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Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.

Genetics, Vol. 174, 1009-1016, October 2006, Copyright © 2006
doi:10.1534/genetics.106.060806

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Using Dominance Relationship Coefficients Based on Linkage Disequilibrium and Linkage With a General Complex Pedigree to Increase Mapping Resolution

S. H. Lee1 and J. H. J. Van der Werf

School of Rural Science and Agriculture and Institute of Genetics and Bioinformatics, University of New England, Armidale, NSW 2351, Australia

1 Corresponding author: School of Rural Science and Agriculture, UNE, Armidale, NSW 2351, Australia. 
E-mail: slee7{at}une.edu.au

Dominance (intralocus allelic interactions) plays often an important role in quantitative trait variation. However, few studies about dominance in QTL mapping have been reported in outbred animal or human populations. This is because common dominance effects can be predicted mainly for many full sibs, which do not often occur in outbred or natural populations with a general pedigree. Moreover, incomplete genotypes for such a pedigree make it infeasible to estimate dominance relationship coefficients between individuals. In this study, identity-by-descent (IBD) coefficients are estimated on the basis of populationwide linkage disequilibrium (LD), which makes it possible to track dominance relationships between unrelated founders. Therefore, it is possible to use dominance effects in QTL mapping without full sibs. Incomplete genotypes with a complex pedigree and many markers can be efficiently dealt with by a Markov chain Monte Carlo method for estimating IBD and dominance relationship matrices (Formula). It is shown by simulation that the use of Formula increases the likelihood ratio at the true QTL position and the mapping accuracy and power with complete dominance, overdominance, and recessive inheritance modes when using 200 genotyped and phenotyped individuals.




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P. Waldmann, J. Hallander, F. Hoti, and M. J. Sillanpaa
Efficient Markov Chain Monte Carlo Implementation of Bayesian Analysis of Additive and Dominance Genetic Variances in Noninbred Pedigrees
Genetics, June 1, 2008; 179(2): 1101 - 1112.
[Abstract] [Full Text] [PDF]


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