One of the current challenges in genetics, even in the age of fully sequenced genomes, is that of moving from a linkage map position to the isolation of the gene or genes that encode a trait. In QTL mapping genes encoding products that have an influence on a particular phenotype can be identified to a given confidence interval on a genetic map. While one might expect that it should be simple to move from the QTL confidence interval to the identification of the segment of DNA that encodes the mapped signal in an organism for which the complete genome DNA sequence has been determined, this has often proved to be a frustrating step. We will describe our bioinformatics approach to addressing this issue that uses data about polymorphism, gene expression and published descriptions of gene function.