Free Access
Genet. Sel. Evol.
Volume 34, Number 6, November-December 2002
Page(s) 657 - 678
Genet. Sel. Evol. 34 (2002) 657-678
DOI: 10.1051/gse:2002030

The covariance between relatives conditional on genetic markers

Yuefu Liua, Gerald B. Jansena and Ching Y. Lina, b

a  Department of Animal and Poultry Science, University of Guelph, Guelph, ON N1G 2W1, Canada
b  Dairy and Swine Research and Development Centre, Agriculture and Agri-Food, Canada

(Received 13 August 2001; accepted 3 June 2002)

The development of molecular genotyping techniques makes it possible to analyze quantitative traits on the basis of individual loci. With marker information, the classical theory of estimating the genetic covariance between relatives can be reformulated to improve the accuracy of estimation. In this study, an algorithm was derived for computing the conditional covariance between relatives given genetic markers. Procedures for calculating the conditional relationship coefficients for additive, dominance, additive by additive, additive by dominance, dominance by additive and dominance by dominance effects were developed. The relationship coefficients were computed based on conditional QTL allelic transmission probabilities, which were inferred from the marker allelic transmission probabilities. An example data set with pedigree and linked markers was used to demonstrate the methods developed. Although this study dealt with two QTLs coupled with linked markers, the same principle can be readily extended to the situation of multiple QTL. The treatment of missing marker information and unknown linkage phase between markers for calculating the covariance between relatives was discussed.

Key words: covariance between relatives / molecular marker / QTL / transmission probability / relationship matrix

Correspondence and reprints: Yuefu Liu

© INRA, EDP Sciences 2002