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Simple deterministic identity-by-descent coefficients and estimation of QTL allelic effects in full and half sibs

Published online by Cambridge University Press:  17 February 2003

Y. NAGAMINE
Affiliation:
Roslin Institute (Edinburgh), Midlothian, EH25 9PS, UK Permanent address: National Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan.
S. A. KNOTT
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
P. M. VISSCHER
Affiliation:
Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
C. S. HALEY
Affiliation:
Roslin Institute (Edinburgh), Midlothian, EH25 9PS, UK
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Abstract

Accurate and rapid methods for the detection of quantitative trait loci (QTLs) and evaluation of consequent allelic effects are required to implement marker-assisted selection in outbred populations. In this study, we present a simple deterministic method for estimating identity-by-descent (IBD) coefficients in full- and half-sib families that can be used for the detection of QTLs via a variance-component approach. In a simulated dataset, IBD coefficients among sibs estimated by the simple deterministic and Markov chain Monte Carlo (MCMC) methods with three or four alleles at each marker locus exhibited a correlation of greater than 0·99. This high correlation was also found in QTL analyses of data from an outbred pig population. Variance component analysis used both the simple deterministic and MCMC methods to estimate IBD coefficients. Both procedures detected a QTL at the same position and gave similar test statistics and heritabilities. The MCMC method, however, required much longer computation than the simple method. The conversion of estimated QTL genotypic effects into allelic effects for use in marker-assisted selection is also demonstrated.

Type
Research Article
Copyright
© 2002 Cambridge University Press

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