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Open Access Research

Prediction of identity by descent probabilities from marker-haplotypes

Theo HE Meuwissen1* and Mike E Goddard2

Author Affiliations

1 Research Institute of Animal Science and Health, Box 65, 8200 AB Lelystad, The Netherlands

2 Institute of Land and Food Resources, University of Melbourne, Parkville Victorian Institute of Animal Science, Attwood, Victoria, Australia

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Genetics Selection Evolution 2001, 33:605-634  doi:10.1186/1297-9686-33-6-605

The electronic version of this article is the complete one and can be found online at:

Received:13 February 2001
Accepted:11 June 2001
Published:15 November 2001

© 2001 INRA, EDP Sciences


The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (i.e. all information came from the marker genotypes), and the situation where, say T, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.

identity by descent; haplotype analysis; coalescence process; linkage disequilibrium; QTL mapping


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