Free Access
Genet. Sel. Evol.
Volume 33, Number 5, September-October 2001
Page(s) 453 - 471
DOI: 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 Haley

Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK

(Received 1st September 2000; accepted 9 April 2001)

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:

© INRA, EDP Sciences 2001