Biometrics 54: 1334-1347.
26. THALLER, G., and I. HOESCHELE, 1996 A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. 1. Methodology. Theor. Appl. Genet. 93:1161-1166.
27. UIMARI, P., and I. HOESCHELE, 1997 Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics 146: 735-743.
28. WELLER, J. I., Y. KASHI and M. SOLLER, 1990 Power of "daughter" and "granddaughter" designs for genetic mapping of quantitative traits in dairy cattle using genetic markers. J. Dairy Sci. 73: 2525-2537.
29. XU, S., 1996 Mapping quantitative trait loci using four-way crosses. Genet. Res. 68: 175-181.
30. XU, S., 1998a Further investigation on the regression method of mapping quantitative trait loci. Heredity 80: 364-373.
31. XU, S., 1998b Mapping quantitative trait loci using multiple families of line crosses. Genetics 148: 517-524.
32. XU, S., 2002 QTL Analysis in Plants. Humana Press, Totowa, NJ.
33. XU, S., 2003 Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
34. XU, C., X. HE and S. XU, 2003 Mapping quantitative trait loci underlying triploid endosperm traits. Heredity 90: 228-235.
35. YI, N., and S. XU, 2001 Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157: 1759-1771.
36. 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.
37. ZENG, Z-B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
38. ZHANG, T., Y. YUAN, J. YU, W. Z. GUO and R.J. KOHEL, 2003 Molecular tagging of a major QTL for fiber strong in upland cotton and its marker-assisted selection. Theor. Appl. Genet. 106: 262-268.
39. ZHANG, Y. M., J. Y. GAI and Y. H. YANG, 2003 The EIM algorithm in the joint segregation analysis of quantitative traits. Genet. Res. 81: 157-163.