precision of methods for calculating identity-by-descent matrices using multiple markers计算精度的方法identity-by-descent矩阵使用多个标记.pdf

Genet. Sel. Evol. 34 (2002) 557–579 557 © INRA, EDP Sciences, 2002 DOI: 10.1051/gse:2002023 Original article Precision of methods for calculating identity-by-descent matrices using multiple markers Anders Christian SØRENSENa ,b ,c ∗, Ricardo PONG-WONGa , Jack J. WINDIGd , John A. WOOLLIAMSa a 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 ≥ 95% relative to MCMC. Relative precision declined for the