Issue |
Genet. Sel. Evol.
Volume 34, Number 5, September-October 2002
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|
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Page(s) | 557 - 579 | |
DOI | https://doi.org/10.1051/gse:2002023 |
DOI: 10.1051/gse:2002023
Precision of methods for calculating identity-by-descent matrices using multiple markers
Anders Christian Sørensena, b, c, Ricardo Pong-Wonga, Jack J. Windigd and John A. Woolliamsaa Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK
b Department of Animal Breeding and Genetics, Danish Institute of Agricultural Science, P.O. Box 50, 8830 Tjele, Denmark
c Department of Animal Science and Animal Health, Royal Veterinary and Agricultural University, Grønnegårdsvej 2, 1870 Frederiksberg C, Denmark
d Institute for Animal Science, ID-Lelystad, P.O. Box 65, 8200 AB Lelystad, The Netherlands
(Received 13 November 2001; accepted 22 April 2002)
Abstract
A rapid, deterministic method (DET) based on a recursive algorithm and
a stochastic method based on Markov Chain Monte Carlo (MCMC) for
calculating identity-by-descent (IBD) matrices conditional on multiple
markers were compared using stochastic simulation. Precision was
measured by the mean squared error (MSE) of the relationship
coefficients in predicting the true IBD relationships, relative to
MSE obtained from using pedigree only. Comparisons were made
when varying marker density, allele numbers, allele frequencies, and
the size of full-sib families. The precision of DET was 75-99%
relative to MCMC, but was not simply related to the informativeness of
individual loci. For situations mimicking microsatellite markers or
dense SNP, the precision of DET was
relative to
MCMC. Relative precision declined for the SNP, but not microsatellites
as marker density decreased. Full-sib family size did not affect the
precision. The methods were tested in interval mapping and marker
assisted selection, and the performance was very largely determined by
the MSE. A multi-locus information index considering the
type, number, and position of markers was developed to assess
precision. It showed a marked empirical relationship with the observed
precision for DET and MCMC and explained the complex relationship
between relative precision and the informativeness of individual loci.
Key words: IBD / genetic relationship / multiple markers / complex pedigree / information
Correspondence and reprints: Anders Christian Sørensen E-mail: AndersC.Sorensen@agrsci.dk
© INRA, EDP Sciences 2002