As shown in the Manhattan plot (Fig. 3b and Additional file 7), four SNPs were observed to surpass the genome-wide significance threshold of 1.585 × 10−5, which is strong evidence of association. All four SNPs are located on chromosome (Chr) 5 (Additional file 8). The strongest evidence of association is linked to AX-156994126 (P = 5.99E-6, odds ratio (OR) = 0.2573), AX-156988334 (P = 8.852E-6, odds ratio (OR) = 0.2758) and AX-157000652 (P = 8.074E-6, odds ratio (OR) = 0.2773) (Table 6). On chromosome (Chr) 5, SNPs were positioned at 12.344 cM (centimorgans) for AX-156994126, AX-156989406 and for AX-157000652 and at 13.811 cM for AX-156988334 (Additional file 8A).Table 6Top SNPs associated with Beech Bark diseaseGeneChrPosition (cM)Affymetrix IDOriginal SNPs IDLogistic regression association (P value)AnnotationMt512.344AX-156989406contig03321_5762.46E-6 Fagus sylvatica (European beech) mRNA for methallothionein-like protein, Metal ion bindingMt512.344AX-157000652contig03321_1668.07E-6Mt513.811AX-156988334contig03321_3308.85E-6Mt512.344AX-156994126contig03321_4415.99E-6