Mixed model regression mapping for QTL detection in experimental crosses

Computational Statistics and Data Analysis

Volumn 51, Issue 8, 2007, Pages 3749-3764

  Gilmour, A R ^a  

^a NSW DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

Author keywords

ASReml; Mixed model; MMRM; QTL mapping; REML

Indexed keywords

COMPUTER SOFTWARE; CONFORMAL MAPPING; MATHEMATICAL MODELS; MAXIMUM LIKELIHOOD; RANDOM PROCESSES;

ASREML; MIXED MODEL REGRESSION MAPPING (MMRM); MIXED MODELS; QUANTITATIVE TRAIT LOCI (QTL) MAPPING; REML;

REGRESSION ANALYSIS;

EID: 33947695203     PISSN: 01679473     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.csda.2006.12.031     Document Type: Article

References (32)

1. Almasy L., and Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am. J. Hum. Genet. 62 5 (1998) 1198-1211
2. Bink M.C.A.M., Janss L.L.G., and Quaas R.L. Markov chain Monte Carlo for mapping a quantitative trait locus in outbred populations. Genet. Res. 75 (2000) 231-241
3. Basten, C.J., Weir, B.S., Zeng, Z.-B., 2001. QTL Cartographer: A Reference Manual and Tutorial for QTL Mapping, Bioinformatics Research Centre, North Carolina State University, Raleigh, NC, 27695-7566.
4. Broman K.W., and Speed T.P. A model selection approach for the identification of quantitative trait loci in experimental crosses. J. R. Statist. Soc. B 64 (2002) 641-656
5. Doerge R.W., Zeng Z.-B., and Weir B.S. Statistical Issues in the Search for Genes affecting quantitative traits in experimental populations. Statist. Sci. 12 (1997) 195-219
6. Esmailizadeh, K.A., Pitchford, W.S., Bottema, C.D.K., Verbyla, A.P., Gilmour, A.R., 2006. Mapping multiple QTL for birth weight in cattle growth using a mixed model approach. Eighth World Congress on Genetics Applied to Livestock Production, Brazil. CDROM Article 20-17.
7. Gianola D., Perez-Enciso M., and Toro M.A. On marker assisted prediction of genetic value: beyond the ridge. Genetics 163 (2003) 347-365
8. Gilmour A.R., Thompson R., and Cullis B.R. Average Information REML: an efficient algorithm for Variance Parameter estimation in linear mixed models. Biometrics 51 (1995) 1440-1450
9. Gilmour, A.R., Gogel, B.J., Cullis, B.R., Thompson, R., 2006. ASReml User Guide Release 2.0 VSN International Ltd., Hemel Hempstead, HP1 1ES, UK.
10. Hayes B., and Goddard M.E. The distribution of the effects of genes affecting quantitative traits in livestock. Genet. Selection Evol. 33 (2001) 209-229
11. Horvat S., and Medrano J.F. Interval mapping of high growth (hg), a major locus that increases weight gain in mice. Genetics 139 (1995) 1737-1748
12. Jansen R.C. Interval mapping of multiple quantitative trait loci. Genetics 135 (1993) 205-211
13. Jansen R.C., and Stam P. High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136 (1994) 1447-1455
14. Lander E.S., and Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121 (1989) 185-199
15. Patterson H.D., and Thompson R. Recovery of interblock information when block sizes are unequal. Biometrika 58 (1971) 545-554
16. Perez-Enciso M., and Misztal I. Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 20 16 (2004) 2792-2798
17. Perez-Enciso M., and Varona L. Quantitative trait loci mapping in F-2 crosses between outbred lines. Genetics 155 (2000) 391-405
18. Seaton G.A., Haley C.S., Knott S.A., Kearsey M., and Visscher P.M. QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18 (2002) 1-2
19. Soller M., Brody T., and Genizi A. On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theoret. Appl. Genet. 66 (1976) 255-265
20. Stram D.O., and Lee J.W. Variance components testing in the longitudinal mixed effects setting. Biometrics 50 (1994) 1171-1177
21. Ter Braak C.J.F., Boer M.P., and Bink M.C.A.M. Extending Xu's Bayesian model for estimating polygenic effects using markers of the entire genome. Genetics 170 (2005) 1435-1438
22. Verbyla A.P. A conditional derivation of residual maximum likelihood. Austral. J. Statist. 32 (1990) 227-230
23. Verbyla, A.P., Cullis, B.R., Thompson, R., 2007. The analysis of QTLs by simultaneous use of the full linkage map. Theoret. Appl. Genet. accepted for publication.
24. Wang H., Zhang Y.-M., Li X.M., Masinde G.L., Mohan S., Baylink D.J., and Xu S. Bayesian shrinkage estimation of quantitative trait loci parameters. Genetics 170 (2005) 465-480
25. Weller, J.I., 2001. Quantitative Trait Loci Analysis in Animals. CABI Publishing.
26. Whittaker J.C., Thompson R., and Visscher P.M. On the mapping of QTL by regression of phenotype on genotype. Heredity 77 (1996) 23-32
27. Whittaker J.C., Thompson R., and Denham M.C. Marker assisted selection using ridge regression. Genet. Rese. 75 (2000) 249-252
28. Xu S.Z. Estimating polygenic effects using markers of the entire genome. Genetics 163 (2003) 789-801
29. Xu, S.Z., 2007. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63, in press.
30. Xu S.Z., and Yi N.J. Mixed model analysis of quantitative trait loci. Proc. Natl. Acad. Sci. USA 97 (2000) 14542-14547
31. Zeng Z.-B. Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc. Natl. Acad. Sci. USA 90 (1993) 10972-10976
32. Zeng Z.-B. Precision mapping of quantitative trait loci. Genetics 136 (1994) 1457-1468