Genetics, Vol. 177, 2399-2416, December 2007, Copyright © 2007
doi:10.1534/genetics.106.069955

Quantifying Evidence for Candidate Gene Polymorphisms: Bayesian Analysis Combining Sequence-Specific and Quantitative Trait Loci Colocation Information

Roderick D. Ball1

Scion (New Zealand Forest Research Institute Limited), Rotorua, New Zealand

1 Address for correspondence: Scion (New Zealand Forest Research Institute Limited), 49 Sala St., P.B. 3020, Rotorua, New Zealand.
E-mail: rod.ball{at}scionresearch.com

We calculate posterior probabilities for candidate genes as a function of genomic location. Posterior probabilities for quantitative trait loci (QTL) presence in a small interval are calculated using a Bayesian model-selection approach based on the Bayesian information criterion (BIC) and used to combine QTL colocation information with sequence-specific evidence, e.g., from differential expression and/or association studies. Our method takes into account uncertainty in estimation of number and locations of QTL and estimated map position. Posterior probabilities for QTL presence were calculated for simulated data with n = 100, 300, and 1200 QTL progeny and compared with interval mapping and composite-interval mapping. Candidate genes that mapped to QTL regions had substantially larger posterior probabilities. Among candidates with a given Bayes factor, those that map near a QTL are more promising for further investigation with association studies and functional testing or for use in marker-aided selection. The BIC is shown to correspond very closely to Bayes factors for linear models with a nearly noninformative Zellner prior for the simulated QTL data with n ≥ 100. It is shown how to modify the BIC to use a subjective prior for the QTL effects.