Precision of methods for calculating identity-by-descent matrices using multiple markers

Genetics Selection Evolution

Volumn 34, Issue 5, 2002, Pages 557-579

  Sørensen, Anders Christian ^a,b,c,e   Pong Wong, Ricardo ^a   Windig, Jack J ^d   Woolliams, John A ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e AARHUS UNIVERSITY   (Denmark)

Author keywords

Complex pedigree; Genetic relationship; IBD; Information; Multiple markers

Indexed keywords

ANCESTRY; GENETIC MARKER; MARKOV CHAIN;

ANIMALIA;

EID: 18144440348     PISSN: 0999193X     EISSN: None     Source Type: Journal    
DOI: 10.1051/gse:2002023     Document Type: Article

References (28)

1. Anonymous, NAG Fortran Library Introductory Guide Mark 16, 1st Ed., NAG Ltd, Oxford, 1993.
2. Bijma P., Van Arendonk J.A.M., Woolliams J.A., A general procedure to predict rates of inbreeding in populations undergoing mass selection, Genetics 154 (2000) 1865-1877.
3. Blott S.C., Williams J.L., Haley C.S., Genetic relationships among European cattle breeds, Anim. Genet. 29 (1998) 273-282.
4. Botstein D., White R.L., Skolnick M., Davis R.W., Construction of a genetic linkage map in man using restriction fragment length polymorphisms, Am. J. Hum. Genet. 32 (1980) 314-331.
5. Christensen K., Fredholm M., Winterø A.K., Jørgensen J.N., Andersen S., Joint effect of 21 marker loci and effect of realized inbreeding on growth in pigs, Anim. Sci. 62 (1996) 541-546.
6. Duff I.S., Erisman A.M., Reid J.K., Direct Methods for Sparse Matrices, 1st Ed., Clarendon Press, Oxford, 1986.
7. Feller W., An Introduction to Probability Theory and its Applications, 1st ed., John Wiley & Sons, New York, 1968.
8. Fernando R.L., Grossman M., Marker assisted selection using best linear unbiased prediction, Genet. Sel. Evol. 21 (1989) 467-477.
9. Fisher R.A., The correlation between relatives on the supposition of mendelian inheritance, Trans. Roy Soc. Edin. 52 (1918) 399-433.
10. George A.W., Visscher P.M., Haley C.S., Mapping quantitative trait loci in complex pedigrees: A two-step variance component approach, Genetics 156 (2000) 2081-2092.
11. Gunawan B., James J.W., The use of "bending" in multiple trait selection of Border Leicester-Merino synthetic populations, Aust. J. Agric. Res. 37 (1986) 539-547.
12. Hayes J.F., Hill W.G., Modification of estimates of parameters in the construction of genetic selection indices ("bending"), Biometrics 37 (1981) 483-493.
13. Heath S., Markov chain Monte Carlo segregation and linkage analysis for oligogenic models, Am. J. Hum. Genet. 61 (1997) 748-760.
14. Henderson C.R., A simple method for computing the inverse of a numerator relationship matrix used in the prediction of breeding values, Biometrics 32 (1976) 69-83.
15. Lynch M., Walsh B., Genetics and Analysis of Quantitative Traits, 1st Ed., Sinauer Associates, Sunderland, 1998.
16. Meuwissen T.H.E., Goddard M.E., The use of marker haplotypes in animal breeding schemes, Genet. Sel. Evol. 28 (1996) 161-176.
17. Meuwissen T.H.E., Luo Z., Computing inbreeding coefficients in large populations, Genet. Sel. Evol. 24 (1992) 305-313.
18. Nejati-Javaremi A., Smith C., Gibson J.P., Effect of total allelic relationship on accuracy of evaluation and response to selection, J. Anim. Sci. 75 (1997) 1738-1745.
19. Patterson H.D., Thompson R., Recovery of inter-block information when block sizes are unequal, Biometrika 58 (1971) 545-554.
20. Pong-Wong R., George A.W., Woolliams J.A., Haley C.S., A simple and rapid method for calculating identity-by-descent matrices using multiple markers, Genet. Sel. Evol. 33 (2001) 453-471.
21. Rasmuson M., Variation in genetic identity within kinships, Heredity 70 (1993) 266-268.
22. Searle S.R., Matrix Algebra Useful for Statistics, 1st Ed., John Wiley & Sons, New York, 1982.
23. Self S.G., Liang K.-Y., Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under non-standard conditions, J. Am. Stat. Assoc. 82 (1987) 605-610.
24. Thompson E.A., Heath S.C., Estimation of conditional multilocus gene identity among relatives, in: Seillier-Moiseiwitsch F. (Ed.), Statistics in Molecular Biology and Genetics, Institute of Mathematical Statistics, New York, Lecture Notes-Monograph Series, Vol. 33, 1999, pp. 95-113.
25. Thompson R., Atkins K.D., Sources of information for estimating heritability from selection experiments, Genet. Res. 63 (1994) 49-55.
26. Toro M., Silió L., Rodrigánez J., Rodriguez C., Fernández J., Optimal use of genetic markers in conservation programmes, Genet. Sel. Evol. 31 (1999) 255-261.
27. Vonesh E.F., Chinchilli V.M., Pu K., Goodness-of-fit in generalized nonlinear mixed-effects models, Biometrics 52 (1996) 572-587.
28. Wright S., Coefficients of inbreeding and relationship, Am. Nat. 56 (1922) 330-338.