Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

Genetics Selection Evolution

Volumn 37, Issue 1, 2005, Pages 83-103

  Kerr, R J ^a,d   McLachlan, G M ^b   Henshall, J M ^c  

^a UNIVERSITY OF NEW ENGLAND   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c CSIRO   (Australia)

^d MMI Genomics   (United States)

Author keywords

EM algorithm; Half sib families; Interval mapping; QTL

Indexed keywords

ALGORITHM;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BREEDING; CHROMOSOME MAP; COMPUTER SIMULATION; DOMESTIC ANIMAL; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOTYPE; MALE; METHODOLOGY; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; ANIMALS, DOMESTIC; BREEDING; CHROMOSOME MAPPING; COMPUTER SIMULATION; FEMALE; GENOTYPE; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 11444262227     PISSN: 0999193X     EISSN: None     Source Type: Journal    
DOI: 10.1051/gse:2004037     Document Type: Article

References (16)

1. Carbonell E.A., Gerig T.M., Balansard E., Asins M.J., Interval mapping in the analysis of nonadditive quantitative trait loci, Biometrics 48 (1992) 305-315.
2. Churchill G.A., Doerge R.W., Empirical threshold values for quantitative trait mapping, Genetics 138 (1994) 963-971.
3. Farnir F., Grisart B., Coppieters W., Riquet J., Berzi P., Cambisano N., Karim L., Mni M., Moisio S., Simon P., Wagenaar D., Vilkki J., Georges M., Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14, Genetics 161 (2002) 275-287.
4. Gilbert H., Le Roy P., Comparison of three multitrait methods for QTL detection, Genet. Sel. Evol. 35 (2003) 281-304.
5. Goffinet B., Roy P.L., Boichard D., Elsen J., Mangin B., Alternative models for QTL detection in livestock. III. Heteroskedastic model and models corresponding to several distributions of the QTL effect, Genet. Sel. Evol. 31 (1999) 341-350.
6. Hetzel D.J.S., Davis G.P., Corbet N.J., Shorthose W.R., Stark J., Kuypers R., Scacheri S., Mayne C., Stevenson R., Moore S.S., Byrne K., Detection of gene markers linked to carcass and meat quality traits in a tropical beef herd, in: Proceedings of the Twelth Conference of the Association for the Advancement of Animal Breeding and Genetics, Dubbo, 1997, pp. 442-446.
7. Jansen R., Maximum likelihood in a generalised linear finite mixture model by using the EM algorithm, Biometrics 49 (1993) 227-231.
8. Jansen R.C., Johnson D.L., Arendonk J.A.M.V., A mixture model approach to the mapping of quantitative trait loci in complex populations with an application to multiple cattle families, Genetics 148 (1998) 391-399.
9. Jiang C., Zeng Z.B., Multiple trait analysis of genetic mapping for quantitative trait loci, Genetics 140 (1995) 1111-1127.
10. Kao C.H., Zeng Z.B., General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm, Biometrics 53 (1997) 653-665.
11. Knott S., Haley C., Multitrait least squares for quantitative trait loci detection, Genetics 156 (2000) 899-911.
12. Knott S.A., Elsen J.M., Haley C.S., Methods for multiple-marker mapping of quantitative trait loci in half-sib populations, Theor. Appl. Genet. 93 (1996) 71-80.
13. Lander E.S., Green P., Construction of multilocus genetic linkage maps in humans, Proc. Natl. Acad. Sci. USA 84 (1987) 2363-2367.
14. McLachlan G.J., Krishnan T., The EM algorithm and Extensions, Wiley, New York, 1st edn., 2000.
15. McLachlan G.J., Peel D., Finite Mixture Models, Wiley, New York, 1st edn., 2000.
16. Zeng Z.B., Precision mapping of quantitative trait loci, Genetics 136 (1994) 1457-1468.