## References

Devlin, B. & Risch, N. (1995). A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics
29, 311–322.

Fang, M., Liu, J., Sun, D., Zhang, Y., Zhang, Q., Zhang, Y. & Zhang, S. (2011). QTL mapping in outbred half-sib families using Bayesian model selection. Heredity
107, 265–276.

Fang, M., Liu, S. C. & Jiang, D. (2009). Bayesian composite model space approach for mapping quantitative trait loci in variance component model. Behavior Genetics
39, 337–346.

Goddard, M. E. & Meuwissen, T. H. E. (2005). The use of linkage disequilibrium to map quantitative trait loci. Australian Journal of Experimental Agriculture
45, 837–845.

Grapes, L., Dekkers, J. C., Rothschild, M. F. & Fernando, R. L. (2004). Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci. Genetics
166, 1561–1570.

Hästbacka, J., de la Chapelle, A., Kaitila, I., Sistonen, P., Weaver, A. & Lander, E. (1992). Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nature Genetics
2, 204–211.

Hastings, W. K. (1970). Monte Carlo sampling methods using Markov chains and their applications. Biometrika
57, 97–109.

Hill, W. G. & Hernandez-Sanchez, J. (2007). Prediction of multilocus identity-by-descent. Genetics
176, 2307–2315.

Kaplan, N. L., Hill, W. G. & Weir, B. S. (1995). Likelihood methods for locating disease genes in nonequilibrium populations. American Journal of Human Genetics
56, 18–32.

Lander, E. S. & Bostein, D. (1989). Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics
121, 185–199.

Lee, S. H. & van der Werf, J. H. (2006). Simultaneous fine mapping of multiple closely linked quantitative trait loci using combined linkage disequilibrium and linkage with a general pedigree. Genetics
173, 2329–2337.

Lou, X. Y., Casella, G., Todhunter, R. J., Yang, M. C. K. & Wu, R. (2005). A general statistical framework for unifying interval and linkage disequilibrium mapping. Journal of the American Statistical Association
100, 158–171.

Lund, M. S., Sorensen, P., Guldbrandtsen, B. & Sorensen, D. A. (2003). Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis. Genetics
163, 405–410.

Luo, Z. W., Tao, S. H. & Zeng, Z. B. (2000). Inferring linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations. Genetics
156, 457–467.

Mathew, B., Bauer, A. M., Koistinen, P., Reetz, T. C., Léon, J. & Sillanpää, M. J. (2012). Bayesian adaptive Markov chain Monte Carlo estimation of genetic parameters. Heredity
109, 235–245.

Metropolis, N. A., Rosenbluth, W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. The Journal of Chemical Physics
21, 1087–1091.

Meuwissen, T. H. & Goddard, M. E. (2000). Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci. Genetics
155, 421–430.

Meuwissen, T. H. & Goddard, M. E. (2001). Prediction of identity by descent probabilities from marker-haplotypes. Genetics, Selection, Evolution
33, 605–634.

Meuwissen, T. H. & Goddard, M. E. (2007). Multipoint identity-by-descent prediction using dense markers to map quantitative trait loci and estimate effective population size. Genetics
176, 2551–2560.

Meuwissen, T. H. & Goddard, M. E. (2004). Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genetics, Selection, Evolution
36, 261–279.

Meuwissen, T. H., Hayes, B. J. & Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics
157, 1819–1829.

Sillanpaa, M. J. & Arjas, E. (1998). Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics
148, 1373–1388.

Uleberg, E. & Meuwissen, T. H. E. (2007). Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping – a comparison of single QTL and multi QTL methods. Genetics, Selection, Evolution
39, 285–299.

Wu, R. L., Ma, C. X. & Casella, G. (2002). Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics
160, 779–792.

Wu, R. L. & Zeng, Z. B. (2001). Joint linkage and linkage disequilibrium mapping in natural population. Genetics
157, 899–909.

Xu, S. (2003). Estimating polygenic effects using markers of the entire genome. Genetics
163, 789–801.

Yi, N., Yandell, B. S., Churchill, G. A., Allison, D. B., Eisen, E. J. & Pomp, D. (2005). Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics
170, 1333–1344.

Zeng, Z. B. (1994). Precise mapping quantitative trait loci. Genetics
136, 1457–1468.

Zhao, H. H., Fernando, R. L., Dekkers, J. C. (2007). Power and precision of alternate methods for linkage disequilibrium mapping of quantitative trait loci. Genetics
175, 1975–1986.