Genetics, Vol. 159, 413-422, September 2001, Copyright © 2001
Quantitative Trait Locus Analysis in Crosses Between Outbred Lines With Dominance and Inbreeding
Miguel Pérez-Encisoa,
Rohan L. Fernandob,
Jean-Pierre Bidanelc, and
Pascale Le Royc
a INRA, Station d'Amélioration Génétique des Animaux, BP 27, 31326 Castanet-Tolosan, France,
b Iowa State University, Department of Animal Science, Ames, Iowa, 50011
c INRA, Station de Génétique Quantitative et Appliquée, 78352 Jouy-en-Josas, France
Corresponding author:
Miguel Pérez-Enciso, INRA, Station d'Amélioration Génétique des Animaux, BP 27, 31326 Castanet-Tolosan, France., mperez{at}toulouse.inra.fr (E-mail)
Communicating editor: C. HALEY
We provide a theoretical framework for quantitative trait locus (QTL) analysis of a crossed population where parental lines may be outbred and dominance as well as inbreeding are allowed for. It can be applied to any pedigree. A biallelic QTL is assumed, and the QTL allele frequencies can be different in each breed. The genetic covariance between any two individuals is expressed as a nonlinear function of the probability of up to 15 possible identity modes and of the additive and dominance effects, together with the allelic frequencies in each of the two parental breeds. The probabilities of each identity mode are obtained at the desired genome positions using a Monte Carlo Markov chain method. Unbiased estimates of the actual genetic parameters are recovered in a simulated F2 cross and in a six-generation complex pedigree under a variety of genetic models (allele fixed or segregating in the parental populations and additive or dominance action). Results from analyzing an F2 cross between Meishan and Large White pigs are also presented.
