Genome Wide Association Analysis has identified a single locus contributing to resistance to beech bark disease (BBD). There were four SNPs in chromosome (Chr) 5 significantly associated with the scale resistance trait analyzed. A candidate gene (Mt) encoding for a metallothionein-like protein was found to be physically linked to these genetic markers and may play an important role in the resistance mechanisms against Nectria sp. - beech scale insect. This is consistent with genetic studies of several different small full-sibling families that suggest involvement of a few as two genes [5, 24, 38]. For validation of single locus trait discovery, BLASTn search of the contig EST sequences was performed against the complete NCBI database for those SNPs (see Additional file 8B). A proven functional annotation for these SNPs is essential prior to use in breeding, which will be possible when a reference genome sequence for American Beech is available.