Issue |
Genet. Sel. Evol.
Volume 33, Number 5, September-October 2001
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Page(s) | 453 - 471 | |
DOI | https://doi.org/10.1051/gse:2001127 |
Genet. Sel. Evol. 33 (2001) 453-471
A simple and rapid method for calculating identity-by-descent matrices using multiple markers
Ricardo Pong-Wong, Andrew Winston George, John Arthur Woolliams and Chris Simon HaleyRoslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK
(Received 1st September 2000; accepted 9 April 2001)
Abstract
A fast, partly recursive deterministic method for calculating
Identity-by-Descent (IBD) probabilities was developed with the
objective of using IBD in Quantitative Trait Locus (QTL) mapping. The
method combined a recursive method for a single marker locus with a
method to estimate IBD between sibs using multiple markers. Simulated
data was used to compare the deterministic method developed in the
present paper with a stochastic method (LOKI) for precision in
estimating IBD probabilities and performance in the task of QTL
detection with the variance component approach. This comparison was
made in a variety of situations by varying family size and degree of
polymorphism among marker loci. The following were observed for the
deterministic method relative to MCMC: (i) it was an order of
magnitude faster; (ii) its estimates of IBD probabilities were found
to agree closely, even though it does not extract information when
haplotypes are not known with certainty; (iii) the shape of the
profile for the QTL test statistic as a function of location was
similar, although the magnitude of the test statistic was slightly
smaller; and (iv) the estimates of QTL variance was similar. It was
concluded that the method proposed provided a rapid means of
calculating the IBD matrix with only a small loss in precision, making
it an attractive alternative to the use of stochastic MCMC
methods. Furthermore, developments in marker technology providing
denser maps would enhance the relative advantage of this method.
Key words: IBD / QTL mapping / genetic relationships / marker assisted selection
Correspondence and reprints: Ricardo Pong-Wong E-mail: ricardo.pong-wong@bbsrc.ac.uk
© INRA, EDP Sciences 2001