The initial logistic regression test was performed with 3220 SNPs, however after filtering SNPs to compute PCA and IBS score, an independent set of 2116 SNPs remained. No Genomic inflation from GWAS p-values expected by random chances was detected, except for the top associated SNPs (lambda = 1.13, Fig. 3a). A Fisher’s exact test revealed four markers on chromosome 5 (Fig. 3c), whose P values were above the significant genome-wide threshold of (P value >1.585 × 10−5) (Fig. 3b; Additional file 7). For the association test, the significance threshold for all 3155 SNPs was Bonferroni’s (α* = α/n) based significant threshold to adjust for multiple testing, where α represents Bonferroni’s coefficient 0.05 and n represents the number of SNPs after filtering for quality parameters (0.05 / 3155 = 1.58 × 10−5).Fig. 3 a Quantile-quantile (QQ) plot of GWA p-values. QQ-plot shows only minor deviations from the null distribution, expected for the top associated SNPs. b Manhattan plot from the GWAS analysis of Beech Bark Disease in 327 individuals. Beech bark disease is associated with a locus on chromosome 5. The x-axis represents chromosomal locations and the y-axis, −log10 p-values from genotypic associations. Four markers on chromosome 5 reached genome-wide significance (p-values >1.585 × 10−5)