Fine mapping of quantitative trait loci using linkage disequilibrium in inbred plant populations

Linkage disequilibrium (LD)-based methods capitalize on the number of generations that occurred since the appearance of a mutation at a QTL and can produce extremely accurate estimates of the QTL position. Here, we describe a regression methodology to estimate the effect of marker haplotypes on a quantitative trait for the case of inbred plant populations. The method builds upon probabilities of being 'Identical by Descent' that are obtained via a gene-dropping simulation, where inbreeding is assumed to be due to a single seed descent process. The method was empirically tested via Monte Carlo simulation and results showed that the power to detect the true QTL position depended on the age of the QTL mutation, effective population size and marker distances. Also, increased marker polymorphism dramatically improved power and the method seemed fairly robust to differences in genetic and population assumptions. This revised version was published online in July 2006 with corrections to the Cover Date.