Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale
single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a
commonly used approach due to its simplicity, but is conservative and has low power for large-scale tests. The
permutation test, which is a powerful and popular tool, is computationally expensive and may mislead in the presence of
family structure. We propose a computationally efficient and powerful multiple testing correction approach for Linkage
Disequilibrium (LD) based Quantitative Trait Loci (QTL) mapping on the basis of graphical weighted-Bonferroni
methods. The proposed multiplicity adjustment method synthesizes weighted Bonferroni-based closed testing procedures
into a powerful and versatile graphical approach. By tailoring different priorities for the two hypothesis tests involved in
LD based QTL mapping, we are able to increase power and maintain computational efficiency and conceptual simplicity.
The proposed approach enables strong control of the familywise error rate (FWER). The performance of the proposed
approach as compared to the standard Bonferroni correction is illustrated by simulation and real data. We observe a
consistent and moderate increase in power under all simulated circumstances, among different sample sizes, heritabilities,
and number of SNPs. We also applied the proposed method to a real outbred mouse HDL cholesterol QTL mapping
project where we detected the significant QTLs that were highlighted in the literature, while still ensuring strong control
of the FWER.