Issue |
Genet. Sel. Evol.
Volume 33, Number 6, November-December 2001
|
|
---|---|---|
Page(s) | 605 - 634 | |
DOI | https://doi.org/10.1051/gse:2001134 |
Genet. Sel. Evol. 33 (2001) 605-634
Prediction of identity by descent probabilities from marker-haplotypes
Theo H.E. Meuwissena and Mike E. Goddardba Research Institute of Animal Science and Health, Box 65, 8200 AB Lelystad, The Netherlands
b Institute of Land and Food Resources, University of Melbourne, Parkville Victorian Institute of Animal Science, Attwood, Victoria, Australia
(Received 13 February 2001; accepted 11 June 2001)
Abstract
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.
Key words: identity by descent / haplotype analysis / coalescence process / linkage disequilibrium / QTL mapping
Correspondence and reprints: Theo H.E. Meuwissen
e-mail: t.h.e.meuwissen@id.dlo.nl
© INRA, EDP Sciences 2001