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Bayesian shrinkage analysis is arguably the state-of-the-art technique for large-scale multiple quantitative trait locus (QTL) mapping. However, when the shrinkage model does not involve indicator variables for marker inclusion, QTL detection remains heavily dependent on significance thresholds derived from phenotype permutation under the null hypothesis of no phenotype-to-genotype association. This approach is computationally intensive and more importantly, the hypothetical data generation at the heart of the permutation-based method violates the Bayesian philosophy. Here we propose a fully Bayesian decision rule for QTL detection under the recently introduced extended Bayesian LASSO for QTL mapping. Our new decision rule is free of any hypothetical data generation and relies on the well-established Bayes factors for evaluating the evidence for QTL presence at any locus. Simulation results …