Bayesian analysis of linkage between genetic markers and quantitative trait loci. II. Combining prior knowledge with experimental evidence.

A Bayesian method was developed for identifying genetic markers linked to quantitative trait loci (QTL) by analyzing data from daughter or granddaughter designs and single markers or marker pairs. Traditional methods may yield unrealistic results because linkage tests depend on number of markers and QTL gene effects associated with selected markers are overestimated. The Bayesian or posterior probability of linkage combines information from a daughter or granddaughter design with the prior probability of linkage between a marker locus and a QTL. If the posterior probability exceeds a certain quantity, linkage is declared. Upon linkage acceptance, Bayesian estimates of marker-QTL recombination rate and QTL gene effects and frequencies are obtained. The Bayesian estimates of QTL gene effects account for different amounts of information by shrinking information from data toward the mean or mode of a prior exponential distribution of gene effects. Computation of the Bayesian analysis is feasible. Exact results are given for biallelic QTL, and extensions to multiallelic QTL are suggested.