¹Laboratory of Animal Genome, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba-shi, Ibaraki 305-0901, Japan

Correspondence: T Hayashi, Laboratory of Animal Genome, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba-shi, Ibaraki 305-0901, Japan. E-mail: hayatk@affrc.go.jp

Received 8 December 2003; Accepted 1 October 2004; Published online 26 January 2005.

Abstract

In this paper, we propose a new Bayesian method for QTL analysis in outbred F2 families based on Markov chain Monte Carlo (MCMC) estimation allowing inference about whether each of F0 founders (grandparents) is homozygous or heterozygous at QTL. This, in turn, allows us to select a model accurately explaining observations of phenotypes for F2 individuals. The proposed method performs the fitting a statistical model of the two possible QTL states in each F0 grandparent, that is, homozygous and heterozygous at QTL, and gives a posterior distribution for the QTL states in each F0 grandparent. We confine ourselves to the discrimination of two QTL states, homozygous or heterozygous, for each of the F0 grandparents without taking into consideration whether common alleles are shared by F0 grandparents. The statistical model includes allelic effects and dominance effects for each QTL. The number of parameters representing allelic effects and dominance effects is therefore changed depending on the QTL states. A Reversible Jump MCMC technique is used for transition between the models of different dimensions. The effectiveness of the proposed method was investigated using simulation experiments. It was practicable to estimate the QTL states of F0 grandparents as well as the number, the locations and the effects of QTL segregating in an outbred F2 family.