Open Access

The covariance between relatives conditional on genetic markers

Genetics Selection Evolution200234:657

Received: 13 August 2001

Accepted: 3 June 2002

Published: 15 November 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.


covariance between relatives molecular marker QTL transmission probability relationship matrix

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Authors’ Affiliations

Department of Animal and Poultry Science, University of Guelph
Dairy and Swine Research and Development Centre, Agriculture and Agri-Food


© INRA, EDP Sciences 2002